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Fu Z, Zhang X, Liu J, Li J, Zeng Y, Yang J, Sun Y, Cui J, Zhu Y. Enzymatic synthesis and immunomodulatory activity of highly branched α-D-glucans with glycogen-like structure. Int J Biol Macromol 2023; 237:123882. [PMID: 37015174 DOI: 10.1016/j.ijbiomac.2023.123882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 02/12/2023] [Accepted: 02/26/2023] [Indexed: 04/05/2023]
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Baharifar H, Khoshnevisan K, Maleki H. Compartmentalized Immobilization of Multi-enzyme Systems. Methods Mol Biol 2022; 2487:151-162. [PMID: 35687234 DOI: 10.1007/978-1-0716-2269-8_9] [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] [Indexed: 06/15/2023]
Abstract
The methods of compartmentalized immobilization in multi-enzyme systems containing inorganic complexes and organic scaffolds (i.e. nucleic acid (RNA and DNA), protein and lipid) have been thoroughly investigated. Compartmentalization mostly focuses on dividing individual enzyme(s) into specific location or orientation of the enzymes cooperating in cascade reaction. Organic scaffolds are preferred because of their capability for simultaneous synthesis in biological systems. Besides, the most required methods of horseradish peroxidase (HRP) and glucose oxidase (GOD) enzymes including enzyme activity measurement, enzyme immobilization, removal, and re-hybridization, and enzyme attaching have been provided because they have been extensively applied in multi-enzyme systems. Organic scaffolds have a wide range and properties. Therefore, two methods including dockerin-cohesin linker and nucleotides interaction have been demonstrated for immobilization of enzyme on protein and DNA scaffold, respectively.
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Affiliation(s)
- Hadi Baharifar
- Department of Medical Nanotechnology, Applied Biophotonics Research Center, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Kamyar Khoshnevisan
- Medical Nanotechnology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Hassan Maleki
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
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New Family of Carbohydrate-Binding Modules Defined by a Galactosyl-Binding Protein Module from a Cellvibrio japonicus Endo-Xyloglucanase. Appl Environ Microbiol 2021; 87:e0263420. [PMID: 33355108 DOI: 10.1128/aem.02634-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Carbohydrate-binding modules (CBMs) are usually appended to carbohydrate-active enzymes (CAZymes) and serve to potentiate catalytic activity, for example, by increasing substrate affinity. The Gram-negative soil saprophyte Cellvibrio japonicus is a valuable source for CAZyme and CBM discovery and characterization due to its innate ability to degrade a wide array of plant polysaccharides. Bioinformatic analysis of the CJA_2959 gene product from C. japonicus revealed a modular architecture consisting of a fibronectin type III (Fn3) module, a cryptic module of unknown function (X181), and a glycoside hydrolase family 5 subfamily 4 (GH5_4) catalytic module. We previously demonstrated that the last of these, CjGH5F, is an efficient and specific endo-xyloglucanase (M. A. Attia, C. E. Nelson, W. A. Offen, N. Jain, et al., Biotechnol Biofuels 11:45, 2018, https://doi.org/10.1186/s13068-018-1039-6). In the present study, C-terminal fusion of superfolder green fluorescent protein in tandem with the Fn3-X181 modules enabled recombinant production and purification from Escherichia coli. Native affinity gel electrophoresis revealed binding specificity for the terminal galactose-containing plant polysaccharides galactoxyloglucan and galactomannan. Isothermal titration calorimetry further evidenced a preference for galactoxyloglucan polysaccharide over short oligosaccharides comprising the limit-digest products of CjGH5F. Thus, our results identify the X181 module as the defining member of a new CBM family, CBM88. In addition to directly revealing the function of this CBM in the context of xyloglucan metabolism by C. japonicus, this study will guide future bioinformatic and functional analyses across microbial (meta)genomes. IMPORTANCE This study reveals carbohydrate-binding module family 88 (CBM88) as a new family of galactose-binding protein modules, which are found in series with diverse microbial glycoside hydrolases, polysaccharide lyases, and carbohydrate esterases. The definition of CBM88 in the carbohydrate-active enzymes classification (http://www.cazy.org/CBM88.html) will significantly enable future microbial (meta)genome analysis and functional studies.
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Morales-Quintana L, Beltrán D, Mendez-Yañez Á, Valenzuela-Riffo F, Herrera R, Moya-León MA. Characterization of FcXTH2, a Novel Xyloglucan Endotransglycosylase/Hydrolase Enzyme of Chilean Strawberry with Hydrolase Activity. Int J Mol Sci 2020; 21:E3380. [PMID: 32403246 PMCID: PMC7247008 DOI: 10.3390/ijms21093380] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/01/2020] [Accepted: 05/07/2020] [Indexed: 12/12/2022] Open
Abstract
Xyloglucan endotransglycosylase/hydrolases (XTHs) are cell wall enzymes with hydrolase (XEH) and/or endotransglycosylase (XET) activities. As they are involved in the modification of the xyloglucans, a type of hemicellulose present in the cell wall, they are believed to be very important in different processes, including growth, development, and fruit ripening. Previous studies suggest that XTHs might play a key role in development and ripening of Fragaria chiloensis fruit, and its characterization is pending. Therefore, in order to provide a biochemical characterization of the FcXTH2 enzyme to explain its possible role in strawberry development, the molecular cloning and the heterologous expression of FcXTH2 were performed. The recombinant FcXTH2 was active and displayed mainly XEH activity. The optimal pH and temperature are 5.5 and 37 °C, respectively. A KM value of 0.029 mg mL-1 was determined. Additionally, its protein structural model was built through comparative modeling methodology. The model showed a typically β-jelly-roll type folding in which the catalytic motif was oriented towards the FcXTH2 central cavity. Using molecular docking, protein-ligand interactions were explored, finding better interaction with xyloglucan than with cellulose. The data provided groundwork for understanding, at a molecular level, the enzymatic mechanism of FcXTH2, an important enzyme acting during the development of the Chilean strawberry.
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Affiliation(s)
- Luis Morales-Quintana
- Multidisciplinary Agroindustry Research Laboratory, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, 3460000 Talca, Chile
| | - Dina Beltrán
- Functional Genomics, Biochemistry and Plant Physiology group, Instituto de Ciencias Biológicas, Universidad de Talca, 3460000 Talca, Chile; (D.B.); (R.H.)
| | - Ángela Mendez-Yañez
- Functional Genomics, Biochemistry and Plant Physiology group, Instituto de Ciencias Biológicas, Universidad de Talca, 3460000 Talca, Chile; (D.B.); (R.H.)
- Programa de Doctorado en Ciencias Mención Ingeniería Genética Vegetal, Instituto de Ciencias Biológicas, Universidad de Talca, 3460000 Talca, Chile;
| | - Felipe Valenzuela-Riffo
- Programa de Doctorado en Ciencias Mención Ingeniería Genética Vegetal, Instituto de Ciencias Biológicas, Universidad de Talca, 3460000 Talca, Chile;
| | - Raúl Herrera
- Functional Genomics, Biochemistry and Plant Physiology group, Instituto de Ciencias Biológicas, Universidad de Talca, 3460000 Talca, Chile; (D.B.); (R.H.)
| | - María Alejandra Moya-León
- Functional Genomics, Biochemistry and Plant Physiology group, Instituto de Ciencias Biológicas, Universidad de Talca, 3460000 Talca, Chile; (D.B.); (R.H.)
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5
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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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6
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Jones DR, Xing X, Tingley JP, Klassen L, King ML, Alexander TW, Abbott DW. Analysis of Active Site Architecture and Reaction Product Linkage Chemistry Reveals a Conserved Cleavage Substrate for an Endo-alpha-mannanase within Diverse Yeast Mannans. J Mol Biol 2020; 432:1083-1097. [PMID: 31945375 DOI: 10.1016/j.jmb.2019.12.048] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 01/06/2023]
Abstract
Yeast α-mannan (YM) is a densely branched N-linked glycan that decorates the surface of yeast cell walls. Owing to the high degree of branching, cleavage of the backbone of YM appears to rely on the coupled action of side-chain-cleaving enzymes. Upon examining the genome sequences of bovine-adapted Bacteroides thetaiotaomicron strains, isolated for their ability to degrade YM, we have identified a tandem pair of genes inserted into an orphan pathway predicted to be involved in YM metabolism. Here, we investigated the activity of one of these enzymes, a predicted endo-mannanase from glycoside hydrolase (GH) family 76 (BtGH76-MD40). Purified recombinant BtGH76-MD40 displayed activity on structurally distinct YMs from Saccharomyces cerevisiae and Schizosaccharomyces pombe. Linkage analysis of released oligosaccharide products from S. cerevisiae and S. pombe mannan determined BtGH76-MD40 targets a specific linkage that is conserved in structurally diverse YM substrates. In addition, using two differential derivatization methods, we have shown that there is an absolute requirement for undecorated d-mannopyranose in the -1 subsite. Determination of the BtGH76-MD40 X-ray crystal structure and structural superimposition and molecular docking of a branched alpha-mannopentatose substrate supported these findings. In contrast, BtGH76-MD40 can accommodate extended side chains in the +1 and -2 subsites, highlighting that a single alpha-1,6-mannosyl residue is a prerequisite for activity, and cleavage occurs at the reducing end of the undecorated monosaccharide. Collectively these results demonstrate how acquisition of new enzymes within extant pathways contributes to the functional abilities of saccharolytic bacteria persisting in complex digestive ecosystems.
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Affiliation(s)
- Darryl R Jones
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, T1J 4B1, Canada; Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, T1K 3M4, Canada
| | - Xiaohui Xing
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, T1J 4B1, Canada; Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, T1K 3M4, Canada
| | - Jeffrey P Tingley
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, T1J 4B1, Canada
| | - Leeann Klassen
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, T1J 4B1, Canada
| | - Marissa L King
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, T1J 4B1, Canada
| | - Trevor W Alexander
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, T1J 4B1, Canada
| | - D Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, T1J 4B1, Canada; Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, T1K 3M4, Canada.
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7
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Déjean G, Tauzin AS, Bennett SW, Creagh AL, Brumer H. Adaptation of Syntenic Xyloglucan Utilization Loci of Human Gut Bacteroidetes to Polysaccharide Side Chain Diversity. Appl Environ Microbiol 2019; 85:e01491-19. [PMID: 31420336 PMCID: PMC6805095 DOI: 10.1128/aem.01491-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/08/2019] [Indexed: 12/16/2022] Open
Abstract
Genome sequencing has revealed substantial variation in the predicted abilities of individual species within animal gut microbiota to metabolize the complex carbohydrates comprising dietary fiber. At the same time, a currently limited body of functional studies precludes a richer understanding of how dietary glycan structures affect the gut microbiota composition and community dynamics. Here, using biochemical and biophysical techniques, we identified and characterized differences among recombinant proteins from syntenic xyloglucan utilization loci (XyGUL) of three Bacteroides and one Dysgonomonas species from the human gut, which drive substrate specificity and access to distinct polysaccharide side chains. Enzymology of four syntenic glycoside hydrolase family 5 subfamily 4 (GH5_4) endo-xyloglucanases revealed surprising differences in xyloglucan (XyG) backbone cleavage specificity, including the ability of some homologs to hydrolyze congested branched positions. Further, differences in the complement of GH43 alpha-l-arabinofuranosidases and GH95 alpha-l-fucosidases among syntenic XyGUL confer distinct abilities to fully saccharify plant species-specific arabinogalactoxyloglucan and/or fucogalactoxyloglucan. Finally, characterization of highly sequence-divergent cell surface glycan-binding proteins (SGBPs) across syntenic XyGUL revealed a novel group of XyG oligosaccharide-specific SGBPs encoded within select BacteroidesIMPORTANCE The catabolism of complex carbohydrates that otherwise escape the endogenous digestive enzymes of humans and other animals drives the composition and function of the gut microbiota. Thus, detailed molecular characterization of dietary glycan utilization systems is essential both to understand the ecology of these complex communities and to manipulate their compositions, e.g., to benefit human health. Our research reveals new insight into how ubiquitous members of the human gut microbiota have evolved a set of microheterogeneous gene clusters to efficiently respond to the structural variations of plant xyloglucans. The data here will enable refined functional prediction of xyloglucan utilization among diverse environmental taxa in animal guts and beyond.
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Affiliation(s)
- Guillaume Déjean
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexandra S Tauzin
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stuart W Bennett
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - A Louise Creagh
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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8
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Arnal G, Stogios PJ, Asohan J, Attia MA, Skarina T, Viborg AH, Henrissat B, Savchenko A, Brumer H. Substrate specificity, regiospecificity, and processivity in glycoside hydrolase family 74. J Biol Chem 2019; 294:13233-13247. [PMID: 31324716 DOI: 10.1074/jbc.ra119.009861] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/16/2019] [Indexed: 12/11/2022] Open
Abstract
Glycoside hydrolase family 74 (GH74) is a historically important family of endo-β-glucanases. On the basis of early reports of detectable activity on cellulose and soluble cellulose derivatives, GH74 was originally considered to be a "cellulase" family, although more recent studies have generally indicated a high specificity toward the ubiquitous plant cell wall matrix glycan xyloglucan. Previous studies have indicated that GH74 xyloglucanases differ in backbone cleavage regiospecificities and can adopt three distinct hydrolytic modes of action: exo, endo-dissociative, and endo-processive. To improve functional predictions within GH74, here we coupled in-depth biochemical characterization of 17 recombinant proteins with structural biology-based investigations in the context of a comprehensive molecular phylogeny, including all previously characterized family members. Elucidation of four new GH74 tertiary structures, as well as one distantly related dual seven-bladed β-propeller protein from a marine bacterium, highlighted key structure-function relationships along protein evolutionary trajectories. We could define five phylogenetic groups, which delineated the mode of action and the regiospecificity of GH74 members. At the extremes, a major group of enzymes diverged to hydrolyze the backbone of xyloglucan nonspecifically with a dissociative mode of action and relaxed backbone regiospecificity. In contrast, a sister group of GH74 enzymes has evolved a large hydrophobic platform comprising 10 subsites, which facilitates processivity. Overall, the findings of our study refine our understanding of catalysis in GH74, providing a framework for future experimentation as well as for bioinformatics predictions of sequences emerging from (meta)genomic studies.
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Affiliation(s)
- Gregory Arnal
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Jathavan Asohan
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Mohamed A Attia
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada; Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Alexander Holm Viborg
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille University, 13007 Marseille, France; INRA, USC1408 Architecture et Fonction des Macromolécules Biologiques (AFMB), 13007 Marseille, France
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada; Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, 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, Vancouver, British Columbia V6T 1Z1, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.
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Foley MH, Déjean G, Hemsworth GR, Davies GJ, Brumer H, Koropatkin NM. A Cell-Surface GH9 Endo-Glucanase Coordinates with Surface Glycan-Binding Proteins to Mediate Xyloglucan Uptake in the Gut Symbiont Bacteroides ovatus. J Mol Biol 2019; 431:981-995. [PMID: 30668971 PMCID: PMC6478033 DOI: 10.1016/j.jmb.2019.01.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/14/2018] [Accepted: 01/04/2019] [Indexed: 01/07/2023]
Abstract
Dietary fiber is an important food source for members of the human gut microbiome. Members of the dominant Bacteroidetes phylum capture diverse polysaccharides via the action of multiple cell surface proteins encoded within polysaccharide utilization loci (PUL). The independent activities of PUL-encoded glycoside hydrolases (GHs) and surface glycan-binding proteins (SGBPs) for the harvest of various glycans have been studied in detail, but how these proteins work together to coordinate uptake is poorly understood. Here, we combine genetic and biochemical approaches to discern the interplay between the BoGH9 endoglucanase and the xyloglucan-binding proteins SGBP-A and SGBP-B from the Bacteroides ovatus xyloglucan utilization locus (XyGUL). The expression of BoGH9, a weakly active xyloglucanase in isolation, is required in a strain that expresses a non-binding version of SGBP-A (SGBP-A*). The crystal structure of the BoGH9 enzyme suggests the molecular basis for its robust activity on mixed-linkage β-glucan compared to xyloglucan. However, catalytically inactive site-directed mutants of BoGH9 fail to complement the deletion of the active BoGH9 in a SGBP-A* strain. We also find that SGBP-B is needed in an SGBP-A* background to support growth on xyloglucan, but that the non-binding SGBP-B* protein acts in a dominant negative manner to inhibit growth on xyloglucan. We postulate a model whereby the SGBP-A, SGBP-B, and BoGH9 work together at the cell surface, likely within a discrete complex, and that xyloglucan binding by SGBP-B and BoGH9 may facilitate the orientation of the xyloglucan for transfer across the outer membrane.
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Affiliation(s)
- Matthew H Foley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Guillaume Déjean
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Glyn R Hemsworth
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - 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
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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10
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Morales-Quintana L, Carrasco-Orellana C, Beltrán D, Moya-León MA, Herrera R. Molecular insights of a xyloglucan endo-transglycosylase/hydrolase of radiata pine (PrXTH1) expressed in response to inclination: Kinetics and computational study. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 136:155-161. [PMID: 30684844 DOI: 10.1016/j.plaphy.2019.01.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 12/25/2018] [Accepted: 01/14/2019] [Indexed: 06/09/2023]
Abstract
Xyloglucan endotransglycosylase/hydrolases (XTH) may have endotransglycosylase (XET) and/or hydrolase (XEH) activities. Previous studies confirmed XET activity for PrXTH1 protein from radiata pine. XTHs could interact with many hemicellulose substrates, but the favorite substrate of PrXTH1 is still unknown. The prediction of union type and energy stability of the complexes formed between PrXTH1 and different substrates (XXXGXXXG, XXFGXXFG, XLFGXLFG and cellulose) were determined using bioinformatics tools. Molecular Docking, Molecular Dynamics, MM-GBSA and Electrostatic Potential Calculations were employed to predict the binding modes, free energies of interaction and the distribution of electrostatic charge. The results suggest that the enzyme formed more stable complexes with hemicellulose substrates than cellulose, and the best ligand was the xyloglucan XLFGXLFG (free energy of -58.83 ± 0.8 kcal mol-1). During molecular dynamics trajectories, hemicellulose fibers showed greater stability than cellulose. Aditionally, the kinetic properties of PrXTH1 enzyme were determined. The recombinant protein was active and showed an optimal pH 5.0 and optimal temperature of 37 °C. A Km value of 20.9 mM was determined for xyloglucan oligomer. PrXTH1 is able to interact with different xyloglycans structures but no activity was observed for cellulose as substrate, remodeling cell wall structure in response to inclination.
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Affiliation(s)
- Luis Morales-Quintana
- Functional Genomics, Biochemistry and Plant Physiology, Instituto de Ciencias Biológicas, Universidad de Talca, Campus Lircay s/n, Talca, Chile; Multidisciplinary Agroindustry Research Laboratory, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, 5 poniente #1670, Talca, Chile
| | - Cristian Carrasco-Orellana
- Functional Genomics, Biochemistry and Plant Physiology, Instituto de Ciencias Biológicas, Universidad de Talca, Campus Lircay s/n, Talca, Chile
| | - Dina Beltrán
- Functional Genomics, Biochemistry and Plant Physiology, Instituto de Ciencias Biológicas, Universidad de Talca, Campus Lircay s/n, Talca, Chile
| | - María Alejandra Moya-León
- Functional Genomics, Biochemistry and Plant Physiology, Instituto de Ciencias Biológicas, Universidad de Talca, Campus Lircay s/n, Talca, Chile
| | - Raúl Herrera
- Functional Genomics, Biochemistry and Plant Physiology, Instituto de Ciencias Biológicas, Universidad de Talca, Campus Lircay s/n, Talca, Chile.
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11
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Structural enzymology reveals the molecular basis of substrate regiospecificity and processivity of an exemplar bacterial glycoside hydrolase family 74 endo-xyloglucanase. Biochem J 2018; 475:3963-3978. [PMID: 30463871 DOI: 10.1042/bcj20180763] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/18/2018] [Accepted: 11/21/2018] [Indexed: 12/21/2022]
Abstract
Paenibacillus odorifer produces a single multimodular enzyme containing a glycoside hydrolase (GH) family 74 module (AIQ73809). Recombinant production and characterization of the GH74 module (PoGH74cat) revealed a highly specific, processive endo-xyloglucanase that can hydrolyze the polysaccharide backbone at both branched and unbranched positions. X-ray crystal structures obtained for the free enzyme and oligosaccharide complexes evidenced an extensive hydrophobic binding platform - the first in GH74 extending from subsites -4 to +6 - and unique mobile active-site loops. Site-directed mutagenesis revealed that glycine-476 was uniquely responsible for the promiscuous backbone-cleaving activity of PoGH74cat; replacement with tyrosine, which is conserved in many GH74 members, resulted in exclusive hydrolysis at unbranched glucose units. Likewise, systematic replacement of the hydrophobic platform residues constituting the positive subsites indicated their relative contributions to the processive mode of action. Specifically, W347 (+3 subsite) and W348 (+5 subsite) are essential for processivity, while W406 (+2 subsite) and Y372 (+6 subsite) are not strictly essential, but aid processivity.
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12
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Moroz OV, Jensen PF, McDonald SP, McGregor N, Blagova E, Comamala G, Segura DR, Anderson L, Vasu SM, Rao VP, Giger L, Sørensen TH, Monrad RN, Svendsen A, Nielsen JE, Henrissat B, Davies GJ, Brumer H, Rand KD, Wilson KS. Structural Dynamics and Catalytic Properties of a Multimodular Xanthanase. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00666] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Olga V. Moroz
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom
| | - Pernille F. Jensen
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Sean P. McDonald
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Nicholas McGregor
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Elena Blagova
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom
| | - Gerard Comamala
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | | | - Lars Anderson
- Novozymes A/S, Krogshojvej 36, DK-2880 Bagsvard, Denmark
| | | | | | - Lars Giger
- Novozymes A/S, Krogshojvej 36, DK-2880 Bagsvard, Denmark
| | - Trine Holst Sørensen
- Department of Science and Environment, INM, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark
| | | | - Allan Svendsen
- Novozymes A/S, Krogshojvej 36, DK-2880 Bagsvard, Denmark
| | | | - Bernard Henrissat
- Institut National de la Recherche Agronomique, USC 1408, Architecture et Fonction des Macromolecules Biologiques, F-13288, UMR 7857 CNRS, Aix-Marseille University, F-13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Gideon J. Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom
| | - Harry Brumer
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Kasper D. Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Keith S. Wilson
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom
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13
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Méndez-Yañez Á, Beltrán D, Campano-Romero C, Molinett S, Herrera R, Moya-León MA, Morales-Quintana L. Glycosylation is important for FcXTH1 activity as judged by its structural and biochemical characterization. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 119:200-210. [PMID: 28898745 DOI: 10.1016/j.plaphy.2017.08.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/24/2017] [Accepted: 08/25/2017] [Indexed: 05/23/2023]
Abstract
Xyloglucan endotransglycosylase/hydrolases (XTH) may have endotransglycosylase (XET) and/or hydrolase (XEH) activities. Previous studies suggest that XTHs might play a key role in ripening of Fragaria chiloensis fruit as FcXTH1 transcripts increase as fruit softens. FcXTH1 protein sequence contains a conserved N-glycosylation site adjacent to catalytic residues. The FcXTH1 structure was built through comparative modeling methodology, the structure displays a β-jellyroll-type folding with a curvature generated by eight antiparallel β-sheets that holds the catalytic motif that is oriented towards the central cavity of the protein. Through Molecular Dynamic Simulations (MDS) analyses the protein-ligand interactions of FcXTH1 were explored, finding a better interaction with xyloglucans than cellulose. Nevertheless, the stability of the protein-ligand complex depends on the glycosylation state of FcXTH1: better energy interactions were determined for the glycosylated protein. As a complement, the molecular cloning and heterologous expression of FcXTH1 in Pichia pastoris was performed, and the recombinant protein was active and displayed strict XET activity. A KM value of 17.0 μM was determined for xyloglucan oligomer. The deglycosylation of FcXTH1 by PNGase-F treatment affects its biochemical properties (increase KM and reduce kcat/KM ratio) and reduces its stability. As a conclusion, glycosylation of FcXTH1 is important for its biological function.
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Affiliation(s)
- Ángela Méndez-Yañez
- Functional Genomics, Biochemistry and Plant Physiology Group, Instituto de Ciencias Biológicas, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - Dina Beltrán
- Functional Genomics, Biochemistry and Plant Physiology Group, Instituto de Ciencias Biológicas, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - Constanza Campano-Romero
- Functional Genomics, Biochemistry and Plant Physiology Group, Instituto de Ciencias Biológicas, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - Sebastián Molinett
- Functional Genomics, Biochemistry and Plant Physiology Group, Instituto de Ciencias Biológicas, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - Raúl Herrera
- Functional Genomics, Biochemistry and Plant Physiology Group, Instituto de Ciencias Biológicas, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - María Alejandra Moya-León
- Functional Genomics, Biochemistry and Plant Physiology Group, Instituto de Ciencias Biológicas, Universidad de Talca, 2 Norte 685, Talca, Chile.
| | - Luis Morales-Quintana
- Functional Genomics, Biochemistry and Plant Physiology Group, Instituto de Ciencias Biológicas, Universidad de Talca, 2 Norte 685, Talca, Chile.
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