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Tayi L, Nathawat R, Kumar S, Maku RV, Patel HK, Sankaranarayanan R, Sonti RV. Mutational analysis of predicted active site residues of an exoglucanase secreted by Xanthomonas oryzae pv. oryzae to determine their role in catalysis and in virulence on rice. Enzyme Microb Technol 2024; 174:110372. [PMID: 38104475 DOI: 10.1016/j.enzmictec.2023.110372] [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: 10/11/2023] [Revised: 12/04/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023]
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight disease in rice. As a part of its virulence repertoire, Xoo secretes a cell wall degrading enzyme Cellobiosidase (CbsA), which is a critical virulence factor and also a determinant of tissue specificity. CbsA protein is made up of an N-terminal catalytic domain and a C-terminal fibronectin type III domain. According to the CAZy classification, the catalytic domain of CbsA protein belongs to the glycosyl hydrolase-6 (GH6) family that performs acid-base catalysis. However, the identity of the catalytic acid and the catalytic base of CbsA is not known. Based on the available structural and biochemical data, we identified putative catalytic residues and probed them by site-directed mutagenesis. Intriguingly, the biochemical analysis showed that none of the mutations abolishes the catalytic activity of CbsA, an observation that is contrary to other GH6 family members. All the mutants exhibited altered enzymatic activity and caused significant virulence deficiency in Xoo emphasising the requirement of specific exoglucanase activity of wild-type CbsA for virulence on rice. Our study highlights the need for further studies and the detailed characterisation of bacterial exoglucanases.
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Affiliation(s)
- Lavanya Tayi
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500007, India
| | - Rajkanwar Nathawat
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500007, India
| | - Sushil Kumar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500007, India
| | - Roshan V Maku
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500007, India
| | - Hitendra Kumar Patel
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500007, India
| | - Rajan Sankaranarayanan
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500007, India.
| | - Ramesh V Sonti
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500007, India.
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Mendonça M, Barroca M, Collins T. Endo-1,4-β-xylanase-containing glycoside hydrolase families: Characteristics, singularities and similarities. Biotechnol Adv 2023; 65:108148. [PMID: 37030552 DOI: 10.1016/j.biotechadv.2023.108148] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 04/02/2023] [Accepted: 04/04/2023] [Indexed: 04/09/2023]
Abstract
Endo-1,4-β-xylanases (EC 3.2.1.8) are O-glycoside hydrolases that cleave the internal β-1,4-D-xylosidic linkages of the complex plant polysaccharide xylan. They are produced by a vast array of organisms where they play critical roles in xylan saccharification and plant cell wall hydrolysis. They are also important industrial biocatalysts with widespread application. A large and ever growing number of xylanases with wildly different properties and functionalites are known and a better understanding of these would enable a more effective use in various applications. The Carbohydrate-Active enZYmes database (CAZy), which classifies evolutionarily related proteins into a glycoside hydrolase family-subfamily organisational scheme has proven powerful in understanding these enzymes. Nevertheless, ambiguity currently exists as to the number of glycoside hydrolase families and subfamilies harbouring catalytic domains with true endoxylanase activity and as to the specific characteristics of each of these families/subfamilies. This review seeks to clarify this, identifying 9 glycoside hydrolase families containing enzymes with endo-1,4-β-xylanase activity and discussing their properties, similarities, differences and biotechnological perspectives. In particular, substrate specificities and hydrolysis patterns and the structural determinants of these are detailed, with taxonomic aspects of source organisms being also presented. Shortcomings in current knowledge and research areas that require further clarification are highlighted and suggestions for future directions provided. This review seeks to motivate further research on these enzymes and especially of the lesser known endo-1,4-β-xylanase containing families. A better understanding of these enzymes will serve as a foundation for the knowledge-based development of process-fitted endo-1,4-β-xylanases and will accelerate their development for use with even the most recalcitrant of substrates in the biobased industries of the future.
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Chitin-Active Lytic Polysaccharide Monooxygenases Are Rare in Cellulomonas Species. Appl Environ Microbiol 2022; 88:e0096822. [PMID: 35862679 PMCID: PMC9361826 DOI: 10.1128/aem.00968-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Cellulomonas flavigena is a saprotrophic bacterium that encodes, within its genome, four predicted lytic polysaccharide monooxygenases (LPMOs) from Auxiliary Activity family 10 (AA10). We showed previously that three of these cleave the plant polysaccharide cellulose by oxidation at carbon-1 (J. Li, L. Solhi, E.D. Goddard-Borger, Y. Mattieu et al., Biotechnol Biofuels 14:29, 2021, https://doi.org/10.1186/s13068-020-01860-3). Here, we present the biochemical characterization of the fourth C. flavigena AA10 member (CflaLPMO10D) as a chitin-active LPMO. Both the full-length CflaLPMO10D-Carbohydrate-Binding Module family 2 (CBM2) and catalytic module-only proteins were produced in Escherichia coli using the native general secretory (Sec) signal peptide. To quantify chitinolytic activity, we developed a high-performance anion-exchange chromatography-pulsed amperometric detection (HPAEC-PAD) method as an alternative to the established hydrophilic interaction liquid ion chromatography coupled with UV detection (HILIC-UV) method for separation and detection of released oxidized chito-oligosaccharides. Using this method, we demonstrated that CflaLPMO10D is strictly active on the β-allomorph of chitin, with optimal activity at pH 5 to 6 and a preference for ascorbic acid as the reducing agent. We also demonstrated the importance of the CBM2 member for both mediating enzyme localization to substrates and prolonging LPMO activity. Together with previous work, the present study defines the distinct substrate specificities of the suite of C. flavigena AA10 members. Notably, a cross-genome survey of AA10 members indicated that chitinolytic LPMOs are, in fact, rare among Cellulomonas bacteria. IMPORTANCE Species from the genus Cellulomonas have a long history of study due to their roles in biomass recycling in nature and corresponding potential as sources of enzymes for biotechnological applications. Although Cellulomonas species are more commonly associated with the cleavage and utilization of plant cell wall polysaccharides, here, we show that C. flavigena produces a unique lytic polysaccharide monooxygenase with activity on β-chitin, which is found, for example, in arthropods. The limited distribution of orthologous chitinolytic LPMOs suggests adaptation of individual cellulomonads to specific nutrient niches present in soil ecosystems. This research provides new insight into the biochemical specificity of LPMOs in Cellulomonas species and related bacteria, and it raises new questions about the physiological function of these enzymes.
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Kurotani KI, Huang C, Okayasu K, Suzuki T, Ichihashi Y, Shirasu K, Higashiyama T, Niwa M, Notaguchi M. Interfamily grafting capacity of petunia. HORTICULTURE RESEARCH 2022; 9:uhab056. [PMID: 35048114 PMCID: PMC8969063 DOI: 10.1093/hr/uhab056] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/25/2021] [Indexed: 05/27/2023]
Abstract
In grafting, an agricultural technique for propagating flower species and fruit trees, two plants are combined to exploit their beneficial characteristics, such as rootstock disease tolerance and vigor. Grafting incompatibility has been observed, however, between distantly related plant combinations, which limits the availability of plant resources. A high grafting capacity has been found in Nicotiana, belonging to Solanaceae, but not in Ipomoea nil, a Convolvulaceae species. Here, we found that Petunia hybrida, another solanaceous species, has similar ability of interfamily grafting, which indicates that interfamily grafting capability in Solanaceae is not limited to the genus Nicotiana. RNA sequencing-based comparative time-series transcriptomic analyses of Nicotiana benthamiana, I. nil, and P. hybrida revealed that N. benthamiana and P. hybrida share a common gene expression pattern, with continued elevated expression of the β-1,4-glucanase subclade gene GH9B3 observed after interfamily grafting. During self-grafting, GH9B3 expression in each species was similarly elevated, thus suggesting that solanaceous plants have altered regulatory mechanisms for GH9B3 gene expression that allow tissue fusion even with other species. Finally, we tested the effect of the β-1,4-glucanase inhibitor D-glucono-1,5-lactone, using glucose as a control, on the interfamily grafting usability of P. hybrida with Arabidopsis rootstock. Strong inhibition of graft establishment was observed only with D-glucono-1,5-lactone, thus suggesting the important role of GH9B3 in P. hybrida grafting. The newly discovered grafting compatibility of Petunia with different families enhances the propagation techniques and the production of flower plants.
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Affiliation(s)
- Ken-ichi Kurotani
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Chaokun Huang
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Koji Okayasu
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, Matsumoto-cho, Kasugai 487-8501, Japan
| | - Yasunori Ichihashi
- Center for Sustainable Resource Science, RIKEN, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Ken Shirasu
- Center for Sustainable Resource Science, RIKEN, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Science, University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tetsuya Higashiyama
- Graduate School of Science, University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Masaki Niwa
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- GRA&GREEN Inc., Incubation Facility, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Michitaka Notaguchi
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- GRA&GREEN Inc., Incubation Facility, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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Briganti L, Capetti C, Pellegrini VO, Ghio S, Campos E, Nascimento AS, Polikarpov I. Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in Paenibacillus xylanivorans GH11 xylanase. Comput Struct Biotechnol J 2021; 19:1557-1566. [PMID: 33815691 PMCID: PMC7994722 DOI: 10.1016/j.csbj.2021.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 02/27/2021] [Accepted: 03/01/2021] [Indexed: 12/25/2022] Open
Abstract
Glycoside hydrolases (GHs) are essential for plant biomass deconstruction. GH11 family consist of endo-β-1,4-xylanases which hydrolyze xylan, the second most abundant cell wall biopolymer after cellulose, into small bioavailable oligomers. Structural requirements for enzymatic mechanism of xylan hydrolysis is well described for GH11 members. However, over the last years, it has been discovered that some enzymes from GH11 family have a secondary binding sites (SBS), which modulate the enzymes activities, but mechanistic details of the molecular communication between the active site and SBS of the enzymes remain a conundrum. In the present work we structurally characterized GH11 xylanase from Paenibacillus xylanivorans A57 (PxXyn11B), a microorganism of agricultural importance, using protein crystallography and molecular dynamics simulations. The PxXyn11B structure was solved to 2.5 Å resolution and different substrates (xylo-oligosaccharides from X3 to X6), were modelled in its active and SBS sites. Molecular Dynamics (MD) simulations revealed an important role of SBS in the activity and conformational mobility of PxXyn11B, demonstrating that binding of the reaction products to the SBS of the enzyme stabilizes the N-terminal region and, consequently, the active site. Furthermore, MD simulations showed that the longer the ligand, the better is the stabilization within active site, and the positive subsites contribute less to the stabilization of the substrates than the negative ones. These findings provide rationale for the observed enzyme kinetics, shedding light on the conformational modulation of the GH11 enzymes via their SBS mediated by the positive molecular feedback loop which involve the products of the enzymatic reaction.
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Affiliation(s)
- Lorenzo Briganti
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense 400, 13566-590 São Carlos, SP, Brazil
| | - Caio Capetti
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense 400, 13566-590 São Carlos, SP, Brazil
| | - Vanessa O.A. Pellegrini
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense 400, 13566-590 São Carlos, SP, Brazil
| | - Silvina Ghio
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CONICET-INTA, Los Reseros y Nicolas Repetto (s/n), Hurlingham (1686), Prov. Buenos Aires, Argentina
| | - Eleonora Campos
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CONICET-INTA, Los Reseros y Nicolas Repetto (s/n), Hurlingham (1686), Prov. Buenos Aires, Argentina
| | - Alessandro S. Nascimento
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense 400, 13566-590 São Carlos, SP, Brazil
| | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense 400, 13566-590 São Carlos, SP, Brazil
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Li J, Solhi L, Goddard-Borger ED, Mathieu Y, Wakarchuk WW, Withers SG, Brumer H. Four cellulose-active lytic polysaccharide monooxygenases from Cellulomonas species. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:29. [PMID: 33485381 PMCID: PMC7828015 DOI: 10.1186/s13068-020-01860-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/13/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND The discovery of lytic polysaccharide monooxygenases (LPMOs) has fundamentally changed our understanding of microbial lignocellulose degradation. Cellulomonas bacteria have a rich history of study due to their ability to degrade recalcitrant cellulose, yet little is known about the predicted LPMOs that they encode from Auxiliary Activity Family 10 (AA10). RESULTS Here, we present the comprehensive biochemical characterization of three AA10 LPMOs from Cellulomonas flavigena (CflaLPMO10A, CflaLPMO10B, and CflaLPMO10C) and one LPMO from Cellulomonas fimi (CfiLPMO10). We demonstrate that these four enzymes oxidize insoluble cellulose with C1 regioselectivity and show a preference for substrates with high surface area. In addition, CflaLPMO10B, CflaLPMO10C, and CfiLPMO10 exhibit limited capacity to perform mixed C1/C4 regioselective oxidative cleavage. Thermostability analysis indicates that these LPMOs can refold spontaneously following denaturation dependent on the presence of copper coordination. Scanning and transmission electron microscopy revealed substrate-specific surface and structural morphological changes following LPMO action on Avicel and phosphoric acid-swollen cellulose (PASC). Further, we demonstrate that the LPMOs encoded by Cellulomonas flavigena exhibit synergy in cellulose degradation, which is due in part to decreased autoinactivation. CONCLUSIONS Together, these results advance understanding of the cellulose utilization machinery of historically important Cellulomonas species beyond hydrolytic enzymes to include lytic cleavage. This work also contributes to the broader mapping of enzyme activity in Auxiliary Activity Family 10 and provides new biocatalysts for potential applications in biomass modification.
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Affiliation(s)
- James Li
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Laleh Solhi
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Ethan D Goddard-Borger
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
| | - Yann Mathieu
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Warren W Wakarchuk
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Stephen G Withers
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada.
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada.
- Department of Botany, University of British Columbia, 3200 University Blvd, Vancouver, BC, V6T 1Z4, Canada.
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada.
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Brandt SC, Ellinger B, van Nguyen T, Harder S, Schlüter H, Hahnke RL, Rühl M, Schäfer W, Gand M. Aspergillus sydowii: Genome Analysis and Characterization of Two Heterologous Expressed, Non-redundant Xylanases. Front Microbiol 2020; 11:2154. [PMID: 33071998 PMCID: PMC7531221 DOI: 10.3389/fmicb.2020.573482] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/14/2020] [Indexed: 12/28/2022] Open
Abstract
A prerequisite for the transition toward a biobased economy is the identification and development of efficient enzymes for the usage of renewable resources as raw material. Therefore, different xylanolytic enzymes are important for efficient enzymatic hydrolysis of xylan-heteropolymers. A powerful tool to overcome the limited enzymatic toolbox lies in exhausting the potential of unexplored habitats. By screening a Vietnamese fungal culture collection of 295 undiscovered fungal isolates, 12 highly active xylan degraders were identified. One of the best xylanase producing strains proved to be an Aspergillus sydowii strain from shrimp shell (Fsh102), showing a specific activity of 0.6 U/mg. Illumina dye sequencing was used to identify our Fsh102 strain and determine differences to the A. sydowii CBS 593.65 reference strain. With activity based in-gel zymography and subsequent mass spectrometric identification, three potential proteins responsible for xylan degradation were identified. Two of these proteins were cloned from the cDNA and, furthermore, expressed heterologously in Escherichia coli and characterized. Both xylanases, were entirely different from each other, including glycoside hydrolases (GH) families, folds, substrate specificity, and inhibition patterns. The specific enzyme activity applying 0.1% birch xylan of both purified enzymes were determined with 181.1 ± 37.8 or 121.5 ± 10.9 U/mg for xylanase I and xylanase II, respectively. Xylanase I belongs to the GH11 family, while xylanase II is member of the GH10 family. Both enzymes showed typical endo-xylanase activity, the main products of xylanase I are xylobiose, xylotriose, and xylohexose, while xylobiose, xylotriose, and xylopentose are formed by xylanase II. Additionally, xylanase II showed remarkable activity toward xylotriose. Xylanase I is stable when stored up to 30°C and pH value of 9, while xylanase II started to lose significant activity stored at pH 9 after exceeding 3 days of storage. Xylanase II displayed about 40% activity when stored at 50°C for 24 h. The enzymes are tolerant toward mesophilic temperatures, while acting in a broad pH range. With site directed mutagenesis, the active site residues in both enzymes were confirmed. The presented activity and stability justify the classification of both xylanases as highly interesting for further development.
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Affiliation(s)
- Sophie C. Brandt
- Department of Molecular Phytopathology, University of Hamburg, Hamburg, Germany
| | - Bernhard Ellinger
- Department ScreeningPort, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Hamburg, Germany
| | - Thuat van Nguyen
- Department of Molecular Phytopathology, University of Hamburg, Hamburg, Germany
| | - Sönke Harder
- Mass Spectrometric Proteomics Group, Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hartmut Schlüter
- Mass Spectrometric Proteomics Group, Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Richard L. Hahnke
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Martin Rühl
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Giessen, Germany
| | - Wilhelm Schäfer
- Department of Molecular Phytopathology, University of Hamburg, Hamburg, Germany
| | - Martin Gand
- Department of Molecular Phytopathology, University of Hamburg, Hamburg, Germany
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Giessen, Germany
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Holland C, Simmons TJ, Meulewaeter F, Hudson A, Fry SC. Three highly acidic Equisetum XTHs differ from hetero-trans-β-glucanase in donor substrate specificity and are predominantly xyloglucan homo-transglucosylases. JOURNAL OF PLANT PHYSIOLOGY 2020; 251:153210. [PMID: 32544741 DOI: 10.1016/j.jplph.2020.153210] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 05/20/2020] [Accepted: 05/24/2020] [Indexed: 05/27/2023]
Abstract
Transglycanases are enzymes that remodel the primary cell wall in plants, potentially loosening and/or strengthening it. Xyloglucan endotransglucosylase (XET; EC 2.4.1.207), ubiquitous in land plants, is a homo-transglucanase activity (donor, xyloglucan; acceptor, xyloglucan) exhibited by XTH (xyloglucan endotransglucosylase/hydrolase) proteins. By contrast, hetero-trans-β-glucanase (HTG) is the only known enzyme that is preferentially a hetero-transglucanase. Its two main hetero-transglucanase activities are MLG : xyloglucan endotransglucosylase (MXE) and cellulose : xyloglucan endotransglucosylase (CXE). HTG is highly acidic and found only in the evolutionarily isolated genus of fern-allies, Equisetum. We now report genes for three new highly acidic HTG-related XTHs in E. fluviatile (EfXTH-A, EfXTH-H and EfXTH-I). We expressed them heterologously in Pichia and tested the encoded proteins' enzymic activities to determine whether their acidity and/or their Equisetum-specific sequences might confer high hetero-transglucanase activity. Untransformed Pichia was found to secrete MLG-degrading enzyme(s), which had to be removed for reliable MXE assays. All three acidic EfXTHs exhibited very predominantly XET activity, although low but measurable hetero-transglucanase activities (MXE and CXE) were also detected in EfXTH-H and EfXTH-I. We conclude that the extremely high hetero-transglucanase activities of Equisetum HTG are not emulated by similarly acidic Equisetum XTHs that share up to 55.5% sequence identity with HTG.
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Affiliation(s)
- Claire Holland
- The Edinburgh Cell Wall Group, Institute of Molecular Plant Sciences, The University of Edinburgh, Daniel Rutherford Building, The King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Thomas J Simmons
- The Edinburgh Cell Wall Group, Institute of Molecular Plant Sciences, The University of Edinburgh, Daniel Rutherford Building, The King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Frank Meulewaeter
- BASF Innovation Center Gent- Trait Research, Technologiepark-Zwijnaarde, 9052 Gent, Belgium
| | - Andrew Hudson
- Institute of Molecular Plant Sciences, The University of Edinburgh, Daniel Rutherford Building, The King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Stephen C Fry
- The Edinburgh Cell Wall Group, Institute of Molecular Plant Sciences, The University of Edinburgh, Daniel Rutherford Building, The King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK.
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9
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Kurotani KI, Wakatake T, Ichihashi Y, Okayasu K, Sawai Y, Ogawa S, Cui S, Suzuki T, Shirasu K, Notaguchi M. Host-parasite tissue adhesion by a secreted type of β-1,4-glucanase in the parasitic plant Phtheirospermum japonicum. Commun Biol 2020; 3:407. [PMID: 32733024 PMCID: PMC7393376 DOI: 10.1038/s42003-020-01143-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/10/2020] [Indexed: 01/10/2023] Open
Abstract
Tissue adhesion between plant species occurs both naturally and artificially. Parasitic plants establish intimate relationship with host plants by adhering tissues at roots or stems. Plant grafting, on the other hand, is a widely used technique in agriculture to adhere tissues of two stems. Here we found that the model Orobanchaceae parasitic plant Phtheirospermum japonicum can be grafted on to interfamily species. To understand molecular basis of tissue adhesion between distant plant species, we conducted comparative transcriptome analyses on both infection and grafting by P. japonicum on Arabidopsis. Despite different organs, we identified the shared gene expression profile, where cell proliferation- and cell wall modification-related genes are up-regulated. Among genes commonly induced in tissue adhesion between distant species, we showed a gene encoding a secreted type of β-1,4-glucanase plays an important role for plant parasitism. Our data provide insights into the molecular commonality between parasitism and grafting in plants.
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Affiliation(s)
- Ken-Ichi Kurotani
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Takanori Wakatake
- Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
- Center for Sustainable Resource Science, RIKEN, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Biocenter, Institute for Molecular Plant Physiology and Biophysics, Julius-von-Sachs-Institute, University of Würzburg, 97082, Würzburg, Germany
| | - Yasunori Ichihashi
- Center for Sustainable Resource Science, RIKEN, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Koji Okayasu
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Yu Sawai
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Satoshi Ogawa
- Center for Sustainable Resource Science, RIKEN, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Songkui Cui
- Institute for Research Initiatives, Division for Research Strategy, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, Matsumoto-cho, Kasugai, 487-8501, Japan
| | - Ken Shirasu
- Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.
- Center for Sustainable Resource Science, RIKEN, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
| | - Michitaka Notaguchi
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.
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Zavyalov AV, Rykov SV, Lunina NA, Sushkova VI, Yarotsky SV, Berezina OV. Plant Polysaccharide Xyloglucan and Enzymes That Hydrolyze It (Review). RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162019070148] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Karkehabadi S, Hansson H, Mikkelsen NE, Kim S, Kaper T, Sandgren M, Gudmundsson M. Structural studies of a glycoside hydrolase family 3 β-glucosidase from the model fungus Neurospora crassa. Acta Crystallogr F Struct Biol Commun 2018; 74:787-796. [PMID: 30511673 PMCID: PMC6277957 DOI: 10.1107/s2053230x18015662] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/05/2018] [Indexed: 11/29/2022] Open
Abstract
The glycoside hydrolase family 3 (GH3) β-glucosidases are a structurally diverse family of enzymes. Cel3A from Neurospora crassa (NcCel3A) belongs to a subfamily of key enzymes that are crucial for industrial biomass degradation. β-Glucosidases hydrolyse the β-1,4 bond at the nonreducing end of cellodextrins. The hydrolysis of cellobiose is of special importance as its accumulation inhibits other cellulases acting on crystalline cellulose. Here, the crystal structure of the biologically relevant dimeric form of NcCel3A is reported. The structure has been refined to 2.25 Å resolution, with an Rcryst and Rfree of 0.18 and 0.22, respectively. NcCel3A is an extensively N-glycosylated glycoprotein that shares 46% sequence identity with Hypocrea jecorina Cel3A, the structure of which has recently been published, and 61% sequence identity with the thermophilic β-glucosidase from Rasamsonia emersonii. NcCel3A is a three-domain protein with a number of extended loops that deepen the active-site cleft of the enzyme. These structures characterize this subfamily of GH3 β-glucosidases and account for the high cellobiose specificity of this subfamily.
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Affiliation(s)
- Saeid Karkehabadi
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Henrik Hansson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Nils Egil Mikkelsen
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Steve Kim
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA 94304, USA
| | - Thijs Kaper
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA 94304, USA
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Mikael Gudmundsson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
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12
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Veerakumar S, Manian RP. Recombinant β-agarases: insights into molecular, biochemical, and physiochemical characteristics. 3 Biotech 2018; 8:445. [PMID: 30333947 DOI: 10.1007/s13205-018-1470-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/03/2018] [Indexed: 12/11/2022] Open
Abstract
Agarases (agarose 4-glycanohydrolase; EC 3.2.1.81) are class of enzymes that belong to glycoside hydrolase (GH) family capable of hydrolyzing agar. Their classification depends on hydrolysis pattern and product formation. Among all the agarases, β-agarases and the oligosaccharides formed by its action have fascinated quite a lot of industries. Ample of β-agarase genes have been endowed from marine sources such as algae, sea water, and marine sediments, and the expression of these genes into suitable host gives rise to recombinant β-agarases. These recombinant β-agarases have wide range of industrial applications due to its improved catalytic efficiency and stability in tough environments with ease of production on large scale. In this review, we have perused different types of recombinant β-agarases in consort with their molecular, physiochemical, and kinetic properties in detail and the significant features of those agarases are spotlighted. From the literature reviewed after 2010, we have found that the recombinant β-agarases belonged to the families GH16, GH39, GH50, GH86, and GH118. Among that, GH39, GH50, and GH86 belonged to clan GH-A, while the GH16 family belonged to clan GH-B. It was observed that GH16 is the largest polyspecific glycoside hydrolase family with ample number of β-agarases and the families GH50 and GH118 were found to be monospecific with only β-agarase activity. And, out of 84 non-catalytic carbohydrate-binding modules (CBMs), only CBM6 and CBM13 were professed in β-agarases. We witnessed a larger heterogeneity in molecular, physiochemical, and catalytic characteristics of the recombinant β-agarases including molecular mass: 32-132 kDa, optimum pH: 4.5-9, optimum temperature 16-60 °C, K M: 0.68-59.8 mg/ml, and V max: 0.781-11,400 U/mg. Owing to this extensive range of heterogeneity, they have lion's share in the multibillion dollar enzyme market. This review provides a holistic insight to a few aspects of recombinant β-agarases which can be referred by the upcoming explorers to this area.
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Affiliation(s)
- Sneeha Veerakumar
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, 632014 India
| | - Ramesh Pathy Manian
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, 632014 India
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13
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Meekrathok P, Stubbs KA, Suginta W. Potent inhibition of a GH20 exo-β-N-acetylglucosaminidase from marine Vibrio bacteria by reaction intermediate analogues. Int J Biol Macromol 2018; 115:1165-1173. [DOI: 10.1016/j.ijbiomac.2018.04.193] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/14/2018] [Accepted: 04/30/2018] [Indexed: 02/04/2023]
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14
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Gudmundsson M, Hansson H, Karkehabadi S, Larsson A, Stals I, Kim S, Sunux S, Fujdala M, Larenas E, Kaper T, Sandgren M. Structural and functional studies of the glycoside hydrolase family 3 β-glucosidase Cel3A from the moderately thermophilic fungus Rasamsonia emersonii. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:860-70. [PMID: 27377383 PMCID: PMC4932919 DOI: 10.1107/s2059798316008482] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 05/25/2016] [Indexed: 12/16/2022]
Abstract
Cel3A from the thermophilic fungus R. emersonii has proven to be more efficient in the hydrolysis of β-glycosidic linkages than Cel3A from H. jecorina. The filamentous fungus Hypocrea jecorina produces a number of cellulases and hemicellulases that act in a concerted fashion on biomass and degrade it into monomeric or oligomeric sugars. β-Glucosidases are involved in the last step of the degradation of cellulosic biomass and hydrolyse the β-glycosidic linkage between two adjacent molecules in dimers and oligomers of glucose. In this study, it is shown that substituting the β-glucosidase from H. jecorina (HjCel3A) with the β-glucosidase Cel3A from the thermophilic fungus Rasamsonia emersonii (ReCel3A) in enzyme mixtures results in increased efficiency in the saccharification of lignocellulosic materials. Biochemical characterization of ReCel3A, heterologously produced in H. jecorina, reveals a preference for disaccharide substrates over longer gluco-oligosaccharides. Crystallographic studies of ReCel3A revealed a highly N-glycosylated three-domain dimeric protein, as has been observed previously for glycoside hydrolase family 3 β-glucosidases. The increased thermal stability and saccharification yield and the superior biochemical characteristics of ReCel3A compared with HjCel3A and mixtures containing HjCel3A make ReCel3A an excellent candidate for addition to enzyme mixtures designed to operate at higher temperatures.
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Affiliation(s)
- Mikael Gudmundsson
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
| | - Henrik Hansson
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
| | - Saeid Karkehabadi
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
| | - Anna Larsson
- Department of Cell and Molecular Biology, Uppsala University, Box 596, 751 24 Uppsala, Sweden
| | - Ingeborg Stals
- Laboratory for Protein Biochemistry and Biomolecular Engineering, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Steve Kim
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA 94304, USA
| | - Sergio Sunux
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA 94304, USA
| | - Meredith Fujdala
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA 94304, USA
| | - Edmund Larenas
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA 94304, USA
| | - Thijs Kaper
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA 94304, USA
| | - Mats Sandgren
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
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15
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Schmoll M, Dattenböck C, Carreras-Villaseñor N, Mendoza-Mendoza A, Tisch D, Alemán MI, Baker SE, Brown C, Cervantes-Badillo MG, Cetz-Chel J, Cristobal-Mondragon GR, Delaye L, Esquivel-Naranjo EU, Frischmann A, Gallardo-Negrete JDJ, García-Esquivel M, Gomez-Rodriguez EY, Greenwood DR, Hernández-Oñate M, Kruszewska JS, Lawry R, Mora-Montes HM, Muñoz-Centeno T, Nieto-Jacobo MF, Nogueira Lopez G, Olmedo-Monfil V, Osorio-Concepcion M, Piłsyk S, Pomraning KR, Rodriguez-Iglesias A, Rosales-Saavedra MT, Sánchez-Arreguín JA, Seidl-Seiboth V, Stewart A, Uresti-Rivera EE, Wang CL, Wang TF, Zeilinger S, Casas-Flores S, Herrera-Estrella A. The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species. Microbiol Mol Biol Rev 2016; 80:205-327. [PMID: 26864432 PMCID: PMC4771370 DOI: 10.1128/mmbr.00040-15] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for "hot topic" research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei, T. atroviride, and T. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N-linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma, and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway.
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Affiliation(s)
- Monika Schmoll
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | - Christoph Dattenböck
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Doris Tisch
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Mario Ivan Alemán
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | - Scott E Baker
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher Brown
- University of Otago, Department of Biochemistry and Genetics, Dunedin, New Zealand
| | | | - José Cetz-Chel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - Luis Delaye
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | | | - Alexa Frischmann
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | - Monica García-Esquivel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - David R Greenwood
- The University of Auckland, School of Biological Sciences, Auckland, New Zealand
| | - Miguel Hernández-Oñate
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | - Joanna S Kruszewska
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Robert Lawry
- Lincoln University, Bio-Protection Research Centre, Lincoln, Canterbury, New Zealand
| | | | | | | | | | | | | | - Sebastian Piłsyk
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Kyle R Pomraning
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Aroa Rodriguez-Iglesias
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Verena Seidl-Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | | | - Chih-Li Wang
- National Chung-Hsing University, Department of Plant Pathology, Taichung, Taiwan
| | - Ting-Fang Wang
- Academia Sinica, Institute of Molecular Biology, Taipei, Taiwan
| | - Susanne Zeilinger
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria University of Innsbruck, Institute of Microbiology, Innsbruck, Austria
| | | | - Alfredo Herrera-Estrella
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
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16
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Illuminating the binding interactions of galactonoamidines during the inhibition of β-galactosidase (E. coli). Bioorg Med Chem 2016; 24:661-71. [PMID: 26740154 DOI: 10.1016/j.bmc.2015.12.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 12/08/2015] [Accepted: 12/17/2015] [Indexed: 11/20/2022]
Abstract
Several galactonoamidines were previously identified as very potent competitive inhibitors that exhibit stabilizing hydrophobic interactions of the aglycon in the active site of β-galactosidase (Aspergillus oryzae). To elucidate the contributions of the glycon to the overall inhibition ability of the compounds, three glyconoamidine derivatives with alteration in the glycon at C-2 and C-4 were synthesized and evaluated herein. All amidines are competitive inhibitors of β-galactosidase (Escherichia coli) and show significantly reduced inhibition ability when compared to the parent. The results highlight strong hydrogen-bonding interactions between the hydroxyl group at C-2 of the amidine glycon and the active site of the enzyme. Slightly weaker H-bonds are promoted through the hydroxyl group at C-4. The inhibition constants were determined to be picomolar for the parent galactonoamidine, and nanomolar for the designed derivatives rendering all glyconoamidines very potent inhibitors of glycosidases albeit the derivatized amidines show up to 700-fold lower inhibition activity than the parent.
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17
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The crystal structure of an inverting glycoside hydrolase family 9 exo-β-D-glucosaminidase and the design of glycosynthase. Biochem J 2016; 473:463-72. [DOI: 10.1042/bj20150966] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 11/27/2015] [Indexed: 02/04/2023]
Abstract
The crystal structure of an inverting exo-β-D-glucosaminidase from glycoside hydrolase family 9 was determined. This is the first description of the structure of an exo-type enzyme from this family. A glycosynthase was produced from this enzyme through saturation mutagenesis.
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18
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Deshmukh RA, Jagtap S, Mandal MK, Mandal SK. Purification, biochemical characterization and structural modelling of alkali-stable β-1,4-xylan xylanohydrolase from Aspergillus fumigatus R1 isolated from soil. BMC Biotechnol 2016; 16:11. [PMID: 26847222 PMCID: PMC4743132 DOI: 10.1186/s12896-016-0242-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 01/20/2016] [Indexed: 11/30/2022] Open
Abstract
Background Aspergillus fumigatus R1 produced xylanase under submerged fermentation which degrades the complex hemicelluloses contained in agricultural substrates. Xylanases have gained considerable attention because of their tremendous applications in industries. The purpose of our study was to purify xylanase and study its biochemical properties. We have predicted the secondary structure of purified xylanase and evaluated its active site residues and substrate binding sites based on the global and local structural similarity. Results Various microorganisms were isolated from Puducherry soil and screened by Congo-red test. The best isolate was identified to be Aspergillus fumigatus R1. The production kinetics showed the highest xylanase production (208 IU/ml) by this organism in 96 h using 1 % rice bran as the only carbon source. The purification of extracellular xylanase was carried out by fractional ammonium sulphate precipitation (30–55 %), followed by extensive dialysis and Bio-Gel P-60 Gel-filtration chromatography. The enzyme was purified 58.10 folds with a specific activity of 38196.22 IU/mg. The biochemical characterization of the pure enzyme was carried out for its optimum pH and temperature (5.0 and 500C), pH and temperature stability, molecular mass (Mr) (24.5 kDa) and pI (6.29). The complete sequence of protein was obtained by mass spectrometry analysis. Apparent Km and Vmax values of the xylanase for birchwood xylan were 11.66 mg/ml and 87.6 μmol min−1 mg−1 respectively. Conclusion Purified xylanase was analyzed by mass-spectrometry which revealed 2 unique peptides. Xylanase under current study showed significant production using agricultural residues and a broad range of pH stability in the alkaline region. Xylanase produced by Aspergillus fumigatus R1 could serve as the enzyme of choice in industries.
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Affiliation(s)
- Rehan Ahmed Deshmukh
- Department of Microbiology, School Of Life-Sciences, Pondicherry University, R.V. Nagar, Kalapet, Puducherry, 605014, India.
| | - Sharmili Jagtap
- Department of Microbiology, School Of Life-Sciences, Pondicherry University, R.V. Nagar, Kalapet, Puducherry, 605014, India.
| | - Madan Kumar Mandal
- Department of Microbiology, School Of Life-Sciences, Pondicherry University, R.V. Nagar, Kalapet, Puducherry, 605014, India.
| | - Suraj Kumar Mandal
- Department of Microbiology, School Of Life-Sciences, Pondicherry University, R.V. Nagar, Kalapet, Puducherry, 605014, India.
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19
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Kusaykin MI, Silchenko AS, Zakharenko AM, Zvyagintseva TN. Fucoidanases. Glycobiology 2015; 26:3-12. [PMID: 26347522 DOI: 10.1093/glycob/cwv072] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 08/18/2015] [Indexed: 11/13/2022] Open
Abstract
In recent years, the research of fucoidans has steadily increased. The interest in these substances is due to their various biological activities. Despite a wide range of biological activity and the lack of oral toxicity, fucoidans remain relatively unexploited as a source of medicines because of their heterogeneity. Enzymes that degrade polyanionic polysaccharides are widely used for establishing their structures and structure-activity relationships. Sometimes, to obtain preparations of polysaccharides with standard characteristics, for example, medicines and food supplements, enzymatic treatment can be also applied. Only a few sources of enzymes with fucoidanase activity have been described, and only a few studies regarding the isolation and characterization of fucoidanases have been performed. The data on the specificity of fucoidanases: the type of cleaved glycoside bond, the relation between catalytic activity and the degree of substrate sulfation are scarce. The review summarizes achievements in the research of fucoidanases, mechanisms of enzymatic degradation of fucoidans, as well as of structures of sulfated fucooligosaccharides obtained under the action of fucoidanases.
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Affiliation(s)
- Mikhail I Kusaykin
- G. B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Vladivostok, 159, Prospect 100-let, Vladivostoku 690022, Russia
| | - Artem S Silchenko
- G. B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Vladivostok, 159, Prospect 100-let, Vladivostoku 690022, Russia
| | - Alexander M Zakharenko
- G. B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Vladivostok, 159, Prospect 100-let, Vladivostoku 690022, Russia
| | - Tatyana N Zvyagintseva
- G. B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Vladivostok, 159, Prospect 100-let, Vladivostoku 690022, Russia
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20
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Abstract
SUMMARY Biomass is constructed of dense recalcitrant polymeric materials: proteins, lignin, and holocellulose, a fraction constituting fibrous cellulose wrapped in hemicellulose-pectin. Bacteria and fungi are abundant in soil and forest floors, actively recycling biomass mainly by extracting sugars from holocellulose degradation. Here we review the genome-wide contents of seven Aspergillus species and unravel hundreds of gene models encoding holocellulose-degrading enzymes. Numerous apparent gene duplications followed functional evolution, grouping similar genes into smaller coherent functional families according to specialized structural features, domain organization, biochemical activity, and genus genome distribution. Aspergilli contain about 37 cellulase gene models, clustered in two mechanistic categories: 27 hydrolyze and 10 oxidize glycosidic bonds. Within the oxidative enzymes, we found two cellobiose dehydrogenases that produce oxygen radicals utilized by eight lytic polysaccharide monooxygenases that oxidize glycosidic linkages, breaking crystalline cellulose chains and making them accessible to hydrolytic enzymes. Among the hydrolases, six cellobiohydrolases with a tunnel-like structural fold embrace single crystalline cellulose chains and cooperate at nonreducing or reducing end termini, splitting off cellobiose. Five endoglucanases group into four structural families and interact randomly and internally with cellulose through an open cleft catalytic domain, and finally, seven extracellular β-glucosidases cleave cellobiose and related oligomers into glucose. Aspergilli contain, on average, 30 hemicellulase and 7 accessory gene models, distributed among 9 distinct functional categories: the backbone-attacking enzymes xylanase, mannosidase, arabinase, and xyloglucanase, the short-side-chain-removing enzymes xylan α-1,2-glucuronidase, arabinofuranosidase, and xylosidase, and the accessory enzymes acetyl xylan and feruloyl esterases.
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21
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Payne CM, Knott BC, Mayes HB, Hansson H, Himmel ME, Sandgren M, Ståhlberg J, Beckham GT. Fungal Cellulases. Chem Rev 2015; 115:1308-448. [DOI: 10.1021/cr500351c] [Citation(s) in RCA: 533] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christina M. Payne
- Department
of Chemical and Materials Engineering and Center for Computational
Sciences, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, Kentucky 40506, United States
| | - Brandon C. Knott
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Heather B. Mayes
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Henrik Hansson
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Michael E. Himmel
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Mats Sandgren
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Jerry Ståhlberg
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Gregg T. Beckham
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
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22
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Lakhundi S, Siddiqui R, Khan NA. Cellulose degradation: a therapeutic strategy in the improved treatment of Acanthamoeba infections. Parasit Vectors 2015; 8:23. [PMID: 25586209 PMCID: PMC4300153 DOI: 10.1186/s13071-015-0642-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/05/2015] [Indexed: 11/10/2022] Open
Abstract
Acanthamoeba is an opportunistic free-living amoeba that can cause blinding keratitis and fatal brain infection. Early diagnosis, followed by aggressive treatment is a pre-requisite in the successful treatment but even then the prognosis remains poor. A major drawback during the course of treatment is the ability of the amoeba to enclose itself within a shell (a process known as encystment), making it resistant to chemotherapeutic agents. As the cyst wall is partly made of cellulose, thus cellulose degradation offers a potential therapeutic strategy in the effective targeting of trophozoite encased within the cyst walls. Here, we present a comprehensive report on the structure of cellulose and cellulases, as well as known cellulose degradation mechanisms with an eye to target the Acanthamoeba cyst wall. The disruption of the cyst wall will make amoeba (concealed within) susceptible to chemotherapeutic agents, and at the very least inhibition of the excystment process will impede infection recurrence, as we bring these promising drug targets into focus so that they can be explored to their fullest.
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Affiliation(s)
- Sahreena Lakhundi
- Department of Biological and Biomedical Sciences, Aga Khan University, Stadium Road, Karachi, Pakistan.
| | - Ruqaiyyah Siddiqui
- Department of Biological and Biomedical Sciences, Aga Khan University, Stadium Road, Karachi, Pakistan.
| | - Naveed Ahmed Khan
- Department of Biological and Biomedical Sciences, Aga Khan University, Stadium Road, Karachi, Pakistan.
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Molecular modeling and MM-PBSA free energy analysis of endo-1,4-β-xylanase from Ruminococcus albus 8. Int J Mol Sci 2014; 15:17284-303. [PMID: 25264743 PMCID: PMC4227162 DOI: 10.3390/ijms151017284] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 09/11/2014] [Accepted: 09/15/2014] [Indexed: 11/16/2022] Open
Abstract
Endo-1,4-β-xylanase (EC 3.2.1.8) is the enzyme from Ruminococcus albus 8 (R. albus 8) (Xyn10A), and catalyzes the degradation of arabinoxylan, which is a major cell wall non-starch polysaccharide of cereals. The crystallographic structure of Xyn10A is still unknown. For this reason, we report a computer-assisted homology study conducted to build its three-dimensional structure based on the known sequence of amino acids of this enzyme. In this study, the best similarity was found with the Clostridium thermocellum (C. thermocellum) N-terminal endo-1,4-β-D-xylanase 10 b. Following the 100 ns molecular dynamics (MD) simulation, a reliable model was obtained for further studies. Molecular Mechanics/Poisson-Boltzmann Surface Area (MM-PBSA) methods were used for the substrate xylotetraose having the reactive sugar, which was bound in the -1 subsite of Xyn10A in the 4C1 (chair) and 2SO (skew boat) ground state conformations. According to the simulations and free energy analysis, Xyn10A binds the substrate with the -1 sugar in the 2SO conformation 39.27 kcal·mol(-1) tighter than the substrate with the sugar in the 4C1 conformation. According to the Xyn10A-2SO Xylotetraose (X4(sb) interaction energies, the most important subsite for the substrate binding is subsite -1. The results of this study indicate that the substrate is bound in a skew boat conformation with Xyn10A and the -1 sugar subsite proceeds from the 4C1 conformation through 2SO to the transition state. MM-PBSA free energy analysis indicates that Asn187 and Trp344 in subsite -1 may an important residue for substrate binding. Our findings provide fundamental knowledge that may contribute to further enhancement of enzyme performance through molecular engineering.
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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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Gomez del Pulgar EM, Saadeddin A. The cellulolytic system ofThermobifida fusca. Crit Rev Microbiol 2013; 40:236-47. [DOI: 10.3109/1040841x.2013.776512] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Petersen BO, Olsen O, Beeren SR, Hindsgaul O, Meier S. Monitoring pathways of β-glucan degradation by enzyme mixtures in situ. Carbohydr Res 2013; 368:47-51. [DOI: 10.1016/j.carres.2012.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Accepted: 12/07/2012] [Indexed: 11/15/2022]
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Gokhale AA, Lee I. Cellulase Immobilized Nanostructured Supports for Efficient Saccharification of Cellulosic Substrates. Top Catal 2012. [DOI: 10.1007/s11244-012-9891-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Lammerts van Bueren A, Otani S, Friis EP, Wilson KS, Davies GJ. Three-dimensional structure of a thermophilic family GH11 xylanase from Thermobifida fusca. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:141-4. [PMID: 22297985 PMCID: PMC3274389 DOI: 10.1107/s1744309111049608] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 11/21/2011] [Indexed: 11/10/2022]
Abstract
Thermostable enzymes employ various structural features dictated at the amino-acid sequence level that allow them to maintain their integrity at higher temperatures. Many hypotheses as to the nature of thermal stability have been proposed, including optimized core hydrophobicity and an increase in charged surface residues to enhance polar solvent interactions for solubility. Here, the three-dimensional structure of the family GH11 xylanase from the moderate thermophile Thermobifida fusca in its trapped covalent glycosyl-enzyme intermediate complex is presented. Interactions with the bound ligand show fewer direct hydrogen bonds from ligand to protein than observed in previous complexes from other species and imply that binding of the xylan substrate involves several water-mediated hydrogen bonds.
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Affiliation(s)
| | - Suzie Otani
- Novozymes A/S, Krogshoejvej 36, 2880 Bagsvaerd, Denmark
| | | | - Keith S. Wilson
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
| | - Gideon J. Davies
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
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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: 275] [Impact Index Per Article: 21.2] [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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32
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Naumoff DG. Hierarchical classification of glycoside hydrolases. BIOCHEMISTRY (MOSCOW) 2011; 76:622-35. [PMID: 21639842 DOI: 10.1134/s0006297911060022] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This review deals with structural and functional features of glycoside hydrolases, a widespread group of enzymes present in almost all living organisms. Their catalytic domains are grouped into 120 amino acid sequence-based families in the international classification of the carbohydrate-active enzymes (CAZy database). At a higher hierarchical level some of these families are combined in 14 clans. Enzymes of the same clan have common evolutionary origin of their genes and share the most important functional characteristics such as composition of the active center, anomeric configuration of cleaved glycosidic bonds, and molecular mechanism of the catalyzed reaction (either inverting, or retaining). There are now extensive data in the literature concerning the relationship between glycoside hydrolase families belonging to different clans and/or included in none of them, as well as information on phylogenetic protein relationship within particular families. Summarizing these data allows us to propose a multilevel hierarchical classification of glycoside hydrolases and their homologs. It is shown that almost the whole variety of the enzyme catalytic domains can be brought into six main folds, large groups of proteins having the same three-dimensional structure and the supposed common evolutionary origin.
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Affiliation(s)
- D G Naumoff
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, 117312, Russia.
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33
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Goddard-Borger ED, Fiege B, Kwan EM, Withers SG. Glycosynthase-Mediated Assembly of Xylanase Substrates and Inhibitors. Chembiochem 2011; 12:1703-11. [DOI: 10.1002/cbic.201100229] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Indexed: 11/09/2022]
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34
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Li J, Wang L. Why substituting the asparagine at position 35 in Bacillus circulans xylanase with an aspartic acid remarkably improves the enzymatic catalytic activity? A quantum chemistry-based calculation study. Polym Degrad Stab 2011. [DOI: 10.1016/j.polymdegradstab.2011.01.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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35
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Jollymore A, Li H. Measuring “Unmeasurable” Folding Kinetics of Proteins by Single-Molecule Force Spectroscopy. J Mol Biol 2010; 402:610-7. [DOI: 10.1016/j.jmb.2010.07.059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2010] [Revised: 07/29/2010] [Accepted: 07/29/2010] [Indexed: 10/19/2022]
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36
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Reitinger S, Yu Y, Wicki J, Ludwiczek M, D’Angelo I, Baturin S, Okon M, Strynadka NCJ, Lutz S, Withers SG, McIntosh LP. Circular Permutation of Bacillus circulans Xylanase: A Kinetic and Structural Study. Biochemistry 2010; 49:2464-74. [DOI: 10.1021/bi100036f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stephan Reitinger
- 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 1Z1
| | - Ying Yu
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322
| | - Jacqueline Wicki
- 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 1Z1
| | - Martin Ludwiczek
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Igor D’Angelo
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Simon Baturin
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Mark Okon
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Natalie C. J. Strynadka
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
- Michael Smith Laboratory, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
- Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Stefan Lutz
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322
| | - Stephen G. Withers
- 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 1Z1
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Lawrence P. McIntosh
- 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 1Z1
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
- Michael Smith Laboratory, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
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Yip VLY, Withers SG. Family 4 glycoside hydrolases are special: The first β-elimination mechanism amongst glycoside hydrolases. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420500515926] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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38
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Vuong TV, Wilson DB. The absence of an identifiable single catalytic base residue inThermobifida fuscaexocellulase Cel6B. FEBS J 2009; 276:3837-45. [DOI: 10.1111/j.1742-4658.2009.07097.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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39
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Soliman MES, Ruggiero GD, Pernía JJR, Greig IR, Williams IH. Computational mutagenesis reveals the role of active-site tyrosine in stabilising a boat conformation for the substrate: QM/MM molecular dynamics studies of wild-type and mutant xylanases. Org Biomol Chem 2009; 7:460-8. [DOI: 10.1039/b814695k] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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van den Broek LAM, Hinz SWA, Beldman G, Vincken JP, Voragen AGJ. Bifidobacterium carbohydrases-their role in breakdown and synthesis of (potential) prebiotics. Mol Nutr Food Res 2008; 52:146-63. [PMID: 18040988 DOI: 10.1002/mnfr.200700121] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
There is an increasing interest to positively influence the human intestinal microbiota through the diet by the use of prebiotics and/or probiotics. It is anticipated that this will balance the microbial composition in the gastrointestinal tract in favor of health promoting genera such as Bifidobacterium and Lactobacillus. Carbohydrates like non-digestible oligosaccharides are potential prebiotics. To understand how these bacteria can grow on these carbon sources, knowledge of the carbohydrate-modifying enzymes is needed. Little is known about the carbohydrate-modifying enzymes of bifidobacteria. The genome sequence of Bifidobacterium adolescentis and Bifidobacterium longum biotype longum has been completed and it was observed that for B. longum biotype longum more than 8% of the annotated genes were involved in carbohydrate metabolism. In addition more sequence data of individual carbohydrases from other Bifidobacterium spp. became available. Besides the degradation of (potential) prebiotics by bifidobacterial glycoside hydrolases, we will focus in this review on the possibilities to produce new classes of non-digestible oligosaccharides by showing the presence and (transglycosylation) activity of the most important carbohydrate modifying enzymes in bifidobacteria. Approaches to use and improve carbohydrate-modifying enzymes in prebiotic design will be discussed.
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Cel9D, an atypical 1,4-beta-D-glucan glucohydrolase from Fibrobacter succinogenes: characteristics, catalytic residues, and synergistic interactions with other cellulases. J Bacteriol 2008; 190:1976-84. [PMID: 18203823 DOI: 10.1128/jb.01667-07] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The increasing demands of renewable energy have led to the critical emphasis on novel enzymes to enhance cellulose biodegradation for biomass conversion. To identify new cellulases in the ruminal bacterium Fibrobacter succinogenes, a cell extract of cellulose-grown cells was separated by ion-exchange chromatography and cellulases were located by zymogram analysis and identified by peptide mass fingerprinting. An atypical family 9 glycoside hydrolase (GH9), Cel9D, with less than 20% identity to typical GH9 cellulases, was identified. Purified recombinant Cel9D enhanced the production of reducing sugar from acid swollen cellulose (ASC) and Avicel by 1.5- to 4-fold when mixed separately with each of four other glucanases, although it had low activity on these substrates. Cel9D degraded ASC and cellodextrins with a degree of polymerization higher than 2 to glucose with no apparent endoglucanase activity, and its activity was restricted to beta-1-->4-linked glucose residues. It catalyzed the hydrolysis of cellulose by an inverting mode of reaction, releasing glucose from the nonreducing end. Unlike many GH9 cellulases, calcium ions were not required for its function. Cel9D had increased kcat/Km values for cello-oligosaccharides with higher degrees of polymerization. The kcat/Km value for cellohexaose was 2,300 times higher than that on cellobiose. This result indicates that Cel9D is a 1,4-beta-D-glucan glucohydrolase (EC 3.2.1.74) in the GH9 family. Site-directed mutagenesis of Cel9D identified Asp166 and Glu612 as the candidate catalytic residues, while Ser168, which is not present in typical GH9 cellulases, has a crucial structural role. This enzyme has an important role in crystalline cellulose digestion by releasing glucose from accessible cello-oligosaccharides.
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Cloning, Expression and Characterization of a Glycoside Hydrolase Family 39 Xylosidase from Bacillus Halodurans C-125. Appl Biochem Biotechnol 2007; 146:69-78. [DOI: 10.1007/s12010-007-8055-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2007] [Accepted: 09/14/2007] [Indexed: 10/22/2022]
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43
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Enhancement of the thermostability and hydrolytic activity of GH10 xylanase by module shuffling between Cellulomonas fimi Cex and Thermomonospora alba XylA. World J Microbiol Biotechnol 2007. [DOI: 10.1007/s11274-006-9263-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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44
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Wagschal K, Franqui-Espiet D, Lee CC, Kibblewhite-Accinelli RE, Robertson GH, Wong DW. Genetic and biochemical characterization of an α-l-arabinofuranosidase isolated from a compost starter mixture. Enzyme Microb Technol 2007. [DOI: 10.1016/j.enzmictec.2006.06.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Ma C, Lu X, Shi C, Li J, Gu Y, Ma Y, Chu Y, Han F, Gong Q, Yu W. Molecular cloning and characterization of a novel beta-agarase, AgaB, from marine Pseudoalteromonas sp. CY24. J Biol Chem 2006; 282:3747-54. [PMID: 17166842 DOI: 10.1074/jbc.m607888200] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Agarases are generally classified into glycoside hydrolase families 16, 50, and 86 and are found to degrade agarose to frequently generate neoagarobiose, neoagarotetraose, or neoagarohexaose as the main products. In this study we have cloned a novel endo-type beta-agarase gene, agaB, from marine Pseudoalteromonas sp. CY24. The novel agarase encoded by agaB gene has no significant sequence similarity with any known proteins including all glycoside hydrolases. It degrades agarose to generate neoagarooctaose and neoagarodecaose as the main end products. Based on the analyses of enzymatic kinetics and degradation patterns of different oligosaccharides, the agarase AgaB appears to have a large substrate binding cleft that accommodates 12 sugar units, with 8 sugar units toward the reducing end spanning subsites +1 to +8 and 4 sugar units toward the non-reducing end spanning subsites -4 to -1, and enzymatic cleavage taking place between subsites -1 and +1. In addition, 1H NMR analysis shows that this enzyme hydrolyzes the glycosidic bond with inversion of anomeric configuration, in contrast to other known agarases that are retaining. Altogether, AgaB is structurally and functionally different from other known agarases and appears to represent a new family of glycoside hydrolase.
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Affiliation(s)
- Cuiping Ma
- Department of Molecular Biology, Marine Drug and Food Institute, Ocean University of China, Qingdao 266003, China
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St John FJ, Rice JD, Preston JF. Characterization of XynC from Bacillus subtilis subsp. subtilis strain 168 and analysis of its role in depolymerization of glucuronoxylan. J Bacteriol 2006; 188:8617-26. [PMID: 17028274 PMCID: PMC1698249 DOI: 10.1128/jb.01283-06] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2006] [Accepted: 09/28/2006] [Indexed: 11/20/2022] Open
Abstract
Secretion of xylanase activities by Bacillus subtilis 168 supports the development of this well-defined genetic system for conversion of methylglucuronoxylan (MeGAXn [where n represents the number of xylose residues]) in the hemicellulose component of lignocellulosics to biobased products. In addition to the characterized glycosyl hydrolase family 11 (GH 11) endoxylanase designated XynA, B. subtilis 168 secretes a second endoxylanase as the translated product of the ynfF gene. This sequence shows remarkable homology to the GH 5 endoxylanase secreted by strains of Erwinia chrysanthemi. To determine its properties and potential role in the depolymerization of MeGAXn, the ynfF gene was cloned and overexpressed to provide an endoxylanase, designated XynC, which was characterized with respect to substrate preference, kinetic properties, and product formation. With different sources of MeGAXn as the substrate, the specific activity increased with increasing methylglucuronosyl substitutions on the beta-1,4-xylan chain. With MeGAXn from sweetgum as a preferred substrate, XynC exhibited a Vmax of 59.9 units/mg XynC, a Km of 1.63 mg MeGAXn/ml, and a k(cat) of 2,635/minute at pH 6.0 and 37 degrees C. Matrix-assisted laser desorption ionization-time of flight mass spectrometry and 1H nuclear magnetic resonance data revealed that each hydrolysis product has a single glucuronosyl substitution penultimate to the reducing terminal xylose. This detailed analysis of XynC from B. subtilis 168 defines the unique depolymerization process catalyzed by the GH 5 endoxylanases. Based upon product analysis, B. subtilis 168 secretes both XynA and XynC. Expression of xynA was subject to MeGAXn induction; xynC expression was constitutive with growth on different substrates. Translation and secretion of both GH 11 and GH 5 endoxylanases by the fully sequenced and genetically malleable B. subtilis 168 recommends this bacterium for the introduction of genes required for the complete utilization of products of the enzyme-catalyzed depolymerization of MeGAXn. B. subtilis may serve as a model platform for development of gram-positive biocatalysts for conversion of lignocellulosic materials to renewable fuels and chemicals.
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Affiliation(s)
- Franz J St John
- Department of Microbiology and Cell Science, University of Florida, Box 110700, Bldg. 981, Museum Rd., Gainesville, FL 32611, USA
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Monterroso B, López-Zumel C, García J, Sáiz J, García P, Campillo N, Menéndez M. Unravelling the structure of the pneumococcal autolytic lysozyme. Biochem J 2006; 391:41-9. [PMID: 15943581 PMCID: PMC1237137 DOI: 10.1042/bj20050612] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The LytC lysozyme of Streptococcus pneumoniae forms part of the autolytic system of this important pathogen. This enzyme is composed of a C-terminal CM (catalytic module), belonging to the GH25 family of glycosyl hydrolases, and an N-terminal CBM (choline-binding module), made of eleven homologous repeats, that specifically recognizes the choline residues that are present in pneumococcal teichoic and lipoteichoic acids. This arrangement inverts the general assembly pattern of the major pneumococcal autolysin, LytA, and the lytic enzymes encoded by pneumococcal bacteriophages that place the CBM (made of six repeats) at the C-terminus. In the present paper, a three-dimensional model of LytC built by homology modelling of each module and consistent with spectroscopic and hydrodynamic studies is shown. In addition, the putative catalytic-pair residues are identified. Despite the inversion in the modular arrangement, LytC and the bacteriophage-encoded Cpl-1 lysozyme most probably adopt a similar global fold. However, the distinct choline-binding ability and their substrate-binding surfaces may reflect a divergent evolution directed by the different roles played by them in the host (LytC) or in the bacteriophage (Cpl-1). The tight binding of LytC to the pneumococcal envelope, mediated by the acquisition of additional choline-binding repeats, could facilitate the regulation of the potentially suicidal activity of this autolysin. In contrast, a looser attachment of Cpl-1 to the cell wall and the establishment of more favourable interactions between its highly negatively charged catalytic surface and the positively charged chains of pneumococcal murein could enhance the lytic activity of the parasite-encoded enzyme and therefore liberation of the phage progeny.
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Affiliation(s)
- Begoña Monterroso
- *Instituto de Química-Física “Rocasolano” (CSIC), Serrano 119, 28006 Madrid, Spain
| | - Consuelo López-Zumel
- *Instituto de Química-Física “Rocasolano” (CSIC), Serrano 119, 28006 Madrid, Spain
| | - José L. García
- †Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - José L. Sáiz
- *Instituto de Química-Física “Rocasolano” (CSIC), Serrano 119, 28006 Madrid, Spain
| | - Pedro García
- †Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Nuria E. Campillo
- ‡Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
- Correspondence may be addressed to either of these authors (email or )
| | - Margarita Menéndez
- *Instituto de Química-Física “Rocasolano” (CSIC), Serrano 119, 28006 Madrid, Spain
- Correspondence may be addressed to either of these authors (email or )
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48
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Fliegmann J, Montel E, Djulić A, Cottaz S, Driguez H, Ebel J. Catalytic properties of the bifunctional soybean beta-glucan-binding protein, a member of family 81 glycoside hydrolases. FEBS Lett 2005; 579:6647-52. [PMID: 16297387 DOI: 10.1016/j.febslet.2005.10.060] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2005] [Revised: 10/28/2005] [Accepted: 10/31/2005] [Indexed: 11/22/2022]
Abstract
The beta-glucan-binding protein (GBP) of soybean (Glycine max L.) has been shown to contain two different activities. As part of the plasma membrane-localized pathogen receptor complex, it binds a microbial cell wall elicitor, triggering the activation of defence responses. Additionally, the GBP is able to hydrolyze beta-1,3-glucans, as present in the cell walls of potential pathogens. The substrate specificity, the mode of action, and the stereochemistry of the catalysis have been elucidated. This defines for the first time the inverting mode of the catalytic mechanism of glycoside hydrolases belonging to family 81.
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Affiliation(s)
- Judith Fliegmann
- Department Biologie I - Botanik, LMU, Menzinger Str. 67, D-80638 München, Germany.
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49
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Cheng CY, Chang CH, Wu YJ, Li YK. Exploration of glycosyl hydrolase family 75, a chitosanase from Aspergillus fumigatus. J Biol Chem 2005; 281:3137-44. [PMID: 16330537 DOI: 10.1074/jbc.m512506200] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A powerful endo-chitosanase (CSN) previously described for a large scale preparation of chito-oligosaccharides (Cheng, C.-Y., and Li, Y.-K. (2000) Biotechnol. Appl. Biochem. 32, 197-203) was cloned from Aspergillus fumigatus and further identified as a member of glycosyl hydrolase family 75. We report here a study of gene expression, functional characterization, and mutation analysis of this enzyme. Gene cloning was accomplished by reverse transcription-PCR and inverse PCR. Within the 1382-bp Aspergillus gene (GenBank accession number AY190324), two introns (67 and 82 bp) and an open reading frame encoding a 238-residue protein containing a 17-residue signal peptide were characterized. The recombinant mature protein was overexpressed as an inclusion body in Escherichia coli, rescued by treatment with 5 m urea, and subsequently purified by cation exchange chromatography. A time course 1H NMR study on the enzymatic formation of chito-oligosaccharides confirmed that this A. fumigatus CSN is an inverting enzyme. Tandem mass spectrum analysis of the enzymatic hydrolysate revealed that the recombinant CSN can cleave linkages of GlcNAc-GlcN and GlcN-GlcN in its substrate, suggesting that it is a subclass I chitosanase. In addition, an extensive site-directed mutagenesis study on 10 conserved carboxylic amino acids of glycosyl hydrolase family 75 was performed. This showed that among these various mutants, D160N and E169Q lost nearly all activity. Further investigation using circular dichroism measurements of D160N, E169Q, wild-type CSN, and other active mutants showed similar spectra, indicating that the loss of enzymatic activity in D160N and E169Q was not because of changes in protein structure but was caused by loss of the catalytic essential residue. We conclude that Asp160 and Glu169 are the essential residues for the action of A. fumigatus endo-chitosanase.
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Affiliation(s)
- Chih-Yu Cheng
- Center for Interdisciplinary Molecular Science and Department of Applied Chemistry, National Chiao Tung University, Hsinchu 30010, Taiwan
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50
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Stam MR, Blanc E, Coutinho PM, Henrissat B. Evolutionary and mechanistic relationships between glycosidases acting on α- and β-bonds. Carbohydr Res 2005; 340:2728-34. [PMID: 16226731 DOI: 10.1016/j.carres.2005.09.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2005] [Accepted: 09/15/2005] [Indexed: 10/25/2022]
Abstract
Because of the fast accumulation of sequences derived from genome sequencing efforts, the sampling of the sequence space in glycosidase and related enzyme families is such that sensitive sequence similarity detection methods like PSI-BLAST are now able to reveal distant, but clear, structural and evolutionary relations between glycosidases acting on alpha- and beta-bonds. We have observed this trend within groups of glycosidases with completely different folds. We postulate that the evolutionary interconversion between alpha- and beta-acting glycosidases was greatly facilitated by the fact that both types share a similar axial orientation of the glycosidic bond in the reactive bound substrate. Glycosides in the beta anomeric configuration, require a sugar ring distortion, resulting in an axial orientation of the glycosidic bond, equivalent to that of an alpha glycosidic bond, prior to displacement by nucleophilic substitution.
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Affiliation(s)
- Mark R Stam
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, Centre National de la Recherche Scientifique, Universités d'Aix-Marseille I & II, Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
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