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Jain N, Tamura K, Déjean G, Van Petegem F, Brumer H. Orthogonal Active-Site Labels for Mixed-Linkage endo-β-Glucanases. ACS Chem Biol 2021; 16:1968-1984. [PMID: 33988963 DOI: 10.1021/acschembio.1c00063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Small molecule irreversible inhibitors are valuable tools for determining catalytically important active-site residues and revealing key details of the specificity, structure, and function of glycoside hydrolases (GHs). β-glucans that contain backbone β(1,3) linkages are widespread in nature, e.g., mixed-linkage β(1,3)/β(1,4)-glucans in the cell walls of higher plants and β(1,3)glucans in yeasts and algae. Commensurate with this ubiquity, a large diversity of mixed-linkage endoglucanases (MLGases, EC 3.2.1.73) and endo-β(1,3)-glucanases (laminarinases, EC 3.2.1.39 and EC 3.2.1.6) have evolved to specifically hydrolyze these polysaccharides, respectively, in environmental niches including the human gut. To facilitate biochemical and structural analysis of these GHs, with a focus on MLGases, we present here the facile chemo-enzymatic synthesis of a library of active-site-directed enzyme inhibitors based on mixed-linkage oligosaccharide scaffolds and N-bromoacetylglycosylamine or 2-fluoro-2-deoxyglycoside warheads. The effectiveness and irreversibility of these inhibitors were tested with exemplar MLGases and an endo-β(1,3)-glucanase. Notably, determination of inhibitor-bound crystal structures of a human-gut microbial MLGase from Glycoside Hydrolase Family 16 revealed the orthogonal labeling of the nucleophile and catalytic acid/base residues with homologous 2-fluoro-2-deoxyglycoside and N-bromoacetylglycosylamine inhibitors, respectively. We anticipate that the selectivity of these inhibitors will continue to enable the structural and mechanistic analyses of β-glucanases from diverse sources and protein families.
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Affiliation(s)
- Namrata Jain
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Kazune Tamura
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Guillaume Déjean
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
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Déjean G, Tamura K, Cabrera A, Jain N, Pudlo NA, Pereira G, Viborg AH, Van Petegem F, Martens EC, Brumer H. Synergy between Cell Surface Glycosidases and Glycan-Binding Proteins Dictates the Utilization of Specific Beta(1,3)-Glucans by Human Gut Bacteroides. mBio 2020; 11:e00095-20. [PMID: 32265336 PMCID: PMC7157763 DOI: 10.1128/mbio.00095-20] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/09/2020] [Indexed: 01/06/2023] Open
Abstract
The human gut microbiota (HGM) has far-reaching impacts on human health and nutrition, which are fueled primarily by the metabolism of otherwise indigestible complex carbohydrates commonly known as dietary fiber. However, the molecular basis of the ability of individual taxa of the HGM to address specific dietary glycan structures remains largely unclear. In particular, the utilization of β(1,3)-glucans, which are widespread in the human diet as yeast, seaweed, and plant cell walls, had not previously been resolved. Through a systems-based approach, here we show that the symbiont Bacteroides uniformis deploys a single, exemplar polysaccharide utilization locus (PUL) to access yeast β(1,3)-glucan, brown seaweed β(1,3)-glucan (laminarin), and cereal mixed-linkage β(1,3)/β(1,4)-glucan. Combined biochemical, enzymatic, and structural analysis of PUL-encoded glycoside hydrolases (GHs) and surface glycan-binding proteins (SGBPs) illuminates a concerted molecular system by which B. uniformis recognizes and saccharifies these distinct β-glucans. Strikingly, the functional characterization of homologous β(1,3)-glucan utilization loci (1,3GUL) in other Bacteroides further demonstrated that the ability of individual taxa to utilize β(1,3)-glucan variants and/or β(1,3)/β(1,4)-glucans arises combinatorially from the individual specificities of SGBPs and GHs at the cell surface, which feed corresponding signals to periplasmic hybrid two-component sensors (HTCSs) via TonB-dependent transporters (TBDTs). These data reveal the importance of cooperativity in the adaptive evolution of GH and SGBP cohorts to address individual polysaccharide structures. We anticipate that this fine-grained knowledge of PUL function will inform metabolic network analysis and proactive manipulation of the HGM. Indeed, a survey of 2,441 public human metagenomes revealed the international, yet individual-specific, distribution of each 1,3GUL.IMPORTANCEBacteroidetes are a dominant phylum of the human gut microbiota (HGM) that target otherwise indigestible dietary fiber with an arsenal of polysaccharide utilization loci (PULs), each of which is dedicated to the utilization of a specific complex carbohydrate. Here, we provide novel insight into this paradigm through functional characterization of homologous PULs from three autochthonous Bacteroides species, which target the family of dietary β(1,3)-glucans. Through detailed biochemical and protein structural analysis, we observed an unexpected diversity in the substrate specificity of PUL glycosidases and glycan-binding proteins with regard to β(1,3)-glucan linkage and branching patterns. In combination, these individual enzyme and protein specificities support taxon-specific growth on individual β(1,3)-glucans. This detailed metabolic insight, together with a comprehensive survey of individual 1,3GULs across human populations, further expands the fundamental roadmap of the HGM, with potential application to the future development of microbial intervention therapies.
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Affiliation(s)
- Guillaume Déjean
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kazune Tamura
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Adriana Cabrera
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Namrata Jain
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Gabriel Pereira
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Alexander Holm Viborg
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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Jain N, Attia MA, Offen WA, Davies GJ, Brumer H. Synthesis and application of a highly branched, mechanism-based 2-deoxy-2-fluoro-oligosaccharide inhibitor of endo-xyloglucanases. Org Biomol Chem 2018; 16:8732-8741. [DOI: 10.1039/c8ob02250j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Xyloglucan (XyG) is a complex polysaccharide that is ubiquitous and often abundant in the cell walls of terrestrial plants.
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Affiliation(s)
- Namrata Jain
- Michael Smith Laboratories
- University of British Columbia
- Vancouver
- Canada
- Department of Chemistry
| | - Mohamed A. Attia
- Michael Smith Laboratories
- University of British Columbia
- Vancouver
- Canada
- Department of Chemistry
| | | | | | - Harry Brumer
- Michael Smith Laboratories
- University of British Columbia
- Vancouver
- Canada
- Department of Chemistry
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Attia MA, Nelson CE, Offen WA, Jain N, Davies GJ, Gardner JG, Brumer H. In vitro and in vivo characterization of three Cellvibrio japonicus glycoside hydrolase family 5 members reveals potent xyloglucan backbone-cleaving functions. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:45. [PMID: 29467823 PMCID: PMC5816542 DOI: 10.1186/s13068-018-1039-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/01/2018] [Indexed: 05/15/2023]
Abstract
BACKGROUND Xyloglucan (XyG) is a ubiquitous and fundamental polysaccharide of plant cell walls. Due to its structural complexity, XyG requires a combination of backbone-cleaving and sidechain-debranching enzymes for complete deconstruction into its component monosaccharides. The soil saprophyte Cellvibrio japonicus has emerged as a genetically tractable model system to study biomass saccharification, in part due to its innate capacity to utilize a wide range of plant polysaccharides for growth. Whereas the downstream debranching enzymes of the xyloglucan utilization system of C. japonicus have been functionally characterized, the requisite backbone-cleaving endo-xyloglucanases were unresolved. RESULTS Combined bioinformatic and transcriptomic analyses implicated three glycoside hydrolase family 5 subfamily 4 (GH5_4) members, with distinct modular organization, as potential keystone endo-xyloglucanases in C. japonicus. Detailed biochemical and enzymatic characterization of the GH5_4 modules of all three recombinant proteins confirmed particularly high specificities for the XyG polysaccharide versus a panel of other cell wall glycans, including mixed-linkage beta-glucan and cellulose. Moreover, product analysis demonstrated that all three enzymes generated XyG oligosaccharides required for subsequent saccharification by known exo-glycosidases. Crystallographic analysis of GH5D, which was the only GH5_4 member specifically and highly upregulated during growth on XyG, in free, product-complex, and active-site affinity-labelled forms revealed the molecular basis for the exquisite XyG specificity among these GH5_4 enzymes. Strikingly, exhaustive reverse-genetic analysis of all three GH5_4 members and a previously biochemically characterized GH74 member failed to reveal a growth defect, thereby indicating functional compensation in vivo, both among members of this cohort and by other, yet unidentified, xyloglucanases in C. japonicus. Our systems-based analysis indicates distinct substrate-sensing (GH74, GH5E, GH5F) and attack-mounting (GH5D) functions for the endo-xyloglucanases characterized here. CONCLUSIONS Through a multi-faceted, molecular systems-based approach, this study provides a new insight into the saccharification pathway of xyloglucan utilization system of C. japonicus. The detailed structural-functional characterization of three distinct GH5_4 endo-xyloglucanases will inform future bioinformatic predictions across species, and provides new CAZymes with defined specificity that may be harnessed in industrial and other biotechnological applications.
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Affiliation(s)
- Mohamed A. Attia
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4 Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1 Canada
| | - Cassandra E. Nelson
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250 USA
| | - Wendy A. Offen
- Department of Chemistry, University of York, Heslington, York, YO10 5DD UK
| | - Namrata Jain
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4 Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1 Canada
| | - Gideon J. Davies
- Department of Chemistry, University of York, Heslington, York, YO10 5DD UK
| | - Jeffrey G. Gardner
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250 USA
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4 Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1 Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada
- Department of Botany, University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4 Canada
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Nelson CE, Attia MA, Rogowski A, Morland C, Brumer H, Gardner JG. Comprehensive functional characterization of the glycoside hydrolase family 3 enzymes from Cellvibrio japonicus reveals unique metabolic roles in biomass saccharification. Environ Microbiol 2017; 19:5025-5039. [PMID: 29052930 DOI: 10.1111/1462-2920.13959] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/27/2017] [Accepted: 10/08/2017] [Indexed: 12/16/2022]
Abstract
Lignocellulose degradation is central to the carbon cycle and renewable biotechnologies. The xyloglucan (XyG), β(1→3)/β(1→4) mixed-linkage glucan (MLG) and β(1→3) glucan components of lignocellulose represent significant carbohydrate energy sources for saprophytic microorganisms. The bacterium Cellvibrio japonicus has a robust capacity for plant polysaccharide degradation, due to a genome encoding a large contingent of Carbohydrate-Active enZymes (CAZymes), many of whose specific functions remain unknown. Using a comprehensive genetic and biochemical approach, we have delineated the physiological roles of the four C. japonicus glycoside hydrolase family 3 (GH3) members on diverse β-glucans. Despite high protein sequence similarity and partially overlapping activity profiles on disaccharides, these β-glucosidases are not functionally equivalent. Bgl3A has a major role in MLG and sophorose utilization, and supports β(1→3) glucan utilization, while Bgl3B underpins cellulose utilization and supports MLG utilization. Bgl3C drives β(1→3) glucan utilization. Finally, Bgl3D is the crucial β-glucosidase for XyG utilization. This study not only sheds the light on the metabolic machinery of C. japonicus, but also expands the repertoire of characterized CAZymes for future deployment in biotechnological applications. In particular, the precise functional analysis provided here serves as a reference for informed bioinformatics on the genomes of other Cellvibrio and related species.
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Affiliation(s)
- Cassandra E Nelson
- Department of Biological Sciences, University of Maryland, Baltimore County, MD, USA
| | - Mohamed A Attia
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada.,Department of Chemistry, University of British Columbia, Vancouver, Canada
| | - Artur Rogowski
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Carl Morland
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada.,Department of Chemistry, University of British Columbia, Vancouver, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada.,Department of Botany, University of British Columbia, Vancouver, Canada
| | - Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland, Baltimore County, MD, USA
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McGregor N, Yin V, Tung CC, Van Petegem F, Brumer H. Crystallographic insight into the evolutionary origins of xyloglucan endotransglycosylases and endohydrolases. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:651-670. [PMID: 27859885 PMCID: PMC5315667 DOI: 10.1111/tpj.13421] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 10/14/2016] [Accepted: 11/04/2016] [Indexed: 05/22/2023]
Abstract
The xyloglucan endotransglycosylase/hydrolase (XTH) gene family encodes enzymes of central importance to plant cell wall remodeling. The evolutionary history of plant XTH gene products is incompletely understood vis-à-vis the larger body of bacterial endoglycanases in Glycoside Hydrolase Family 16 (GH16). To provide molecular insight into this issue, high-resolution X-ray crystal structures and detailed enzyme kinetics of an extant transitional plant endoglucanase (EG) were determined. Functionally intermediate between plant XTH gene products and bacterial licheninases of GH16, Vitis vinifera EG16 (VvEG16) effectively catalyzes the hydrolysis of the backbones of two dominant plant cell wall matrix glycans, xyloglucan (XyG) and β(1,3)/β(1,4)-mixed-linkage glucan (MLG). Crystallographic complexes with extended oligosaccharide substrates reveal the structural basis for the accommodation of both unbranched, mixed-linked (MLG) and highly decorated, linear (XyG) polysaccharide chains in a broad, extended active-site cleft. Structural comparison with representative bacterial licheninases, a xyloglucan endotranglycosylase (XET), and a xyloglucan endohydrolase (XEH) outline the functional ramifications of key sequence deletions and insertions across the phylogenetic landscape of GH16. Although the biological role(s) of EG16 orthologs remains to be fully resolved, the present biochemical and tertiary structural characterization provides key insight into plant cell wall enzyme evolution, which will continue to inform genomic analyses and functional studies across species.
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Affiliation(s)
- Nicholas McGregor
- Michael Smith Laboratories, University of British Columbia,
2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia,
2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Victor Yin
- Michael Smith Laboratories, University of British Columbia,
2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia,
2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Ching-Chieh Tung
- Department of Biochemistry and Molecular Biology,
University of British Columbia, 2350 Health Sciences Mall, Vancouver, British
Columbia V6T 1Z3, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology,
University of British Columbia, 2350 Health Sciences Mall, Vancouver, British
Columbia V6T 1Z3, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia,
2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia,
2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
- Department of Biochemistry and Molecular Biology,
University of British Columbia, 2350 Health Sciences Mall, Vancouver, British
Columbia V6T 1Z3, Canada
- Department of Botany, University of British Columbia, 6270
University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
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Attia M, Stepper J, Davies GJ, Brumer H. Functional and structural characterization of a potent GH74 endo-xyloglucanase from the soil saprophyte Cellvibrio japonicus unravels the first step of xyloglucan degradation. FEBS J 2016; 283:1701-19. [PMID: 26929175 DOI: 10.1111/febs.13696] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/09/2016] [Accepted: 02/25/2016] [Indexed: 11/27/2022]
Abstract
UNLABELLED The heteropolysaccharide xyloglucan (XyG) comprises up to one-quarter of the total carbohydrate content of terrestrial plant cell walls and, as such, represents a significant reservoir in the global carbon cycle. The complex composition of XyG requires a consortium of backbone-cleaving endo-xyloglucanases and side-chain cleaving exo-glycosidases for complete saccharification. The biochemical basis for XyG utilization by the model Gram-negative soil saprophytic bacterium Cellvibrio japonicus is incompletely understood, despite the recent characterization of associated side-chain cleaving exo-glycosidases. We present a detailed functional and structural characterization of a multimodular enzyme encoded by gene locus CJA_2477. The CJA_2477 gene product comprises an N-terminal glycoside hydrolase family 74 (GH74) endo-xyloglucanase module in train with two carbohydrate-binding modules (CBMs) from families 10 and 2 (CBM10 and CBM2). The GH74 catalytic domain generates Glc4 -based xylogluco-oligosaccharide (XyGO) substrates for downstream enzymes through an endo-dissociative mode of action. X-ray crystallography of the GH74 module, alone and in complex with XyGO products spanning the entire active site, revealed a broad substrate-binding cleft specifically adapted to XyG recognition, which is composed of two seven-bladed propeller domains characteristic of the GH74 family. The appended CBM10 and CBM2 members notably did not bind XyG, nor other soluble polysaccharides, and instead were specific cellulose-binding modules. Taken together, these data shed light on the first step of xyloglucan utilization by C. japonicus and expand the repertoire of GHs and CBMs for selective biomass analysis and utilization. DATABASE Structural data have been deposited in the RCSB protein database under the Protein Data Bank codes: 5FKR, 5FKS, 5FKT and 5FKQ.
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Affiliation(s)
- Mohamed Attia
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, Canada
| | | | | | - Harry Brumer
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, Canada
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McGregor N, Morar M, Fenger TH, Stogios P, Lenfant N, Yin V, Xu X, Evdokimova E, Cui H, Henrissat B, Savchenko A, Brumer H. Structure-Function Analysis of a Mixed-linkage β-Glucanase/Xyloglucanase from the Key Ruminal Bacteroidetes Prevotella bryantii B(1)4. J Biol Chem 2015; 291:1175-97. [PMID: 26507654 DOI: 10.1074/jbc.m115.691659] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Indexed: 11/06/2022] Open
Abstract
The recent classification of glycoside hydrolase family 5 (GH5) members into subfamilies enhances the prediction of substrate specificity by phylogenetic analysis. However, the small number of well characterized members is a current limitation to understanding the molecular basis of the diverse specificity observed across individual GH5 subfamilies. GH5 subfamily 4 (GH5_4) is one of the largest, with known activities comprising (carboxymethyl)cellulases, mixed-linkage endo-glucanases, and endo-xyloglucanases. Through detailed structure-function analysis, we have revisited the characterization of a classic GH5_4 carboxymethylcellulase, PbGH5A (also known as Orf4, carboxymethylcellulase, and Cel5A), from the symbiotic rumen Bacteroidetes Prevotella bryantii B14. We demonstrate that carboxymethylcellulose and phosphoric acid-swollen cellulose are in fact relatively poor substrates for PbGH5A, which instead exhibits clear primary specificity for the plant storage and cell wall polysaccharide, mixed-linkage β-glucan. Significant activity toward the plant cell wall polysaccharide xyloglucan was also observed. Determination of PbGH5A crystal structures in the apo-form and in complex with (xylo)glucan oligosaccharides and an active-site affinity label, together with detailed kinetic analysis using a variety of well defined oligosaccharide substrates, revealed the structural determinants of polysaccharide substrate specificity. In particular, this analysis highlighted the PbGH5A active-site motifs that engender predominant mixed-linkage endo-glucanase activity vis à vis predominant endo-xyloglucanases in GH5_4. However the detailed phylogenetic analysis of GH5_4 members did not delineate particular clades of enzymes sharing these sequence motifs; the phylogeny was instead dominated by bacterial taxonomy. Nonetheless, our results provide key enzyme functional and structural reference data for future bioinformatics analyses of (meta)genomes to elucidate the biology of complex gut ecosystems.
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Affiliation(s)
- Nicholas McGregor
- From the Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Mariya Morar
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5G 1L6, Canada
| | - Thomas Hauch Fenger
- From the Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Peter Stogios
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5G 1L6, Canada
| | - Nicolas Lenfant
- the Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille 13288, France
| | - Victor Yin
- From the Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Xiaohui Xu
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5G 1L6, Canada
| | - Elena Evdokimova
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5G 1L6, Canada
| | - Hong Cui
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5G 1L6, Canada
| | - Bernard Henrissat
- the Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille 13288, France, the Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia, and INRA, USC 1408 AFMB, F-13288 Marseille, France
| | - Alexei Savchenko
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5G 1L6, Canada,
| | - Harry Brumer
- From the Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada,
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Fenger TH, Brumer H. Synthesis and Analysis of Specific Covalent Inhibitors ofendo-Xyloglucanases. Chembiochem 2015; 16:575-83. [DOI: 10.1002/cbic.201402663] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Indexed: 01/09/2023]
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10
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Larsbrink J, Thompson AJ, Lundqvist M, Gardner JG, Davies GJ, Brumer H. A complex gene locus enables xyloglucan utilization in the model saprophyte Cellvibrio japonicus. Mol Microbiol 2014; 94:418-33. [PMID: 25171165 PMCID: PMC4285296 DOI: 10.1111/mmi.12776] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2014] [Indexed: 12/17/2022]
Abstract
The degradation of plant biomass by saprophytes is an ecologically important part of the global carbon cycle, which has also inspired a vast diversity of industrial enzyme applications. The xyloglucans (XyGs) constitute a family of ubiquitous and abundant plant cell wall polysaccharides, yet the enzymology of XyG saccharification is poorly studied. Here, we present the identification and molecular characterization of a complex genetic locus that is required for xyloglucan utilization by the model saprophyte Cellvibrio japonicus. In harness, transcriptomics, reverse genetics, enzyme kinetics, and structural biology indicate that the encoded cohort of an α-xylosidase, a β-galactosidase, and an α-l-fucosidase is specifically adapted for efficient, concerted saccharification of dicot (fucogalacto)xyloglucan oligosaccharides following import into the periplasm via an associated TonB-dependent receptor. The data support a biological model of xyloglucan degradation by C. japonicus with striking similarities – and notable differences – to the complex polysaccharide utilization loci of the Bacteroidetes.
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Affiliation(s)
- Johan Larsbrink
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91, Stockholm, Sweden
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Larsbrink J, Rogers TE, Hemsworth GR, McKee LS, Tauzin AS, Spadiut O, Klinter S, Pudlo NA, Urs K, Koropatkin NM, Creagh AL, Haynes CA, Kelly AG, Cederholm SN, Davies GJ, Martens EC, Brumer H. A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes. Nature 2014; 506:498-502. [PMID: 24463512 PMCID: PMC4282169 DOI: 10.1038/nature12907] [Citation(s) in RCA: 338] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 11/22/2013] [Indexed: 01/16/2023]
Abstract
A well-balanced human diet includes a significant intake of non-starch polysaccharides, collectively termed 'dietary fibre', from the cell walls of diverse fruits and vegetables. Owing to the paucity of alimentary enzymes encoded by the human genome, our ability to derive energy from dietary fibre depends on the saccharification and fermentation of complex carbohydrates by the massive microbial community residing in our distal gut. The xyloglucans (XyGs) are a ubiquitous family of highly branched plant cell wall polysaccharides whose mechanism(s) of degradation in the human gut and consequent importance in nutrition have been unclear. Here we demonstrate that a single, complex gene locus in Bacteroides ovatus confers XyG catabolism in this common colonic symbiont. Through targeted gene disruption, biochemical analysis of all predicted glycoside hydrolases and carbohydrate-binding proteins, and three-dimensional structural determination of the vanguard endo-xyloglucanase, we reveal the molecular mechanisms through which XyGs are hydrolysed to component monosaccharides for further metabolism. We also observe that orthologous XyG utilization loci (XyGULs) serve as genetic markers of XyG catabolism in Bacteroidetes, that XyGULs are restricted to a limited number of phylogenetically diverse strains, and that XyGULs are ubiquitous in surveyed human metagenomes. Our findings reveal that the metabolism of even highly abundant components of dietary fibre may be mediated by niche species, which has immediate fundamental and practical implications for gut symbiont population ecology in the context of human diet, nutrition and health.
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Affiliation(s)
- Johan Larsbrink
- 1] Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden [2]
| | - Theresa E Rogers
- 1] Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA [2]
| | - Glyn R Hemsworth
- 1] Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK [2]
| | - Lauren S McKee
- 1] Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden [2] Wallenberg Wood Science Center, Royal Institute of Technology (KTH), Teknikringen 56-58, 100 44 Stockholm, Sweden
| | - Alexandra S Tauzin
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Oliver Spadiut
- 1] Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden [2] Wallenberg Wood Science Center, Royal Institute of Technology (KTH), Teknikringen 56-58, 100 44 Stockholm, Sweden
| | - Stefan Klinter
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden
| | - Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Karthik Urs
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - A Louise Creagh
- Michael Smith Laboratories and Department of Chemical and Biological Engineering, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Charles A Haynes
- Michael Smith Laboratories and Department of Chemical and Biological Engineering, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Amelia G Kelly
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Stefan Nilsson Cederholm
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden
| | - Gideon J Davies
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Harry Brumer
- 1] Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden [2] Michael Smith Laboratories and Department of Chemistry, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
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12
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Kaewthai N, Gendre D, Eklöf JM, Ibatullin FM, Ezcurra I, Bhalerao RP, Brumer H. Group III-A XTH genes of Arabidopsis encode predominant xyloglucan endohydrolases that are dispensable for normal growth. PLANT PHYSIOLOGY 2013; 161:440-54. [PMID: 23104861 PMCID: PMC3532273 DOI: 10.1104/pp.112.207308] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 10/25/2012] [Indexed: 05/05/2023]
Abstract
The molecular basis of primary wall extension endures as one of the central enigmas in plant cell morphogenesis. Classical cell wall models suggest that xyloglucan endo-transglycosylase activity is the primary catalyst (together with expansins) of controlled cell wall loosening through the transient cleavage and religation of xyloglucan-cellulose cross links. The genome of Arabidopsis (Arabidopsis thaliana) contains 33 phylogenetically diverse XYLOGLUCAN ENDO-TRANSGLYCOSYLASE/HYDROLASE (XTH) gene products, two of which were predicted to be predominant xyloglucan endohydrolases due to clustering into group III-A. Enzyme kinetic analysis of recombinant AtXTH31 confirmed this prediction and indicated that this enzyme had similar catalytic properties to the nasturtium (Tropaeolum majus) xyloglucanase1 responsible for storage xyloglucan hydrolysis during germination. Global analysis of Genevestigator data indicated that AtXTH31 and the paralogous AtXTH32 were abundantly expressed in expanding tissues. Microscopy analysis, utilizing the resorufin β-glycoside of the xyloglucan oligosaccharide XXXG as an in situ probe, indicated significant xyloglucan endohydrolase activity in specific regions of both roots and hypocotyls, in good correlation with transcriptomic data. Moreover, this hydrolytic activity was essentially completely eliminated in AtXTH31/AtXTH32 double knockout lines. However, single and double knockout lines, as well as individual overexpressing lines, of AtXTH31 and AtXTH32 did not demonstrate significant growth or developmental phenotypes. These results suggest that although xyloglucan polysaccharide hydrolysis occurs in parallel with primary wall expansion, morphological effects are subtle or may be compensated by other mechanisms. We hypothesize that there is likely to be an interplay between these xyloglucan endohydrolases and recently discovered apoplastic exo-glycosidases in the hydrolytic modification of matrix xyloglucans.
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Affiliation(s)
| | | | - Jens M. Eklöf
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology, AlbaNova University Centre, S–106 91 Stockholm, Sweden (N.K., J.M.E., F.M.I., I.E., H.B.); Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE–901 83 Umea, Sweden (D.G., R.P.B.); Biophysics Division, Petersburg Nuclear Physics Institute, National Research Center Kurchatov Institute, Gatchina 188300, Russia (F.M.I.); and Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (H.B.)
| | - Farid M. Ibatullin
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology, AlbaNova University Centre, S–106 91 Stockholm, Sweden (N.K., J.M.E., F.M.I., I.E., H.B.); Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE–901 83 Umea, Sweden (D.G., R.P.B.); Biophysics Division, Petersburg Nuclear Physics Institute, National Research Center Kurchatov Institute, Gatchina 188300, Russia (F.M.I.); and Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (H.B.)
| | - Ines Ezcurra
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology, AlbaNova University Centre, S–106 91 Stockholm, Sweden (N.K., J.M.E., F.M.I., I.E., H.B.); Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE–901 83 Umea, Sweden (D.G., R.P.B.); Biophysics Division, Petersburg Nuclear Physics Institute, National Research Center Kurchatov Institute, Gatchina 188300, Russia (F.M.I.); and Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (H.B.)
| | - Rishikesh P. Bhalerao
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology, AlbaNova University Centre, S–106 91 Stockholm, Sweden (N.K., J.M.E., F.M.I., I.E., H.B.); Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE–901 83 Umea, Sweden (D.G., R.P.B.); Biophysics Division, Petersburg Nuclear Physics Institute, National Research Center Kurchatov Institute, Gatchina 188300, Russia (F.M.I.); and Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (H.B.)
| | - Harry Brumer
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology, AlbaNova University Centre, S–106 91 Stockholm, Sweden (N.K., J.M.E., F.M.I., I.E., H.B.); Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE–901 83 Umea, Sweden (D.G., R.P.B.); Biophysics Division, Petersburg Nuclear Physics Institute, National Research Center Kurchatov Institute, Gatchina 188300, Russia (F.M.I.); and Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada (H.B.)
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13
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Abstract
The ability of β-glucanases to cleave xyloglucans, a family of highly decorated β-glucans ubiquitous in plant biomass, has traditionally been overlooked in functional biochemical studies. An emerging body of data indicates, however, that a spectrum of xyloglucan specificity resides in diverse glycoside hydrolases from a range of carbohydrate-active enzyme families-including classic "cellulase" families. This chapter outlines a series of enzyme kinetic and product analysis methods to establish degrees of xyloglucan specificity and modes of action of glycosidases emerging from enzyme discovery projects.
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Affiliation(s)
- Jens M Eklöf
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, Canada
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14
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Mark P, Zhang Q, Czjzek M, Brumer H, Ågren H. Molecular dynamics simulations of a branched tetradecasaccharide substrate in the active site of a xyloglucanendo-transglycosylase. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2011.566605] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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15
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Ariza A, Eklöf JM, Spadiut O, Offen WA, Roberts SM, Besenmatter W, Friis EP, Skjøt M, Wilson KS, Brumer H, Davies G. Structure and activity of Paenibacillus polymyxa xyloglucanase from glycoside hydrolase family 44. J Biol Chem 2011; 286:33890-900. [PMID: 21795708 PMCID: PMC3190823 DOI: 10.1074/jbc.m111.262345] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 07/12/2011] [Indexed: 11/06/2022] Open
Abstract
The enzymatic degradation of plant polysaccharides is emerging as one of the key environmental goals of the early 21st century, impacting on many processes in the textile and detergent industries as well as biomass conversion to biofuels. One of the well known problems with the use of nonstarch (nonfood)-based substrates such as the plant cell wall is that the cellulose fibers are embedded in a network of diverse polysaccharides, including xyloglucan, that renders access difficult. There is therefore increasing interest in the "accessory enzymes," including xyloglucanases, that may aid biomass degradation through removal of "hemicellulose" polysaccharides. Here, we report the biochemical characterization of the endo-β-1,4-(xylo)glucan hydrolase from Paenibacillus polymyxa with polymeric, oligomeric, and defined chromogenic aryl-oligosaccharide substrates. The enzyme displays an unusual specificity on defined xyloglucan oligosaccharides, cleaving the XXXG-XXXG repeat into XXX and GXXXG. Kinetic analysis on defined oligosaccharides and on aryl-glycosides suggests that both the -4 and +1 subsites show discrimination against xylose-appended glucosides. The three-dimensional structures of PpXG44 have been solved both in apo-form and as a series of ligand complexes that map the -3 to -1 and +1 to +5 subsites of the extended ligand binding cleft. Complex structures are consistent with partial intolerance of xylosides in the -4' subsites. The atypical specificity of PpXG44 may thus find use in industrial processes involving xyloglucan degradation, such as biomass conversion, or in the emerging exciting applications of defined xyloglucans in food, pharmaceuticals, and cellulose fiber modification.
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Affiliation(s)
- Antonio Ariza
- From the Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Jens M. Eklöf
- the Division of Glycoscience, School of Biotechnology, and
| | - Oliver Spadiut
- the Division of Glycoscience, School of Biotechnology, and
- Wallenberg Wood Science Center, Royal Institute of Technology, SE-106 91 Stockholm, Sweden, and
| | - Wendy A. Offen
- From the Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Shirley M. Roberts
- From the Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | | | | | | | - Keith S. Wilson
- From the Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Harry Brumer
- the Division of Glycoscience, School of Biotechnology, and
- Wallenberg Wood Science Center, Royal Institute of Technology, SE-106 91 Stockholm, Sweden, and
| | - Gideon Davies
- From the Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
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16
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Spadiut O, Ibatullin FM, Peart J, Gullfot F, Martinez-Fleites C, Ruda M, Xu C, Sundqvist G, Davies GJ, Brumer H. Building custom polysaccharides in vitro with an efficient, broad-specificity xyloglucan glycosynthase and a fucosyltransferase. J Am Chem Soc 2011; 133:10892-900. [PMID: 21618981 PMCID: PMC3135005 DOI: 10.1021/ja202788q] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Indexed: 11/29/2022]
Abstract
The current drive for applications of biomass-derived compounds, for energy and advanced materials, has led to a resurgence of interest in the manipulation of plant polymers. The xyloglucans, a family of structurally complex plant polysaccharides, have attracted significant interest due to their intrinsic high affinity for cellulose, both in muro and in technical applications. Moreover, current cell wall models are limited by the lack of detailed structure-property relationships of xyloglucans, due to a lack of molecules with well-defined branching patterns. Here, we have developed a new, broad-specificity "xyloglucan glycosynthase", selected from active-site mutants of a bacterial endoxyloglucanase, which catalyzed the synthesis of high molar mass polysaccharides, with complex side-chain structures, from suitable glycosyl fluoride donor substrates. The product range was further extended by combination with an Arabidopsis thaliana α(1→2)-fucosyltransferase to achieve the in vitro synthesis of fucosylated xyloglucans typical of dicot primary cell walls. These enzymes thus comprise a toolkit for the controlled enzymatic synthesis of xyloglucans that are otherwise impossible to obtain from native sources. Moreover, this study demonstrates the validity of a chemo-enzymatic approach to polysaccharide synthesis, in which the simplicity and economy of glycosynthase technology is harnessed together with the exquisite specificity of glycosyltransferases to control molecular complexity.
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Affiliation(s)
- Oliver Spadiut
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), 106 91 Stockholm, Sweden
- Wallenberg Wood Science Center, Royal Institute of Technology (KTH), 100 44 Stockholm, Sweden
| | - Farid M. Ibatullin
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), 106 91 Stockholm, Sweden
| | - Jonelle Peart
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), 106 91 Stockholm, Sweden
| | - Fredrika Gullfot
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), 106 91 Stockholm, Sweden
| | - Carlos Martinez-Fleites
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Marcus Ruda
- Swetree Technologies AB, P.O. Box 4095, 904 03 Umeå, Sweden
| | - Chunlin Xu
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), 106 91 Stockholm, Sweden
- Wallenberg Wood Science Center, Royal Institute of Technology (KTH), 100 44 Stockholm, Sweden
| | - Gustav Sundqvist
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), 106 91 Stockholm, Sweden
| | - Gideon J. Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Harry Brumer
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), 106 91 Stockholm, Sweden
- Wallenberg Wood Science Center, Royal Institute of Technology (KTH), 100 44 Stockholm, Sweden
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17
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Tanaka T, Noguchi M, Ishihara M, Kobayashi A, Shoda SI. Synthesis of Non-natural Xyloglucans by Polycondensation of 4,6-Dimethoxy-1,3,5-triazin-2-yl Oligosaccharide Monomers Catalyzed by Endo-β
-1,4-glucanase. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/masy.200900083] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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18
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Eklöf JM, Brumer H. The XTH gene family: an update on enzyme structure, function, and phylogeny in xyloglucan remodeling. PLANT PHYSIOLOGY 2010; 153:456-66. [PMID: 20421457 PMCID: PMC2879796 DOI: 10.1104/pp.110.156844] [Citation(s) in RCA: 217] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Accepted: 04/23/2010] [Indexed: 05/18/2023]
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19
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4,6-dimethoxy-1,3,5-triazine oligoxyloglucans: novel one-step preparable substrates for studying action of endo-beta-1,4-glucanase III from Trichoderma reesei. Bioorg Med Chem Lett 2010; 20:3588-91. [PMID: 20529686 DOI: 10.1016/j.bmcl.2010.04.122] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 04/23/2010] [Accepted: 04/27/2010] [Indexed: 11/22/2022]
Abstract
Two kinds of 4,6-dimethoxy-1,3,5-triazine (DMT) oligoxyloglucans, DMT-beta-XXXG and DMT-beta-XLLG, have been synthesized via one-step procedure starting from the corresponding unprotected oligoxyloglucans in water. The resulting DMT derivatives were found to be hydrolyzed by endo-beta-1,4-D-glucanase III from Trichoderma reesei (EGIII) and utilized as substrates for determination of the kinetic parameters of EGIII. The present DMT-method would be a convenient analytical tool for studying the action of glycosyl hydrolases due to the extremely simple synthetic process of DMT-glycosides without using protecting groups.
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20
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Wong DDWS, Chan VJ, McCormack AA, Batt SB. A novel xyloglucan-specific endo-β-1,4-glucanase: biochemical properties and inhibition studies. Appl Microbiol Biotechnol 2009; 86:1463-71. [DOI: 10.1007/s00253-009-2364-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 11/12/2009] [Accepted: 11/12/2009] [Indexed: 11/30/2022]
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21
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Powlowski J, Mahajan S, Schapira M, Master ER. Substrate recognition and hydrolysis by a fungal xyloglucan-specific family 12 hydrolase. Carbohydr Res 2009; 344:1175-9. [PMID: 19433323 DOI: 10.1016/j.carres.2009.04.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Revised: 04/16/2009] [Accepted: 04/19/2009] [Indexed: 11/30/2022]
Abstract
Biochemical studies to elucidate the structural basis for xyloglucan specificity among GH12 xyloglucanases are lacking. Accordingly, the substrate specificity of a GH12 xyloglucanase from Aspergillus niger (AnXEG12A) was investigated using pea xyloglucan and 12 xylogluco-oligosaccharides, and data were compared to a structural model of the enzyme. The specific activity of AnXEG12A with pea xyloglucan was 113 micromol min(-1)mg(-1), and apparent k(cat) and K(m) values were 49 s(-1) and 0.54 mg mL(-1), respectively. These values are similar to previously published results using xyloglucan from tamarind seed, and suggest that substrate fucosylation does not affect the specific activity of this enzyme. AnXEG12A preferred xylogluco-oligosaccharides containing more than six glucose units, and with xylose substitution at the -3 and +1 subsites. The specific activities of AnXEG12A on 100 microM XXXGXXXG and 100 microM XLLGXLLG were 60+/-4 and 72+/-9 micromol min(-1)mg(-1), respectively. AnXEG12A did not hydrolyze XXXXXXXG, consistent with other data that demonstrate the requirement for an unbranched glucose residue for hydrolysis by this enzyme.
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Affiliation(s)
- Justin Powlowski
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke St. West, Montreal, Quebec, Canada H4B 1R6
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22
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Gullfot F, Ibatullin FM, Sundqvist G, Davies GJ, Brumer H. Functional Characterization of Xyloglucan Glycosynthases from GH7, GH12, and GH16 Scaffolds. Biomacromolecules 2009; 10:1782-8. [DOI: 10.1021/bm900215p] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fredrika Gullfot
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden, Petersburg Nuclear Physics Institute, Molecular and Radiation Biology Division, Russian Academy of Science, Gatchina, St. Petersburg 188300, Russia, and York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, United Kingdom
| | - Farid M. Ibatullin
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden, Petersburg Nuclear Physics Institute, Molecular and Radiation Biology Division, Russian Academy of Science, Gatchina, St. Petersburg 188300, Russia, and York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, United Kingdom
| | - Gustav Sundqvist
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden, Petersburg Nuclear Physics Institute, Molecular and Radiation Biology Division, Russian Academy of Science, Gatchina, St. Petersburg 188300, Russia, and York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, United Kingdom
| | - Gideon J. Davies
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden, Petersburg Nuclear Physics Institute, Molecular and Radiation Biology Division, Russian Academy of Science, Gatchina, St. Petersburg 188300, Russia, and York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, United Kingdom
| | - Harry Brumer
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden, Petersburg Nuclear Physics Institute, Molecular and Radiation Biology Division, Russian Academy of Science, Gatchina, St. Petersburg 188300, Russia, and York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5YW, United Kingdom
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