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Sivan P, Heinonen E, Escudero L, Gandla ML, Jiménez-Quero A, Jönsson LJ, Mellerowicz EJ, Vilaplana F. Unraveling the unique structural motifs of glucuronoxylan from hybrid aspen wood. Carbohydr Polym 2024; 343:122434. [PMID: 39174079 DOI: 10.1016/j.carbpol.2024.122434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/11/2024] [Accepted: 06/24/2024] [Indexed: 08/24/2024]
Abstract
Xylan is a fundamental structural polysaccharide in plant secondary cell walls and a valuable resource for biorefinery applications. Deciphering the molecular motifs of xylans that mediate their interaction with cellulose and lignin is fundamental to understand the structural integrity of plant cell walls and to design lignocellulosic materials. In the present study, we investigated the pattern of acetylation and glucuronidation substitution in hardwood glucuronoxylan (GX) extracted from aspen wood using subcritical water and alkaline conditions. Enzymatic digestions of GX with β-xylanases from glycosyl hydrolase (GH) families GH10, GH11 and GH30 generated xylo-oligosaccharides with controlled structures amenable for mass spectrometric glycan sequencing. We identified the occurrence of intramolecular motifs in aspen GX with block repeats of even glucuronidation (every 2 xylose units) and consecutive glucuronidation, which are unique features for hardwood xylans. The acetylation pattern of aspen GX shows major domains with evenly-spaced decorations, together with minor stretches of highly acetylated domains. These heterogenous patterns of GX can be correlated with its extractability and with its potential interaction with lignin and cellulose. Our study provides new insights into the molecular structure of xylan in hardwood species, which has fundamental implications for overcoming lignocellulose recalcitrance during biochemical conversion.
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Affiliation(s)
- Pramod Sivan
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91 Stockholm, Sweden
| | - Emilia Heinonen
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91 Stockholm, Sweden; Wallenberg Wood Science Centre (WWSC), KTH Royal Institute of Technology, 100 44 Stockholm, Sweden
| | - Louis Escudero
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91 Stockholm, Sweden
| | | | - Amparo Jiménez-Quero
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91 Stockholm, Sweden
| | - Leif J Jönsson
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Ewa J Mellerowicz
- Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Department of Forest Genetics and Plant Physiology, 901 83 Umeå, Sweden
| | - Francisco Vilaplana
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, 106 91 Stockholm, Sweden; Wallenberg Wood Science Centre (WWSC), KTH Royal Institute of Technology, 100 44 Stockholm, Sweden.
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2
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Tryfona T, Pankratova Y, Petrik D, Rebaque Moran D, Wightman R, Yu X, Echevarría-Poza A, Deralia PK, Vilaplana F, Anderson CT, Hong M, Dupree P. Altering the substitution and cross-linking of glucuronoarabinoxylans affects cell wall architecture in Brachypodium distachyon. THE NEW PHYTOLOGIST 2024; 242:524-543. [PMID: 38413240 DOI: 10.1111/nph.19624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 02/05/2024] [Indexed: 02/29/2024]
Abstract
The Poaceae family of plants provides cereal crops that are critical for human and animal nutrition, and also, they are an important source of biomass. Interacting plant cell wall components give rise to recalcitrance to digestion; thus, understanding the wall molecular architecture is important to improve biomass properties. Xylan is the main hemicellulose in grass cell walls. Recently, we reported structural variation in grass xylans, suggesting functional specialisation and distinct interactions with cellulose and lignin. Here, we investigated the functions of these xylans by perturbing the biosynthesis of specific xylan types. We generated CRISPR/Cas9 knockout mutants in Brachypodium distachyon XAX1 and GUX2 genes involved in xylan substitution. Using carbohydrate gel electrophoresis, we identified biochemical changes in different xylan types. Saccharification, cryo-SEM, subcritical water extraction and ssNMR were used to study wall architecture. BdXAX1A and BdGUX2 enzymes modify different types of grass xylan. Brachypodium mutant walls are likely more porous, suggesting the xylan substitutions directed by both BdXAX1A and GUX2 enzymes influence xylan-xylan and/or xylan-lignin interactions. Since xylan substitutions influence wall architecture and digestibility, our findings open new avenues to improve cereals for food and to use grass biomass for feed and the production of bioenergy and biomaterials.
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Affiliation(s)
- Theodora Tryfona
- Department of Biochemistry, School of Biological Sciences, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Yanina Pankratova
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, NW14-3212, USA
| | - Deborah Petrik
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Diego Rebaque Moran
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, Stockholm, SE-106, Sweden
- Centro de Biotecnologia y Genomica de Plants (UPM-INIA/CSIC), Universidad Politecnica de Madrid, Pozuelo de Alarcon (Madrid), 28223, Spain
| | | | - Xiaolan Yu
- Department of Biochemistry, School of Biological Sciences, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Alberto Echevarría-Poza
- Department of Biochemistry, School of Biological Sciences, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Parveen Kumar Deralia
- Department of Biochemistry, School of Biological Sciences, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Francisco Vilaplana
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, Stockholm, SE-106, Sweden
- Wallenberg Wood Science Centre, KTH Royal Institute of Technology, Stockholm, SE-11, Sweden
| | - Charles T Anderson
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, NW14-3212, USA
| | - Paul Dupree
- Department of Biochemistry, School of Biological Sciences, University of Cambridge, Cambridge, CB2 1QW, UK
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3
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Wang X, Sheng Y, Cui H, Qiao J, Song Y, Li X, Huang H. Corner Engineering: Tailoring Enzymes for Enhanced Resistance and Thermostability in Deep Eutectic Solvents. Angew Chem Int Ed Engl 2024; 63:e202315125. [PMID: 38010210 DOI: 10.1002/anie.202315125] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023]
Abstract
Deep eutectic solvents (DESs), heralded for their synthesis simplicity, economic viability, and reduced volatility and flammability, have found increasing application in biocatalysis. However, challenges persist due to a frequent diminution in enzyme activity and stability. Herein, we developed a general protein engineering strategy, termed corner engineering, to acquire DES-resistant and thermostable enzymes via precise tailoring of the transition region in enzyme structure. Employing Bacillus subtilis lipase A (BSLA) as a model, we delineated the engineering process, yielding five multi-DESs resistant variants with highly improved thermostability, such as K88E/N89 K exhibited up to a 10.0-fold catalytic efficiency (kcat /KM ) increase in 30 % (v/v) choline chloride (ChCl): acetamide and 4.1-fold in 95 % (v/v) ChCl: ethylene glycol accompanying 6.7-fold thermal resistance improvement than wild type at ≈50 °C. The generality of the optimized approach was validated by two extra industrial enzymes, endo-β-1,4-glucanase PvCel5A (used for biofuel production) and esterase Bs2Est (used for plastics degradation). The molecular investigations revealed that increased water molecules at substrate binding cleft and finetuned helix formation at the corner region are two dominant determinants governing elevated resistance and thermostability. This study, coupling corner engineering with obtained molecular insights, illuminates enzyme-DES interaction patterns and fosters the rational design of more DES-resistant and thermostable enzymes in biocatalysis and biotransformation.
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Affiliation(s)
- Xinyue Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Yijie Sheng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Haiyang Cui
- RWTH Aachen University, Templergraben 55, 52062, Aachen, Germany
- Current address: Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA
| | - Jie Qiao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Yibo Song
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Xiujuan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
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4
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Panwar D, Shubhashini A, Kapoor M. Complex alpha and beta mannan foraging by the human gut bacteria. Biotechnol Adv 2023; 66:108166. [PMID: 37121556 DOI: 10.1016/j.biotechadv.2023.108166] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/02/2023]
Abstract
The human gut microbiota (HGM), a community of trillions of microbes, underscores its contribution by impacting many facets of host health and disease. In the HGM, Bacteroidota and Bacillota represent dominant bacterial phyla, which mainly rely on the glycans recalcitrant to host digestion to meet their energy requirements. Accordingly, the impact of dietary and host-derived glycans in the assembly and operation of these dominant microbial communities continues to be an area of active research. Among various glycans, mannans represent an integral component of the human diet. Apart from their health effects, the diverse and complex mannan structures bears molecular signatures that alter the expression of specific gene clusters in selected Bacteroidota and Bacillota species. Both the phyla possess variable and sophisticated loci of mannan recognition proteins, hydrolytic enzymes, transporters, and other metabolic proteins to sense, capture and utilize mannans as an energy source. The current review summarizes mannan structural diversity, and strategies adopted by select species of the HGM bacteria to forage mannans by focusing primarily on glycoside hydrolases and their effects on host health and metabolism.
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Affiliation(s)
- Deepesh Panwar
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysuru 570 020, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Ghaziabad, UP 201 002, India
| | - A Shubhashini
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysuru 570 020, India
| | - Mukesh Kapoor
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysuru 570 020, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Ghaziabad, UP 201 002, India.
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5
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Tryfona T, Bourdon M, Delgado Marques R, Busse‐Wicher M, Vilaplana F, Stott K, Dupree P. Grass xylan structural variation suggests functional specialization and distinctive interaction with cellulose and lignin. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:1004-1020. [PMID: 36602010 PMCID: PMC10952629 DOI: 10.1111/tpj.16096] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Xylan is the most abundant non-cellulosic polysaccharide in grass cell walls, and it has important structural roles. The name glucuronoarabinoxylan (GAX) is used to describe this variable hemicellulose. It has a linear backbone of β-1,4-xylose (Xyl) residues that may be substituted with α-1,2-linked (4-O-methyl)-glucuronic acid (GlcA), α-1,3-linked arabinofuranose (Araf), and sometimes acetylation at the O-2 and/or O-3 positions. The role of these substitutions remains unclear, although there is increasing evidence that they affect the way xylan interacts with other cell wall components, particularly cellulose and lignin. Here, we used substitution-dependent endo-xylanase enzymes to investigate the variability of xylan substitution in grass culm cell walls. We show that there are at least three different types of xylan: (i) an arabinoxylan with evenly distributed Araf substitutions without GlcA (AXe); (ii) a glucuronoarabinoxylan with clustered GlcA modifications (GAXc); and (iii) a highly substituted glucuronoarabinoxylan (hsGAX). Immunolocalization of AXe and GAXc in Brachypodium distachyon culms revealed that these xylan types are not restricted to a few cell types but are instead widely detected in Brachypodium cell walls. We hypothesize that there are functionally specialized xylan types within the grass cell wall. The even substitutions of AXe may permit folding and binding on the surface of cellulose fibrils, whereas the more complex substitutions of the other xylans may support a role in the matrix and interaction with other cell wall components.
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Affiliation(s)
- Theodora Tryfona
- Department of Biochemistry, School of Biological SciencesUniversity of CambridgeCambridgeCB2 1QWUK
| | | | - Rita Delgado Marques
- Department of Biochemistry, School of Biological SciencesUniversity of CambridgeCambridgeCB2 1QWUK
| | - Marta Busse‐Wicher
- Department of Biochemistry, School of Biological SciencesUniversity of CambridgeCambridgeCB2 1QWUK
| | - Francisco Vilaplana
- Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and HealthKTH Royal Institute of TechnologyStockholmSE‐10691Sweden
| | - Katherine Stott
- Department of Biochemistry, School of Biological SciencesUniversity of CambridgeCambridgeCB2 1QWUK
| | - Paul Dupree
- Department of Biochemistry, School of Biological SciencesUniversity of CambridgeCambridgeCB2 1QWUK
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6
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Mon ML, Marrero Díaz de Villegas R, Campos E, Soria MA, Talia PM. Characterization of a novel GH10 alkali-thermostable xylanase from a termite microbiome. BIORESOUR BIOPROCESS 2022; 9:84. [PMID: 38647897 PMCID: PMC10992782 DOI: 10.1186/s40643-022-00572-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/02/2022] [Indexed: 11/10/2022] Open
Abstract
The aim of the present study was to assess the biochemical and molecular structural characteristics of a novel alkali-thermostable GH10 xylanase (Xyl10B) identified in a termite gut microbiome by a shotgun metagenomic approach. This endoxylanase candidate was amplified, cloned, heterologously expressed in Escherichia coli and purified. The recombinant enzyme was active at a broad range of temperatures (37-60 ºC) and pH values (4-10), with optimal activity at 50 ºC and pH 9. Moreover, its activity remained at more than 80% of its maximum at 50 °C for 8 h. In addition, Xyl10B was found to be stable in the presence of salt and several ions and chemical reagents frequently used in the industry. These characteristics make this enzyme an interesting candidate for pulp and paper bleaching industries, since this process requires enzymes without cellulase activity and resistant to high temperatures and alkaline pH (thermo-alkaliphilic enzymes). The products of xylan hydrolysis by Xyl10B (short xylooligosaccharides, xylose and xylobiose) could be suitable for application as prebiotics and in the production of bioethanol.
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Affiliation(s)
- Maria Laura Mon
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Rubén Marrero Díaz de Villegas
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Eleonora Campos
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Marcelo A Soria
- Facultad de Agronomía, Cátedra de Microbiología Agrícola, Universidad de Buenos Aires, INBA UBA-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Paola M Talia
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina.
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7
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Teze D, Zhao J, Wiemann M, Kazi ZGA, Lupo R, Zeuner B, Vuillemin M, Rønne ME, Carlström G, Duus JØ, Sanejouand YH, O'Donohue MJ, Nordberg Karlsson E, Fauré R, Stålbrand H, Svensson B. Rational Enzyme Design without Structural Knowledge: A Sequence-Based Approach for Efficient Generation of Transglycosylases. Chemistry 2021; 27:10323-10334. [PMID: 33914359 DOI: 10.1002/chem.202100110] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Indexed: 12/22/2022]
Abstract
Glycobiology is dogged by the relative scarcity of synthetic, defined oligosaccharides. Enzyme-catalysed glycosylation using glycoside hydrolases is feasible but is hampered by the innate hydrolytic activity of these enzymes. Protein engineering is useful to remedy this, but it usually requires prior structural knowledge of the target enzyme, and/or relies on extensive, time-consuming screening and analysis. Here, a straightforward strategy that involves rational rapid in silico analysis of protein sequences is described. The method pinpoints 6-12 single-mutant candidates to improve transglycosylation yields. Requiring very little prior knowledge of the target enzyme other than its sequence, the method is generic and procures catalysts for the formation of glycosidic bonds involving various d/l-, α/β-pyranosides or furanosides, and exo or endo action. Moreover, mutations validated in one enzyme can be transposed to others, even distantly related enzymes.
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Affiliation(s)
- David Teze
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
| | - Jiao Zhao
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, 135 avenue de Rangueil, 31077, Toulouse CEDEX 04, France
| | - Mathias Wiemann
- Department of Biochemistry and Structural Biology, Lund University, 221 00, Lund, Sweden
| | - Zubaida G A Kazi
- Department of Chemistry, Lund University, PO Box 124, 22100, Lund, Sweden
| | - Rossana Lupo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
| | - Birgitte Zeuner
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
| | - Marlène Vuillemin
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
| | - Mette E Rønne
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
| | - Göran Carlström
- Department of Chemistry, Lund University, PO Box 124, 22100, Lund, Sweden
| | - Jens Ø Duus
- Department of Chemistry, Technical University of Denmark, Kemitorvet, bulding 207, DK-2800, Kongens Lyngby, Denmark
| | - Yves-Henri Sanejouand
- UFIP, UMR 6286, Université de Nantes, CNRS, 2, chemin de la Houssiniere, Nantes, France
| | - Michael J O'Donohue
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, 135 avenue de Rangueil, 31077, Toulouse CEDEX 04, France
| | | | - Régis Fauré
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, 135 avenue de Rangueil, 31077, Toulouse CEDEX 04, France
| | - Henrik Stålbrand
- Department of Biochemistry and Structural Biology, Lund University, 221 00, Lund, Sweden
| | - Birte Svensson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, building 224, DK-2800, Kongens Lyngby, Denmark
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Multimodularity of a GH10 Xylanase Found in the Termite Gut Metagenome. Appl Environ Microbiol 2021; 87:AEM.01714-20. [PMID: 33187992 PMCID: PMC7848910 DOI: 10.1128/aem.01714-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/03/2020] [Indexed: 01/01/2023] Open
Abstract
Xylan is the major hemicellulosic polysaccharide in cereals and contributes to the recalcitrance of the plant cell wall toward degradation. Bacteroidetes, one of the main phyla in rumen and human gut microbiota, have been shown to encode polysaccharide utilization loci dedicated to the degradation of xylan. Here, we present the biochemical characterization of a xylanase encoded by a bacteroidetes strain isolated from the termite gut metagenome. The functional screening of a Pseudacanthotermes militaris termite gut metagenomic library revealed an array of xylan-degrading enzymes, including P. militaris 25 (Pm25), a multimodular glycoside hydrolase family 10 (GH10). Sequence analysis showed details of the unusual domain organization of this enzyme. It consists of one catalytic domain, which is intercalated by two carbohydrate binding modules (CBMs) from family 4. The genes upstream of the genes encoding Pm25 are susC-susD-unk, suggesting Pm25 is a Xyn10C-like enzyme belonging to a polysaccharide utilization locus. The majority of Xyn10C-like enzymes shared the same interrupted domain architecture and were vastly distributed in different xylan utilization loci found in gut Bacteroidetes, indicating the importance of this enzyme in glycan acquisition for gut microbiota. To understand its unusual multimodularity and the possible role of the CBMs, a detailed characterization of the full-length Pm25 and truncated variants was performed. Results revealed that the GH10 catalytic module is specific toward the hydrolysis of xylan. Ligand binding results indicate that the GH10 module and the CBMs act independently, whereas the tandem CBM4s act synergistically with each other and improve enzymatic activity when assayed on insoluble polysaccharides. In addition, we show that the UNK protein upstream of Pm25 is able to bind arabinoxylan. Altogether, these findings contribute to a better understanding of the potential role of Xyn10C-like proteins in xylan utilization systems of gut bacteria. IMPORTANCE Xylan is the major hemicellulosic polysaccharide in cereals and contributes to the recalcitrance of the plant cell wall toward degradation. Members of the Bacteroidetes, one of the main phyla in rumen and human gut microbiota, have been shown to encode polysaccharide utilization loci dedicated to the degradation of xylan. Here, we present the biochemical characterization of a xylanase encoded by a Bacteroidetes strain isolated from the termite gut metagenome. This xylanase is a multimodular enzyme, the sequence of which is interrupted by the insertion of two CBMs from family 4. Our results show that this enzyme resembles homologues that were shown to be important for xylan degradation in rumen or human diet and show that the CBM insertion in the middle of the sequence seems to be a common feature in xylan utilization systems. This study shed light on our understanding of xylan degradation and plant cell wall deconstruction, which can be applied to several applications in food, feed, and bioeconomy.
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Storani A, Guerrero SA, Iglesias AA. On the functionality of the N-terminal domain in xylanase 10A from Ruminococcus albus 8. Enzyme Microb Technol 2020; 142:109673. [PMID: 33220861 DOI: 10.1016/j.enzmictec.2020.109673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/02/2020] [Accepted: 09/17/2020] [Indexed: 10/23/2022]
Abstract
We analyzed the structure to function relationships in Ruminococcus albus 8 xylanase 10A (RalXyn10A) finding that the N-terminus 34-amino acids sequence (N34) in the protein is particularly functional. We performed the recombinant wild type enzyme's characterization and that of the truncated mutant lacking the N34 extreme (RalΔN34Xyn10A). The truncated enzyme exhibited about half of the activity and reduced affinity for binding to insoluble saccharides. These suggest a (CBM)-like function for the N34 motif. Besides, RalXyn10A activity was diminished by redox agent dithiothreitol, a characteristic absent in RalΔN34Xyn10A. The N34 sequence exhibited a significant similarity with protein components of the ABC transporter of the bacterial membrane, and this motif is present in other proteins of R. albus 8. Data suggest that N34 would confer RalXyn10A the capacity to interact with polysaccharides and components of the cell membrane, enhancing the degradation of the substrate and uptake of the products by the bacterium.
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Affiliation(s)
- Alem Storani
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET - UNL). Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Sergio A Guerrero
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET - UNL). Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Alberto A Iglesias
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET - UNL). Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina.
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10
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Sepulchro AGV, Pellegrini VO, Briganti L, de Araujo EA, de Araujo SS, Polikarpov I. Transformation of xylan into value-added biocommodities using Thermobacillus composti GH10 xylanase. Carbohydr Polym 2020; 247:116714. [DOI: 10.1016/j.carbpol.2020.116714] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/13/2020] [Accepted: 07/01/2020] [Indexed: 12/14/2022]
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11
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Tryfona T, Sorieul M, Feijao C, Stott K, Rubtsov DV, Anders N, Dupree P. Development of an oligosaccharide library to characterise the structural variation in glucuronoarabinoxylan in the cell walls of vegetative tissues in grasses. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:109. [PMID: 31080516 PMCID: PMC6501314 DOI: 10.1186/s13068-019-1451-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 04/25/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND Grass glucuronoarabinoxylan (GAX) substitutions can inhibit enzymatic degradation and are involved in the interaction of xylan with cell wall cellulose and lignin, factors which contribute to the recalcitrance of biomass to saccharification. Therefore, identification of xylan characteristics central to biomass biorefining improvement is essential. However, the task of assessing biomass quality is complicated and is often hindered by the lack of a reference for a given crop. RESULTS In this study, we created a reference library, expressed in glucose units, of Miscanthus sinensis GAX stem and leaf oligosaccharides, using DNA sequencer-Assisted Saccharide analysis in high throughput (DASH), supported by liquid chromatography (LC), nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS). Our analysis of a number of grass species highlighted variations in substitution type and frequency of stem and leaf GAX. In miscanthus, for example, the β-Xylp-(1 → 2)-α-Araf-(1 → 3) side chain is more abundant in leaf than stem. CONCLUSIONS The reference library allows fast identification and comparison of GAX structures from different plants and tissues. Ultimately, this reference library can be used in directing biomass selection and improving biorefining.
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Affiliation(s)
- Theodora Tryfona
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge, CB2 1QW UK
| | - Mathias Sorieul
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge, CB2 1QW UK
- Present Address: Scion, 49 Sala Street, Private Bag 3020, Rotorua, 3046 New Zealand
| | - Carolina Feijao
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge, CB2 1QW UK
- Present Address: Frontiers, WeWork, 1 Fore St, London, EC2Y 5EJ UK
| | - Katherine Stott
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA UK
| | - Denis V. Rubtsov
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge, CB2 1QW UK
- Present Address: ideaSpace South, Cambridge Biomedical Campus, Bay 13 Hills Road, Cambridge, CB2 0SP UK
| | - Nadine Anders
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge, CB2 1QW UK
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Hopkins Building, The Downing Site, Tennis Court Road, Cambridge, CB2 1QW UK
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12
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Fowler CA, Hemsworth GR, Cuskin F, Hart S, Turkenburg J, Gilbert HJ, Walton PH, Davies GJ. Structure and function of a glycoside hydrolase family 8 endoxylanase from Teredinibacter turnerae. Acta Crystallogr D Struct Biol 2018; 74:946-955. [PMID: 30289404 PMCID: PMC6173055 DOI: 10.1107/s2059798318009737] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/09/2018] [Indexed: 12/13/2022] Open
Abstract
The biological conversion of lignocellulosic matter into high-value chemicals or biofuels is of increasing industrial importance as the sector slowly transitions away from nonrenewable sources. Many industrial processes involve the use of cellulolytic enzyme cocktails - a selection of glycoside hydrolases and, increasingly, polysaccharide oxygenases - to break down recalcitrant plant polysaccharides. ORFs from the genome of Teredinibacter turnerae, a symbiont hosted within the gills of marine shipworms, were identified in order to search for enzymes with desirable traits. Here, a putative T. turnerae glycoside hydrolase from family 8, hereafter referred to as TtGH8, is analysed. The enzyme is shown to be active against β-1,4-xylan and mixed-linkage (β-1,3,β-1,4) marine xylan. Kinetic parameters, obtained using high-performance anion-exchange chromatography with pulsed amperometric detection and 3,5-dinitrosalicyclic acid reducing-sugar assays, show that TtGH8 catalyses the hydrolysis of β-1,4-xylohexaose with a kcat/Km of 7.5 × 107 M-1 min-1 but displays maximal activity against mixed-linkage polymeric xylans, hinting at a primary role in the degradation of marine polysaccharides. The three-dimensional structure of TtGH8 was solved in uncomplexed and xylobiose-, xylotriose- and xylohexaose-bound forms at approximately 1.5 Å resolution; the latter was consistent with the greater kcat/Km for hexasaccharide substrates. A 2,5B boat conformation observed in the -1 position of bound xylotriose is consistent with the proposed conformational itinerary for this class of enzyme. This work shows TtGH8 to be effective at the degradation of xylan-based substrates, notably marine xylan, further exemplifying the potential of T. turnerae for effective and diverse biomass degradation.
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Affiliation(s)
- Claire A. Fowler
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Glyn R. Hemsworth
- School of Molecular and Cellular Biology, The Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, England
| | - Fiona Cuskin
- School of Natural and Environmental Science, Newcastle University, Newcastle upon Tyne NE1 7RU, England
| | - Sam Hart
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Johan Turkenburg
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Harry J. Gilbert
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, England
| | - Paul H. Walton
- Department of Chemistry, The University of York, York YO10 5DD, England
| | - Gideon J. Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
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13
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Yang J, Han Z. Understanding the Positional Binding and Substrate Interaction of a Highly Thermostable GH10 Xylanase from Thermotoga maritima by Molecular Docking. Biomolecules 2018; 8:biom8030064. [PMID: 30061529 PMCID: PMC6163442 DOI: 10.3390/biom8030064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/24/2018] [Accepted: 07/26/2018] [Indexed: 11/16/2022] Open
Abstract
Glycoside hydrolase family 10 (GH10) xylanases are responsible for enzymatic cleavage of the internal glycosidic linkages of the xylan backbone, to generate xylooligosaccharides (XOS) and xyloses. The topologies of active-site cleft determine the substrate preferences and product profiles of xylanases. In this study, positional bindings and substrate interactions of TmxB, one of the most thermostable xylanases characterized from Thermotoga maritima to date, was investigated by docking simulations. XOS with backbone lengths of two to five (X2–X5) were docked into the active-site cleft of TmxB by AutoDock The modeled complex structures provided a series of snapshots of the interactions between XOS and TmxB. Changes in binding energy with the length of the XOS backbone indicated the existence of four effective subsites in TmxB. The interaction patterns at subsites −2 to +1 in TmxB were conserved among GH10 xylanases whereas those at distal aglycone subsite +2, consisting of the hydrogen bond network, was unique for TmxB. This work helps in obtaining an in-depth understanding of the substrate-binding property of TmxB and provides a basis for rational design of mutants with desired product profiles.
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Affiliation(s)
- Jiangke Yang
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China.
| | - Zhenggang Han
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China.
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14
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A plasmid borne, functionally novel glycoside hydrolase family 30 subfamily 8 endoxylanase from solventogenic Clostridium. Biochem J 2018; 475:1533-1551. [PMID: 29626157 PMCID: PMC5934979 DOI: 10.1042/bcj20180050] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/28/2018] [Accepted: 04/03/2018] [Indexed: 11/24/2022]
Abstract
Glycoside hydrolase family 30 subfamily 8 (GH30-8) β-1,4-endoxylanases are known for their appendage-dependent function requiring recognition of an α-1,2-linked glucuronic acid (GlcA) common to glucuronoxylans for hydrolysis. Structural studies have indicated that the GlcA moiety of glucuronoxylans is coordinated through six hydrogen bonds and a salt bridge. These GlcA-dependent endoxylanases do not have significant activity on xylans that do not bear GlcA substitutions such as unsubstituted linear xylooligosaccharides or cereal bran arabinoxylans. In the present study, we present the structural and biochemical characteristics of xylanase 30A from Clostridium acetobutylicum (CaXyn30A) which was originally selected for study due to predicted structural differences within the GlcA coordination loops. Amino acid sequence comparisons indicated that this Gram-positive-derived GH30-8 more closely resembles Gram-negative derived forms of these endoxylanases: a hypothesis borne out in the developed crystallographic structure model of the CaXyn30A catalytic domain (CaXyn30A-CD). CaXyn30A-CD hydrolyzes xylans to linear and substituted oligoxylosides showing the greatest rate with the highly arabinofuranose (Araf)-substituted cereal arabinoxylans. CaXyn30A-CD hydrolyzes xylooligosaccharides larger than xylotriose and shows an increased relative rate of hydrolysis for xylooligosaccharides containing α-1,2-linked arabinofuranose substitutions. Biochemical analysis confirms that CaXyn30A benefits from five xylose-binding subsites which extend from the −3 subsite to the +2 subsite of the binding cleft. These studies indicate that CaXyn30A is a GlcA-independent endoxylanase that may have evolved for the preferential recognition of α-1,2-Araf substitutions on xylan chains.
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15
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Xiong K, Xiong S, Gao S, Li Q, Sun B, Li X. Improving Hydrolysis Characteristics of Xylanases by Site-Directed Mutagenesis in Binding-Site Subsites from Streptomyces L10608. Int J Mol Sci 2018. [PMID: 29533991 PMCID: PMC5877695 DOI: 10.3390/ijms19030834] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The preparation of oligosaccharides via xylan hydrolysis is an effective way to add value to hemicellulosic material of agricultural waste. The bacterial strain Streptomyces L10608, isolated from soil, contains genes encoding xylanases of glucoside hydrolase family 10/11 (GH10/11), and these have been cloned to catalyze the production of xylooligosaccharide (XOS). To improve the XOS proportion of hydrolysates produced by xylanase, four amino acid residues were substituted by site-directed mutagenesis, and the mutant genes were overexpressed in Escherichia coli. Mutations replaced the codons encoding Asn214 (+2) and Asn86 (−2) by Ala and removed the Ricin B-lectin domain in GH10-xyn, and mutants Y115A (−2) and Y123A (−2) were produced for GH11-xyn. Interestingly, GH10-N86Q had significantly increased hydrolysis of XOS and almost eliminated xylose (X1) to <2.5%, indicating that the −2 binding site of GH10-xyn of L10608 is required for binding with xylotriose (X3). The hydrolytic activity of GH10-N86Q was increased approximately 1.25-fold using beechwood xylan as a substrate and had high affinity for the substrate with a low Km of about 1.85 mg·mL−1. Otherwise, there were no significant differences in enzymatic properties between GH10-N86Q and GH10-xyn. These mutants offer great potential for modification of xylanase with desired XOS hydrolysis.
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Affiliation(s)
- Ke Xiong
- Beijing Innovation Centre of Food Nutrition and Human, Beijing Technology & Business University (BTBU), No. 33 Fucheng Road, Haidian, Beijing 100048, China.
- Beijing Laboratory for Food Quality and Safety, Beijing Technology & Business University (BTBU), No. 33 Fucheng Road, Haidian, Beijing 100048, China.
| | - Suyue Xiong
- Beijing Innovation Centre of Food Nutrition and Human, Beijing Technology & Business University (BTBU), No. 33 Fucheng Road, Haidian, Beijing 100048, China.
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), No. 33 Fucheng Road, Haidian, Beijing 100048, China.
| | - Siyu Gao
- Beijing Innovation Centre of Food Nutrition and Human, Beijing Technology & Business University (BTBU), No. 33 Fucheng Road, Haidian, Beijing 100048, China.
- Beijing Key Laboratory of Flavor Chemistry, Beijing Technology and Business University (BTBU), No. 33 Fucheng Road, Haidian, Beijing 100048, China.
| | - Qin Li
- Beijing Innovation Centre of Food Nutrition and Human, Beijing Technology & Business University (BTBU), No. 33 Fucheng Road, Haidian, Beijing 100048, China.
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University (BTBU), No. 33 Fucheng Road, Haidian, Beijing 100048, China.
| | - Baoguo Sun
- Beijing Innovation Centre of Food Nutrition and Human, Beijing Technology & Business University (BTBU), No. 33 Fucheng Road, Haidian, Beijing 100048, China.
- Beijing Laboratory for Food Quality and Safety, Beijing Technology & Business University (BTBU), No. 33 Fucheng Road, Haidian, Beijing 100048, China.
| | - Xiuting Li
- Beijing Innovation Centre of Food Nutrition and Human, Beijing Technology & Business University (BTBU), No. 33 Fucheng Road, Haidian, Beijing 100048, China.
- Beijing Laboratory for Food Quality and Safety, Beijing Technology & Business University (BTBU), No. 33 Fucheng Road, Haidian, Beijing 100048, China.
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16
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Chu Y, Tu T, Penttinen L, Xue X, Wang X, Yi Z, Gong L, Rouvinen J, Luo H, Hakulinen N, Yao B, Su X. Insights into the roles of non-catalytic residues in the active site of a GH10 xylanase with activity on cellulose. J Biol Chem 2017; 292:19315-19327. [PMID: 28974575 PMCID: PMC5702671 DOI: 10.1074/jbc.m117.807768] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/20/2017] [Indexed: 11/06/2022] Open
Abstract
Bifunctional glycoside hydrolases have potential for cost-savings in enzymatic decomposition of plant cell wall polysaccharides for biofuels and bio-based chemicals. The N-terminal GH10 domain of a bifunctional multimodular enzyme CbXyn10C/Cel48B from Caldicellulosiruptor bescii is an enzyme able to degrade xylan and cellulose simultaneously. However, the molecular mechanism underlying its substrate promiscuity has not been elucidated. Herein, we discovered that the binding cleft of CbXyn10C would have at least six sugar-binding subsites by using isothermal titration calorimetry analysis of the inactive E140Q/E248Q mutant with xylo- and cello-oligosaccharides. This was confirmed by determining the catalytic efficiency of the wild-type enzyme on these oligosaccharides. The free form and complex structures of CbXyn10C with xylose- or glucose-configured oligosaccharide ligands were further obtained by crystallographic analysis and molecular modeling and docking. CbXyn10C was found to have a typical (β/α)8-TIM barrel fold and "salad-bowl" shape of GH10 enzymes. In complex structures with xylo-oligosaccharides, seven sugar-binding subsites were found, and many residues responsible for substrate interactions were identified. Site-directed mutagenesis indicated that 6 and 10 amino acid residues were key residues for xylan and cellulose hydrolysis, respectively. The most important residues are centered on subsites -2 and -1 near the cleavage site, whereas residues playing moderate roles could be located at more distal regions of the binding cleft. Manipulating the residues interacting with substrates in the distal regions directly or indirectly improved the activity of CbXyn10C on xylan and cellulose. Most of the key residues for cellulase activity are conserved across GH10 xylanases. Revisiting randomly selected GH10 enzymes revealed unreported cellulase activity, indicating that the dual function may be a more common phenomenon than has been expected.
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Affiliation(s)
- Yindi Chu
- From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tao Tu
- From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Leena Penttinen
- the Department of Chemistry, University of Eastern Finland, Joensuu Campus, Joensuu FIN-80101, Finland
| | - Xianli Xue
- From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoyu Wang
- From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhuolin Yi
- the Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China, and
| | - Li Gong
- From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- the Key Laboratory of Molecular Animal Nutrition and Feed Sciences, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Juha Rouvinen
- the Department of Chemistry, University of Eastern Finland, Joensuu Campus, Joensuu FIN-80101, Finland
| | - Huiying Luo
- From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Nina Hakulinen
- the Department of Chemistry, University of Eastern Finland, Joensuu Campus, Joensuu FIN-80101, Finland,
| | - Bin Yao
- From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China,
| | - Xiaoyun Su
- From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China,
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17
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Temple MJ, Cuskin F, Baslé A, Hickey N, Speciale G, Williams SJ, Gilbert HJ, Lowe EC. A Bacteroidetes locus dedicated to fungal 1,6-β-glucan degradation: Unique substrate conformation drives specificity of the key endo-1,6-β-glucanase. J Biol Chem 2017; 292:10639-10650. [PMID: 28461332 PMCID: PMC5481569 DOI: 10.1074/jbc.m117.787606] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 04/25/2017] [Indexed: 12/13/2022] Open
Abstract
Glycans are major nutrients available to the human gut microbiota. The Bacteroides are generalist glycan degraders, and this function is mediated largely by polysaccharide utilization loci (PULs). The genomes of several Bacteroides species contain a PUL, PUL1,6-β-glucan, that was predicted to target mixed linked plant 1,3;1,4-β-glucans. To test this hypothesis we characterized the proteins encoded by this locus in Bacteroides thetaiotaomicron, a member of the human gut microbiota. We show here that PUL1,6-β-glucan does not orchestrate the degradation of a plant polysaccharide but targets a fungal cell wall glycan, 1,6-β-glucan, which is a growth substrate for the bacterium. The locus is up-regulated by 1,6-β-glucan and encodes two enzymes, a surface endo-1,6-β-glucanase, BT3312, and a periplasmic β-glucosidase that targets primarily 1,6-β-glucans. The non-catalytic proteins encoded by PUL1,6-β-glucan target 1,6-β-glucans and comprise a surface glycan-binding protein and a SusD homologue that delivers glycans to the outer membrane transporter. We identified the central role of the endo-1,6-β-glucanase in 1,6-β-glucan depolymerization by deleting bt3312, which prevented the growth of B. thetaiotaomicron on 1,6-β-glucan. The crystal structure of BT3312 in complex with β-glucosyl-1,6-deoxynojirimycin revealed a TIM barrel catalytic domain that contains a deep substrate-binding cleft tailored to accommodate the hook-like structure adopted by 1,6-β-glucan. Specificity is driven by the complementarity of the enzyme active site cleft and the conformation of the substrate. We also noted that PUL1,6-β-glucan is syntenic to many PULs from other Bacteroidetes, suggesting that utilization of yeast and fungal cell wall 1,6-β-glucans is a widespread adaptation within the human microbiota.
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Affiliation(s)
- Max J Temple
- From the Institute of Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE4 2HH, United Kingdom and
| | - Fiona Cuskin
- From the Institute of Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE4 2HH, United Kingdom and
| | - Arnaud Baslé
- From the Institute of Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE4 2HH, United Kingdom and
| | - Niall Hickey
- From the Institute of Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE4 2HH, United Kingdom and
| | - Gaetano Speciale
- the School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Spencer J Williams
- the School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Harry J Gilbert
- From the Institute of Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE4 2HH, United Kingdom and
| | - Elisabeth C Lowe
- From the Institute of Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE4 2HH, United Kingdom and
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18
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Senf D, Ruprecht C, de Kruijff GHM, Simonetti SO, Schuhmacher F, Seeberger PH, Pfrengle F. Active Site Mapping of Xylan-Deconstructing Enzymes with Arabinoxylan Oligosaccharides Produced by Automated Glycan Assembly. Chemistry 2017; 23:3197-3205. [PMID: 28092124 DOI: 10.1002/chem.201605902] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Indexed: 11/10/2022]
Abstract
Xylan-degrading enzymes are crucial for the deconstruction of hemicellulosic biomass, making the hydrolysis products available for various industrial applications such as the production of biofuel. To determine the substrate specificities of these enzymes, we prepared a collection of complex xylan oligosaccharides by automated glycan assembly. Seven differentially protected building blocks provided the basis for the modular assembly of 2-substituted, 3-substituted, and 2-/3-substituted arabino- and glucuronoxylan oligosaccharides. Elongation of the xylan backbone relied on iterative additions of C4-fluorenylmethoxylcarbonyl (Fmoc) protected xylose building blocks to a linker-functionalized resin. Arabinofuranose and glucuronic acid residues have been selectively attached to the backbone using fully orthogonal 2-(methyl)naphthyl (Nap) and 2-(azidomethyl)benzoyl (Azmb) protecting groups at the C2 and C3 hydroxyls of the xylose building blocks. The arabinoxylan oligosaccharides are excellent tools to map the active site of glycosyl hydrolases involved in xylan deconstruction. The substrate specificities of several xylanases and arabinofuranosidases were determined by analyzing the digestion products after incubation of the oligosaccharides with glycosyl hydrolases.
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Affiliation(s)
- Deborah Senf
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Colin Ruprecht
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Goswinus H M de Kruijff
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany.,Current address: Institute of Organic Chemistry, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Sebastian O Simonetti
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Current address: Rosario Chemistry Institute (IQUIR, CONICET-UNR), Suipacha 570, S2002LRK, Rosario, Argentina
| | - Frank Schuhmacher
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Fabian Pfrengle
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
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19
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Zhang Y, An J, Yang G, Zhang X, Xie Y, Chen L, Feng Y. Structure features of GH10 xylanase from Caldicellulosiruptor bescii: implication for its thermophilic adaption and substrate binding preference. Acta Biochim Biophys Sin (Shanghai) 2016; 48:948-957. [PMID: 27563004 DOI: 10.1093/abbs/gmw086] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 07/27/2016] [Indexed: 12/11/2022] Open
Abstract
Caldicellulosiruptor bescii is the most thermophilic cellulolytic species of organisms known to date. In our previous study, GH10 xylanase CbXyn10B from C. bescii displayed outstanding hydrolytic activity toward various xylans at high temperatures. To understand the structural basis for this protein's catalysis and thermostability, we solved the crystal structures of CbXyn10B and its complexes with xylooligosaccharides. These structural models were used to guide comparison with its mesophilic counterpart PbXyn10B. A distinctive structural feature is that thermophilic CbXyn10B presents a relatively stable interaction between the extended loops L7 and L8 in the catalytic cleft by an extensive hydrogen bonding network, which is mediated by Lys306, Arg314 and three well-ordered water molecules. Moreover, a unique aromatic cluster consisting of Try17, Phe20, Phe21, and Phe337 may enhance the interaction between the N- and C- terminus. Targeted mutagenesis demonstrated that these interactions substantially contribute to enzyme stabilization, as indicated by a considerable decrease in the melting temperature (Tm) of CbXyn10B by substituting critical residues with Ala. Therefore, it was shown that not only the aromatic interaction connecting protein termini but also the extensive hydrogen bonding network formed between surface loops could restrict the local structural flexibility and contribute significantly to the overall stability of enzymes. Furthermore, the xylooligosaccharides were found to tightly bind to the glycone subsites of xylanase, indicating higher affinities at these subsites and reflecting its substrate binding preference. Our results suggest that CbXyn10B is stabilized with distinct rigidity at the catalytic cleft as well as the terminal regions, which provides insights into the evolutionary strategy for accommodating the functional needs of GH10 enzymes to high temperature.
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Affiliation(s)
- Yong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiao An
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guangyu Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaofei Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuan Xie
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liuqing Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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20
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Labourel A, Crouch LI, Brás JLA, Jackson A, Rogowski A, Gray J, Yadav MP, Henrissat B, Fontes CMGA, Gilbert HJ, Najmudin S, Baslé A, Cuskin F. The Mechanism by Which Arabinoxylanases Can Recognize Highly Decorated Xylans. J Biol Chem 2016; 291:22149-22159. [PMID: 27531750 PMCID: PMC5063996 DOI: 10.1074/jbc.m116.743948] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Indexed: 12/15/2022] Open
Abstract
The enzymatic degradation of plant cell walls is an important biological process of increasing environmental and industrial significance. Xylan, a major component of the plant cell wall, consists of a backbone of β-1,4-xylose (Xylp) units that are often decorated with arabinofuranose (Araf) side chains. A large penta-modular enzyme, CtXyl5A, was shown previously to specifically target arabinoxylans. The mechanism of substrate recognition displayed by the enzyme, however, remains unclear. Here we report the crystal structure of the arabinoxylanase and the enzyme in complex with ligands. The data showed that four of the protein modules adopt a rigid structure, which stabilizes the catalytic domain. The C-terminal non-catalytic carbohydrate binding module could not be observed in the crystal structure, suggesting positional flexibility. The structure of the enzyme in complex with Xylp-β-1,4-Xylp-β-1,4-Xylp-[α-1,3-Araf]-β-1,4-Xylp showed that the Araf decoration linked O3 to the xylose in the active site is located in the pocket (−2* subsite) that abuts onto the catalytic center. The −2* subsite can also bind to Xylp and Arap, explaining why the enzyme can utilize xylose and arabinose as specificity determinants. Alanine substitution of Glu68, Tyr92, or Asn139, which interact with arabinose and xylose side chains at the −2* subsite, abrogates catalytic activity. Distal to the active site, the xylan backbone makes limited apolar contacts with the enzyme, and the hydroxyls are solvent-exposed. This explains why CtXyl5A is capable of hydrolyzing xylans that are extensively decorated and that are recalcitrant to classic endo-xylanase attack.
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Affiliation(s)
- Aurore Labourel
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Lucy I Crouch
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Joana L A Brás
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal, NZYTech Genes & Enzymes, 1649-038 Lisboa, Portugal
| | - Adam Jackson
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Artur Rogowski
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Joseph Gray
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Madhav P Yadav
- the Eastern Regional Research Center, United States Department of Agriculture-Agricultural Research Service, Wyndmoor, Pennsylvania 19038
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR7857 CNRS, Aix-Marseille University, F-13288 Marseille, France, USC1408 Architecture et Fonction des Macromolécules Biologiques, INRA, F-13288 Marseille, France, and the Department of Biological Sciences, King Abdulaziz University, Jedda 21589, Saudi Arabia
| | - Carlos M G A Fontes
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal, NZYTech Genes & Enzymes, 1649-038 Lisboa, Portugal
| | - Harry J Gilbert
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Shabir Najmudin
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal,
| | - Arnaud Baslé
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom,
| | - Fiona Cuskin
- From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom,
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21
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Zheng F, Huang J, Liu X, Hu H, Long L, Chen K, Ding S. N- and C-terminal truncations of a GH10 xylanase significantly increase its activity and thermostability but decrease its SDS resistance. Appl Microbiol Biotechnol 2015; 100:3555-65. [DOI: 10.1007/s00253-015-7176-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 11/09/2015] [Accepted: 11/13/2015] [Indexed: 11/28/2022]
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22
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Tirion MM. On the sensitivity of protein data bank normal mode analysis: an application to GH10 xylanases. Phys Biol 2015; 12:066013. [PMID: 26599799 DOI: 10.1088/1478-3975/12/6/066013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Protein data bank entries obtain distinct, reproducible flexibility characteristics determined by normal mode analyses of their three dimensional coordinate files. We study the effectiveness and sensitivity of this technique by analyzing the results on one class of glycosidases: family 10 xylanases. A conserved tryptophan that appears to affect access to the active site can be in one of two conformations according to x-ray crystallographic electron density data. The two alternate orientations of this active site tryptophan lead to distinct flexibility spectra, with one orientation thwarting the oscillations seen in the other. The particular orientation of this sidechain furthermore affects the appearance of the motility of a distant, C terminal region we term the mallet. The mallet region is known to separate members of this family of enzymes into two classes.
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Affiliation(s)
- Monique M Tirion
- Physics Department, Clarkson University, Potsdam, New York 13699-5820, USA
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23
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Paenibacillus curdlanolyticus B-6 xylanase Xyn10C capable of producing a doubly arabinose-substituted xylose, α-l-Araf-(1→2)-[α-l-Araf-(1→3)]-d-Xylp, from rye arabinoxylan. Enzyme Microb Technol 2015; 72:1-9. [DOI: 10.1016/j.enzmictec.2015.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 01/31/2015] [Accepted: 02/05/2015] [Indexed: 11/18/2022]
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24
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Cuskin F, Lowe EC, Temple MJ, Zhu Y, Cameron E, Pudlo NA, Porter NT, Urs K, Thompson AJ, Cartmell A, Rogowski A, Hamilton BS, Chen R, Tolbert TJ, Piens K, Bracke D, Vervecken W, Hakki Z, Speciale G, Munōz-Munōz JL, Day A, Peña MJ, McLean R, Suits MD, Boraston AB, Atherly T, Ziemer CJ, Williams SJ, Davies GJ, Abbott DW, Martens EC, Gilbert HJ. Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism. Nature 2015; 517:165-169. [PMID: 25567280 PMCID: PMC4978465 DOI: 10.1038/nature13995] [Citation(s) in RCA: 362] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 10/22/2014] [Indexed: 12/28/2022]
Abstract
Yeasts, which have been a component of the human diet for at least 7,000 years, possess an elaborate cell wall α-mannan. The influence of yeast mannan on the ecology of the human microbiota is unknown. Here we show that yeast α-mannan is a viable food source for the Gram-negative bacterium Bacteroides thetaiotaomicron, a dominant member of the microbiota. Detailed biochemical analysis and targeted gene disruption studies support a model whereby limited cleavage of α-mannan on the surface generates large oligosaccharides that are subsequently depolymerized to mannose by the action of periplasmic enzymes. Co-culturing studies showed that metabolism of yeast mannan by B. thetaiotaomicron presents a 'selfish' model for the catabolism of this difficult to breakdown polysaccharide. Genomic comparison with B. thetaiotaomicron in conjunction with cell culture studies show that a cohort of highly successful members of the microbiota has evolved to consume sterically-restricted yeast glycans, an adaptation that may reflect the incorporation of eukaryotic microorganisms into the human diet.
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Affiliation(s)
- Fiona Cuskin
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Elisabeth C. Lowe
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Max J. Temple
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Yanping Zhu
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Elizabeth Cameron
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nicholas A. Pudlo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nathan T. Porter
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Karthik Urs
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Alan Cartmell
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Artur Rogowski
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Brian S. Hamilton
- Dept. of Pharmaceutical Chemistry, University of Kansas School of Pharmacy, 2095 Constant Ave, Lawrence, KS 66047, USA
| | - Rui Chen
- Dept. of Pharmaceutical Chemistry, University of Kansas School of Pharmacy, 2095 Constant Ave, Lawrence, KS 66047, USA
| | - Thomas J. Tolbert
- Dept. of Pharmaceutical Chemistry, University of Kansas School of Pharmacy, 2095 Constant Ave, Lawrence, KS 66047, USA
| | | | | | | | - Zalihe Hakki
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Gaetano Speciale
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jose L. Munōz-Munōz
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Andrew Day
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Maria J. Peña
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Richard McLean
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB, Canada
| | - Michael D. Suits
- Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Alisdair B. Boraston
- Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Todd Atherly
- USDA, Agricultural Research Service, National Laboratory for Agriculture and the Environment, Ames, Iowa, USA
| | - Cherie J. Ziemer
- USDA, Agricultural Research Service, National Laboratory for Agriculture and the Environment, Ames, Iowa, USA
| | - Spencer J. Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | | | - D. Wade Abbott
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB, Canada
| | - Eric C. Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Harry J. Gilbert
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
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25
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Sugimura M, Nishimoto M, Kitaoka M. Characterization of Glycosynthase Mutants Derived from Glycoside Hydrolase Family 10 Xylanases. Biosci Biotechnol Biochem 2014; 70:1210-7. [PMID: 16717424 DOI: 10.1271/bbb.70.1210] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Four xylanases belonging to glycoside hydrolase family 10-Thermotoga maritima XylB (TM), Clostridium stercorarium XynB (CS), Bacillus halodurans XynA (BH), and Cellulomonas fimi Cex (CF)-were converted to glycosynthases by substituting the nucleophilic glutamic acid residues with glycine, alanine, and serine. The glycine mutants exhibited the highest levels of glycosynthase activity with all four enzymes. All the glycine mutants formed polymeric beta-1,4-linked xylopyranose as a precipitate during reaction with alpha-xylobiosyl fluoride. Two glycine mutants (TM and CF) recognized X(2) as an effective acceptor molecule to prohibit the formation of the polymer, while the other two (CS and BH) did not. The difference in acceptor specificity is considered to reflect the difference in substrate affinity at their +2 subsites. The results agreed with the structural predictions of the subsite, where TM and CF exhibit high affinity at subsite 2, suggesting that the glycosynthase technique is useful for investigating the affinity of +subsites.
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26
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Rogowski A, Baslé A, Farinas CS, Solovyova A, Mortimer JC, Dupree P, Gilbert HJ, Bolam DN. Evidence that GH115 α-glucuronidase activity, which is required to degrade plant biomass, is dependent on conformational flexibility. J Biol Chem 2013; 289:53-64. [PMID: 24214982 PMCID: PMC3879575 DOI: 10.1074/jbc.m113.525295] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The microbial degradation of the plant cell wall is an important biological process that is highly relevant to environmentally significant industries such as the bioenergy and biorefining sectors. A major component of the wall is glucuronoxylan, a β1,4-linked xylose polysaccharide that is decorated with α-linked glucuronic and/or methylglucuronic acid (GlcA/MeGlcA). Recently three members of a glycoside hydrolase family, GH115, were shown to hydrolyze MeGlcA side chains from the internal regions of xylan, an activity that has not previously been described. Here we show that a dominant member of the human microbiota, Bacteroides ovatus, contains a GH115 enzyme, BoAgu115A, which displays glucuronoxylan α-(4-O-methyl)-glucuronidase activity. The enzyme is significantly more active against substrates in which the xylose decorated with GlcA/MeGlcA is flanked by one or more xylose residues. The crystal structure of BoAgu115A revealed a four-domain protein in which the active site, comprising a pocket that abuts a cleft-like structure, is housed in the second domain that adopts a TIM barrel-fold. The third domain, a five-helical bundle, and the C-terminal β-sandwich domain make inter-chain contacts leading to protein dimerization. Informed by the structure of the enzyme in complex with GlcA in its open ring form, in conjunction with mutagenesis studies, the potential substrate binding and catalytically significant amino acids were identified. Based on the catalytic importance of residues located on a highly flexible loop, the enzyme is required to undergo a substantial conformational change to form a productive Michaelis complex with glucuronoxylan.
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Affiliation(s)
- Artur Rogowski
- From the Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH United Kingdom and
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27
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Balazs YS, Lisitsin E, Carmiel O, Shoham G, Shoham Y, Schmidt A. Identifying critical unrecognized sugar-protein interactions in GH10 xylanases fromGeobacillus stearothermophilususing STD NMR. FEBS J 2013; 280:4652-65. [DOI: 10.1111/febs.12437] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 07/01/2013] [Accepted: 07/05/2013] [Indexed: 12/29/2022]
Affiliation(s)
- Yael S. Balazs
- Schulich Faculty of Chemistry and Russell Berrie Nanotechnology Institute; Technion - Israel Institute of Technology; Haifa Israel
| | - Elina Lisitsin
- Schulich Faculty of Chemistry and Russell Berrie Nanotechnology Institute; Technion - Israel Institute of Technology; Haifa Israel
| | - Oshrat Carmiel
- Schulich Faculty of Chemistry and Russell Berrie Nanotechnology Institute; Technion - Israel Institute of Technology; Haifa Israel
| | - Gil Shoham
- Schulich Faculty of Chemistry and Russell Berrie Nanotechnology Institute; Technion - Israel Institute of Technology; Haifa Israel
| | - Yuval Shoham
- Schulich Faculty of Chemistry and Russell Berrie Nanotechnology Institute; Technion - Israel Institute of Technology; Haifa Israel
| | - Asher Schmidt
- Schulich Faculty of Chemistry and Russell Berrie Nanotechnology Institute; Technion - Israel Institute of Technology; Haifa Israel
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28
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Du Y, Shi P, Huang H, Zhang X, Luo H, Wang Y, Yao B. Characterization of three novel thermophilic xylanases from Humicola insolens Y1 with application potentials in the brewing industry. BIORESOURCE TECHNOLOGY 2013; 130:161-167. [PMID: 23306124 DOI: 10.1016/j.biortech.2012.12.067] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 12/08/2012] [Accepted: 12/10/2012] [Indexed: 06/01/2023]
Abstract
Three xylanase genes (xynA, xynB, xynC) of glycosyl hydrolase family 10 were identified in Humicola insolens Y1. The deduced protein sequences showed the highest identity of ⩽83% to known fungal xylanases and of ⩽38% with each other. Recombinant XynA-C produced in Pichia pastoris showed optimal activities at pH 6.0-7.0 and at high temperature (70-80°C), and exhibited good stability over a broad pH range and temperatures at 60°C. The gene xynC produced by H. insolens Y1 (named XynW) was similar in enzyme properties with XynC expressed by Pichia. XynA exhibited better alkaline adaptation and thermostability, and had higher catalytic efficiency and wider substrate specificity. Under simulated mashing conditions, addition of XynA-C showed better performance on filtration acceleration (37.4%) and viscosity reduction (13.5%) than Ultraflo from Novozyme. Thus the three xylanases represent good candidates for application in the brewing industry.
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Affiliation(s)
- Yanlong Du
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
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29
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Novel structural features of xylanase A1 from Paenibacillus sp. JDR-2. J Struct Biol 2012; 180:303-11. [PMID: 23000703 DOI: 10.1016/j.jsb.2012.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 08/28/2012] [Accepted: 09/03/2012] [Indexed: 11/24/2022]
Abstract
The Gram-positive bacterium Paenibacillus sp. JDR-2 (PbJDR2) has been shown to have novel properties in the utilization of the abundant but chemically complex hemicellulosic sugar glucuronoxylan. Xylanase A1 of PbJDR2 (PbXynA1) has been implicated in an efficient process in which extracellular depolymerization of this polysaccharide is coupled to assimilation and intracellular metabolism. PbXynA1is a 154kDa cell wall anchored multimodular glycosyl hydrolase family 10 (GH10) xylanase. In this work, the 38kDa catalytic module of PbXynA1 has been structurally characterized revealing several new features not previously observed in structures of GH10 xylanases. These features are thought to facilitate hydrolysis of highly substituted, chemically complex xylans that may be the form found in close proximity to the cell wall of PbJDR2, an organism shown to have a preference for growth on polymeric glucuronoxylan.
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30
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van Gool MP, van Muiswinkel GCJ, Hinz SWA, Schols HA, Sinitsyn AP, Gruppen H. Two GH10 endo-xylanases from Myceliophthora thermophila C1 with and without cellulose binding module act differently towards soluble and insoluble xylans. BIORESOURCE TECHNOLOGY 2012; 119:123-32. [PMID: 22728192 DOI: 10.1016/j.biortech.2012.05.117] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 05/22/2012] [Accepted: 05/22/2012] [Indexed: 05/02/2023]
Abstract
Xylanases are mostly classified as belonging to glycoside hydrolase (GH) family 10 and 11, which differ in catalytic properties and structures. However, within one family, differences may also be present. The influence of solubility and molecular structure of substrates towards the efficiency of two GH10 xylanases from Myceliophthora thermophila C1 was investigated. The xylanases differed in degradation of high and low substituted substrate and the substitution pattern was an important factor influencing their efficiency. Alkali-labile interactions, as well as the presence of cellulose within the complex cell wall structure hindered efficient hydrolysis for both xylanases. The presence of a carbohydrate binding module did not enhance the degradation of the substrates. The differences in degradation could be related to the protein structure of the two xylanases. The study shows that the classification of enzymes does not predict their performance towards various substrates.
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Affiliation(s)
- M P van Gool
- Laboratory of Food Chemistry, Wageningen University, P.O. Box 8129, 6700 EV Wageningen, The Netherlands
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31
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Characterization and pH-dependent substrate specificity of alkalophilic xylanase from Bacillus alcalophilus. J Ind Microbiol Biotechnol 2012; 39:1465-75. [PMID: 22763748 DOI: 10.1007/s10295-012-1159-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Accepted: 06/11/2012] [Indexed: 10/28/2022]
Abstract
The gene of endo-beta-1-4 xylanase, xynT, was cloned from Bacillus alcalophilus AX2000 and expressed in Escherichia coli. This XynT, which belongs to glycoside hydrolase (GH) family 10, was found to have a molecular weight of approximately 37 kDa and exhibit optimal activity at pH 7-9 and 50 °C. It exhibits a high activity towards birchwood xylan and has the ability to bind avicel. Under optimal conditions, XynT hydrolyzes all xylooligomers into xylobiose as an end product with a preference for cleavage sites at the second or third glycosidic bond from the reducing end. XynT has a different substrate affinity on xylooligomers at pH 5.0, which contributes to its low activity toward xylotriose and its derived intermediate products. This low activity may be due to an unstable interaction with the amino acids that constitute subsites of the active site. Interestingly, the addition of Co(2+) and Mn(2+) led to a significant increase in activity by up to 40 and 50 %, respectively. XynT possesses a high binding affinity and hydrolytic activity toward the insoluble xylan, for which it exhibits high activity at pH 7-9, giving rise to its efficient biobleaching effect on Pinus densiflora kraft pulp.
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32
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QM/MM study of catalytic mechanism of Xylanase Cex from Cellulomonas fimi. J Mol Graph Model 2012; 37:67-76. [DOI: 10.1016/j.jmgm.2012.04.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 04/01/2012] [Accepted: 04/17/2012] [Indexed: 12/13/2022]
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33
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St John FJ, Hurlbert JC, Rice JD, Preston JF, Pozharski E. Ligand bound structures of a glycosyl hydrolase family 30 glucuronoxylan xylanohydrolase. J Mol Biol 2011; 407:92-109. [PMID: 21256135 DOI: 10.1016/j.jmb.2011.01.010] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Revised: 01/04/2011] [Accepted: 01/05/2011] [Indexed: 10/18/2022]
Abstract
Xylanases of glycosyl hydrolase family 30 (GH30) have been shown to cleave β-1,4 linkages of 4-O-methylglucuronoxylan (MeGX(n)) as directed by the position along the xylan chain of an α-1,2-linked 4-O-methylglucuronate (MeGA) moiety. Complete hydrolysis of MeGX(n) by these enzymes results in singly substituted aldouronates having a 4-O-methylglucuronate moiety linked to a xylose penultimate from the reducing terminal xylose and some number of xylose residues toward the nonreducing terminus. This novel mode of action distinguishes GH30 xylanases from the more common xylanase families that cleave MeGX(n) in accessible regions. To help understand this unique biochemical function, we have determined the structure of XynC in its native and ligand-bound forms. XynC structure models derived from diffraction data of XynC crystal soaks with the simple sugar glucuronate (GA) and the tetrameric sugar 4-O-methyl-aldotetrauronate resulted in models containing GA and 4-O-methyl-aldotriuronate, respectively. Each is observed in two locations within XynC surface openings. Ligand coordination occurs within the XynC catalytic substrate binding cleft and on the structurally fused side β-domain, demonstrating a substrate targeting role for this putative carbohydrate binding module. Structural data reveal that GA acts as a primary functional appendage for recognition and hydrolysis of the MeGX(n) polymer by the protein. This work compares the structure of XynC with a previously reported homologous enzyme, XynA, from Erwinia chrysanthemi and analyzes the ligand binding sites. Our results identify the molecular interactions that define the unique function of XynC and homologous GH30 enzymes.
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Affiliation(s)
- Franz J St John
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA.
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34
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Stütz AE, Wrodnigg TM. Imino sugars and glycosyl hydrolases: historical context, current aspects, emerging trends. Adv Carbohydr Chem Biochem 2011; 66:187-298. [PMID: 22123190 DOI: 10.1016/b978-0-12-385518-3.00004-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Forty years of discoveries and research on imino sugars, which are carbohydrate analogues having a basic nitrogen atom instead of oxygen in the sugar ring and, acting as potent glycosidase inhibitors, have made considerable impact on our contemporary understanding of glycosidases. Imino sugars have helped to elucidate the catalytic machinery of glycosidases and have refined our methods and concepts of utilizing them. A number of new aspects have emerged for employing imino sugars as pharmaceutical compounds, based on their profound effects on metabolic activities in which glycosidases are involved. From the digestion of starch to the fight against viral infections, from research into malignant diseases to potential improvements in hereditary storage disorders, glycosidase action and inhibition are essential issues. This account aims at combining general developments with a focus on some niches where imino sugars have become useful tools for glycochemistry and glycobiology.
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Affiliation(s)
- Arnold E Stütz
- Institut für Organische Chemie, Technische Universität Graz, Austria
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35
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Nishimoto M, Kobayashi A, Honda Y, Kitaoka M, Hayashi K. p-Nitrophenyl β-Glycosides of β-1,4-Gluco/xylo-disaccharides for the Characterization of Subsites in Endo-xylanases. J Appl Glycosci (1999) 2011. [DOI: 10.5458/jag.jag.jag-2010_024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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SAKSONO BUDI, SUKMARINI LINDA. Structural Analysis of Xylanase from Marine Thermophilic Geobacillus stearothermophilus in Tanjung Api, Poso, Indonesia. HAYATI JOURNAL OF BIOSCIENCES 2010. [DOI: 10.4308/hjb.17.4.189] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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37
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Nagao C, Nagano N, Mizuguchi K. Relationships between functional subclasses and information contained in active-site and ligand-binding residues in diverse superfamilies. Proteins 2010; 78:2369-84. [PMID: 20544971 DOI: 10.1002/prot.22750] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
To investigate the relationships between functional subclasses and sequence and structural information contained in the active-site and ligand-binding residues (LBRs), we performed a detailed analysis of seven diverse enzyme superfamilies: aldolase class I, TIM-barrel glycosidases, alpha/beta-hydrolases, P-loop containing nucleotide triphosphate hydrolases, collagenase, Zn peptidases, and glutamine phosphoribosylpyrophosphate, subunit 1, domain 1. These homologous superfamilies, as defined in CATH, were selected from the enzyme catalytic-mechanism database. We defined active-site and LBRs based solely on the literature information and complex structures in the Protein Data Bank. From a structure-based multiple sequence alignment for each CATH homologous superfamily, we extracted subsequences consisting of the aligned positions that were used as an active-site or a ligand-binding site by at least one sequence. Using both the subsequences and full-length alignments, we performed cluster analysis with three sequence distance measures. We showed that the cluster analysis using the subsequences was able to detect functional subclasses more accurately than the clustering using the full-length alignments. The subsequences determined by only the literature information and complex structures, thus, had sufficient information to detect the functional subclasses. Detailed examination of the clustering results provided new insights into the mechanism of functional diversification for these superfamilies.
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Affiliation(s)
- Chioko Nagao
- National Institute of Biomedical Innovation, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
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38
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Wang G, Wang Y, Yang P, Luo H, Huang H, Shi P, Meng K, Yao B. Molecular detection and diversity of xylanase genes in alpine tundra soil. Appl Microbiol Biotechnol 2010; 87:1383-93. [PMID: 20393704 DOI: 10.1007/s00253-010-2564-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Revised: 03/07/2010] [Accepted: 03/14/2010] [Indexed: 11/25/2022]
Abstract
Xylan is a major polysaccharide in plant cell walls, and its degradation is mainly conducted by microbial xylanases in nature. To explore the xylanase diversity in the environment, two sets of degenerate primers were designed based on the microbial xylanase sequences in Pfam database of glycosyl hydrolase (GH) family 10 and 11 and were used to amplify objective gene fragments directly from the alpine tundra soil DNA of the Tianshan Mountains, China. Ninety-six distinct GH 10 and 31 GH 11 xylanase gene fragments were retrieved, and most of them have low identities with known sequences in GenBank. Based on phylogenetic analysis, all of the GH 10 xylanase sequences fell into six clusters and were related to xylanases from Actinobacteria, Proteobacteria, Verrucomicrobia, Bacteroidetes, Firmicutes, and Acidobacteria. Three clusters of GH 11 xylanase sequences were established, and two of them were related with enzymes from fungi. These results indicated the diversity of xylanase genes in this cold environment. Four xylanolytic strains were isolated from the soil, and GH 10 xylanase gene fragments were cloned using the same primers. A full-length gene was obtained and expressed in Escherichia coli, and the recombinant enzyme showed some cold-related characteristics. Our study provides an efficient molecular approach to study xylanase in complex environments and casts an insight into the diversity and distribution of xylanases in a cold environment, which is very meaningful to understand their roles in xylan degradation in nature.
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Affiliation(s)
- Guozeng Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, People's Republic of China
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Najmudin S, Pinheiro BA, Prates JAM, Gilbert HJ, Romão MJ, Fontes CMGA. Putting an N-terminal end to the Clostridium thermocellum xylanase Xyn10B story: crystal structure of the CBM22-1-GH10 modules complexed with xylohexaose. J Struct Biol 2010; 172:353-62. [PMID: 20682344 DOI: 10.1016/j.jsb.2010.07.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 07/26/2010] [Accepted: 07/29/2010] [Indexed: 10/19/2022]
Abstract
In general, plant cell wall degrading enzymes are modular proteins containing catalytic domains linked to one or more non-catalytic carbohydrate-binding modules (CBMs). Xyn10B from Clostridium thermocellum is a typical modular enzyme containing an N-terminal family 22 CBM (CBM22-1), a family 10 glycoside hydrolase catalytic domain (GH10), a second CBM22 (CBM22-2), a dockerin sequence and a C-terminal family 1 carbohydrate esterase (CE1) catalytic domain. The structure of the N-terminal bi-modular CBM22-1-GH10 component of Xyn10B has been determined using a SeMet derivative by SAD to 2.5Å. The data was extended to 2.0Å for the non-SeMet mutant complexed with xylohexaose. CBM22-1-GH10 is a 60kDa protein with an E337A mutation to render the GH10 subunit inactive. Three of the six xylose residues of xylohexaose are shown to be bound in the inactivated GH10 substrate binding cleft, with the other three sugars presumably disordered in the solvent channel. The protein is a dimer in the asymmetric unit with extensive surface contacts between the two GH10 modules and between the CBM22-1 and GH10 modules. Residues from helix H4 of the GH10 module provide the major contacts by fitting into the minor groove of the CBM22-1 module. The orientation of CBM22-1 is such that it would allow the substrate to be loosely bound and subsequently delivered to the active site in a processive manner.
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Affiliation(s)
- Shabir Najmudin
- CIISA - Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal.
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40
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Comparative analyses of two thermophilic enzymes exhibiting both beta-1,4 mannosidic and beta-1,4 glucosidic cleavage activities from Caldanaerobius polysaccharolyticus. J Bacteriol 2010; 192:4111-21. [PMID: 20562312 DOI: 10.1128/jb.00257-10] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The hydrolysis of polysaccharides containing mannan requires endo-1,4-beta-mannanase and 1,4-beta-mannosidase activities. In the current report, the biochemical properties of two endo-beta-1,4-mannanases (Man5A and Man5B) from Caldanaerobius polysaccharolyticus were studied. Man5A is composed of an N-terminal signal peptide (SP), a catalytic domain, two carbohydrate-binding modules (CBMs), and three surface layer homology (SLH) repeats, whereas Man5B lacks the SP, CBMs, and SLH repeats. To gain insights into how the two glycoside hydrolase family 5 (GH5) enzymes may aid the bacterium in energy acquisition and also the potential application of the two enzymes in the biofuel industry, two derivatives of Man5A (Man5A-TM1 [TM1 stands for truncational mutant 1], which lacks the SP and SLH repeats, and Man5A-TM2, which lacks the SP, CBMs, and SLH repeats) and the wild-type Man5B were biochemically analyzed. The Man5A derivatives displayed endo-1,4-beta-mannanase and endo-1,4-beta-glucanase activities and hydrolyzed oligosaccharides with a degree of polymerization (DP) of 4 or higher. Man5B exhibited endo-1,4-beta-mannanase activity and little endo-1,4-beta-glucanase activity; however, this enzyme also exhibited 1,4-beta-mannosidase and cellodextrinase activities. Man5A-TM1, compared to either Man5A-TM2 or Man5B, had higher catalytic activity with soluble and insoluble polysaccharides, indicating that the CBMs enhance catalysis of Man5A. Furthermore, Man5A-TM1 acted synergistically with Man5B in the hydrolysis of beta-mannan and carboxymethyl cellulose. The versatility of the two enzymes, therefore, makes them a resource for depolymerization of mannan-containing polysaccharides in the biofuel industry. Furthermore, on the basis of the biochemical and genomic data, a molecular mechanism for utilization of mannan-containing nutrients by C. polysaccharolyticus is proposed.
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Hekmat O, Lo Leggio L, Rosengren A, Kamarauskaite J, Kolenova K, Stålbrand H. Rational Engineering of Mannosyl Binding in the Distal Glycone Subsites of Cellulomonas fimi Endo-β-1,4-mannanase: Mannosyl Binding Promoted at Subsite −2 and Demoted at Subsite −3,. Biochemistry 2010; 49:4884-96. [DOI: 10.1021/bi100097f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Omid Hekmat
- Department of Biochemistry, Center for Chemistry and Chemical Engineering, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Leila Lo Leggio
- Biophysical Chemistry Group, Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Anna Rosengren
- Department of Biochemistry, Center for Chemistry and Chemical Engineering, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Jurate Kamarauskaite
- Biophysical Chemistry Group, Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Katarina Kolenova
- Department of Biochemistry, Center for Chemistry and Chemical Engineering, Lund University, Box 124, SE-221 00 Lund, Sweden
| | - Henrik Stålbrand
- Department of Biochemistry, Center for Chemistry and Chemical Engineering, Lund University, Box 124, SE-221 00 Lund, Sweden
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Pollet A, Delcour JA, Courtin CM. Structural determinants of the substrate specificities of xylanases from different glycoside hydrolase families. Crit Rev Biotechnol 2010; 30:176-91. [DOI: 10.3109/07388551003645599] [Citation(s) in RCA: 176] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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43
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Catalytic properties of a GH10 endo-β-1,4-xylanase from Streptomyces thermocarboxydus HY-15 isolated from the gut of Eisenia fetida. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.molcatb.2009.08.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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44
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Gallardo O, Pastor FIJ, Polaina J, Diaz P, Łysek R, Vogel P, Isorna P, González B, Sanz-Aparicio J. Structural insights into the specificity of Xyn10B from Paenibacillus barcinonensis and its improved stability by forced protein evolution. J Biol Chem 2009; 285:2721-33. [PMID: 19940147 DOI: 10.1074/jbc.m109.064394] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Paenibacillus barcinonensis is a soil bacterium bearing a complex set of enzymes for xylan degradation, including several secreted enzymes and Xyn10B, one of the few intracellular xylanases reported to date. The crystal structure of Xyn10B has been determined by x-ray analysis. The enzyme folds into the typical (beta/alpha)(8) barrel of family 10 glycosyl hydrolases (GH10), with additional secondary structure elements within the beta/alpha motifs. One of these loops -L7- located at the beta7 C terminus, was essential for xylanase activity as its partial deletion yielded an inactive enzyme. The loop contains residues His(249)-Glu(250), which shape a pocket opened to solvent in close proximity to the +2 subsite, which has not been described in other GH10 enzymes. This wide cavity at the +2 subsite, where methyl-2,4-pentanediol from the crystallization medium was found, is a noteworthy feature of Xyn10B, as compared with the narrow crevice described for other GH10 xylanases. Docking analysis showed that this open cavity can accommodate glucuronic acid decorations of xylo-oligosaccharides. Co-crystallization experiments with conduramine derivative inhibitors supported the importance of this open cavity at the +2 subsite for Xyn10B activity. Several mutant derivatives of Xyn10B with improved thermal stability were obtained by forced evolution. Among them, mutant xylanases S15L and M93V showed increased half-life, whereas the double mutant S15L/M93V exhibited a further increase in stability, showing a 20-fold higher heat resistance than the wild type xylanase. All the mutations obtained were located on the surface of Xyn10B. Replacement of a Ser by a Leu residue in mutant xylanase S15L can increase hydrophobic packing efficiency and fill a superficial indentation of the protein, giving rise to a more compact structure of the enzyme.
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Affiliation(s)
- Oscar Gallardo
- Department of Microbiology, Faculty of Biology, University of Barcelona, Av. Diagonal 645, 08028 Barcelona, Spain
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45
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Tailford LE, Ducros VMA, Flint JE, Roberts SM, Morland C, Zechel DL, Smith N, Bjørnvad ME, Borchert TV, Wilson KS, Davies GJ, Gilbert HJ. Understanding how diverse beta-mannanases recognize heterogeneous substrates. Biochemistry 2009; 48:7009-18. [PMID: 19441796 DOI: 10.1021/bi900515d] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanism by which polysaccharide-hydrolyzing enzymes manifest specificity toward heterogeneous substrates, in which the sequence of sugars is variable, is unclear. An excellent example of such heterogeneity is provided by the plant structural polysaccharide glucomannan, which comprises a backbone of beta-1,4-linked glucose and mannose units. beta-Mannanases, located in glycoside hydrolase (GH) families 5 and 26, hydrolyze glucomannan by cleaving the glycosidic bond of mannosides at the -1 subsite. The mechanism by which these enzymes select for glucose or mannose at distal subsites, which is critical to defining their substrate specificity on heterogeneous polymers, is currently unclear. Here we report the biochemical properties and crystal structures of both a GH5 mannanase and a GH26 mannanase and describe the contributions to substrate specificity in these enzymes. The GH5 enzyme, BaMan5A, derived from Bacillus agaradhaerens, can accommodate glucose or mannose at both its -2 and +1 subsites, while the GH26 Bacillus subtilis mannanase, BsMan26A, displays tight specificity for mannose at its negative binding sites. The crystal structure of BaMan5A reveals that a polar residue at the -2 subsite can make productive contact with the substrate 2-OH group in either its axial (as in mannose) or its equatorial (as in glucose) configuration, while other distal subsites do not exploit the 2-OH group as a specificity determinant. Thus, BaMan5A is able to hydrolyze glucomannan in which the sequence of glucose and mannose is highly variable. The crystal structure of BsMan26A in light of previous studies on the Cellvibrio japonicus GH26 mannanases CjMan26A and CjMan26C reveals that the tighter mannose recognition at the -2 subsite is mediated by polar interactions with the axial 2-OH group of a (4)C(1) ground state mannoside. Mutagenesis studies showed that variants of CjMan26A, from which these polar residues had been removed, do not distinguish between Man and Glc at the -2 subsite, while one of these residues, Arg 361, confers the elevated activity displayed by the enzyme against mannooligosaccharides. The biological rationale for the variable recognition of Man- and Glc-configured sugars by beta-mannanases is discussed.
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Affiliation(s)
- Louise E Tailford
- Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne NE2 4HH, UK
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46
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Anderson L, Hägglund P, Stoll D, Lo Leggio L, Drakenberg T, Stålbrand H. Kinetics and stereochemistry of theCellulomonas fimiβ-mannanase studied using1H-NMR. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420701788835] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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47
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Moreno-Clavijo E, Carmona AT, Vera-Ayoso Y, Moreno-Vargas AJ, Bello C, Vogel P, Robina I. Synthesis of novel pyrrolidine 3,4-diol derivatives as inhibitors of α-L-fucosidases. Org Biomol Chem 2009; 7:1192-202. [DOI: 10.1039/b819867e] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Kaneko S, Ichinose H, Fujimoto Z, Iwamatsu S, Kuno A, Hasegawa T. Substrate Recognition of a Family 10 Xylanase from Streptomyces olivaceoviridis E-86: A Study by Site-directed Mutagenesis to Make an Hindrance around the Entrance toward the Substrate-binding Cleft. J Appl Glycosci (1999) 2009. [DOI: 10.5458/jag.56.173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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49
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Seipke RF, Loria R. Streptomyces scabies 87-22 possesses a functional tomatinase. J Bacteriol 2008; 190:7684-92. [PMID: 18835993 PMCID: PMC2583622 DOI: 10.1128/jb.01010-08] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Accepted: 09/22/2008] [Indexed: 11/20/2022] Open
Abstract
The actinomycete Streptomyces scabies 87-22 is the causal agent of common scab, an economically important disease of potato and taproot crops. Sequencing of the S. scabies 87-22 genome revealed the presence of a gene with high homology to the gene encoding the alpha-tomatine-detoxifying enzyme tomatinase found in fungal tomato pathogens. The tomA gene from S. scabies 87-22 was cotranscribed with a putative family 1 glycosyl hydrolase gene, and purified TomA protein was active only on alpha-tomatine and not potato glycoalkaloids or xylans. Tomatinase-null mutants were more sensitive to alpha-tomatine than the wild-type strain in a disk diffusion assay. Interestingly, tomatine affected only aerial mycelium and not vegetative mycelium, suggesting that the target(s) of alpha-tomatine is not present during vegetative growth. Severities of disease for tomato seedlings affected by S. scabies 87-22 wild-type and DeltatomA1 strains were indistinguishable, suggesting that tomatinase is not important in pathogenicity on tomato plants. However, conservation of tomA on a pathogenicity island in S. acidiscabies and S. turgidiscabies suggests a role in plant-microbe interaction.
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Affiliation(s)
- Ryan F Seipke
- Department of Plant Pathology, Cornell University, 334 Plant Science Building, Ithaca, NY 14853, USA
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50
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Wu AT, Wu PJ, Zou W, Chir JL, Chang YC, Tsai SY, Guo CQ, Chang WS, Hsieh YC. Synthesis of iminoalditol and N-alkyl iminoalditol derivatives of ribopyranosides. Carbohydr Res 2008; 343:2887-93. [DOI: 10.1016/j.carres.2008.08.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Revised: 07/24/2008] [Accepted: 08/03/2008] [Indexed: 10/21/2022]
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