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McGregor NGS, Turkenburg JP, Mørkeberg Krogh KBR, Nielsen JE, Artola M, Stubbs KA, Overkleeft HS, Davies GJ. Structure of a GH51 α-L-arabinofuranosidase from Meripilus giganteus: conserved substrate recognition from bacteria to fungi. Acta Crystallogr D Struct Biol 2020; 76:1124-1133. [PMID: 33135683 PMCID: PMC7604909 DOI: 10.1107/s205979832001253x] [Citation(s) in RCA: 6] [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: 07/14/2020] [Accepted: 09/14/2020] [Indexed: 03/17/2023] Open
Abstract
α-L-Arabinofuranosidases from glycoside hydrolase family 51 use a stereochemically retaining hydrolytic mechanism to liberate nonreducing terminal α-L-arabinofuranose residues from plant polysaccharides such as arabinoxylan and arabinan. To date, more than ten fungal GH51 α-L-arabinofuranosidases have been functionally characterized, yet no structure of a fungal GH51 enzyme has been solved. In contrast, seven bacterial GH51 enzyme structures, with low sequence similarity to the fungal GH51 enzymes, have been determined. Here, the crystallization and structural characterization of MgGH51, an industrially relevant GH51 α-L-arabinofuranosidase cloned from Meripilus giganteus, are reported. Three crystal forms were grown in different crystallization conditions. The unliganded structure was solved using sulfur SAD data collected from a single crystal using the I23 in vacuo diffraction beamline at Diamond Light Source. Crystal soaks with arabinose, 1,4-dideoxy-1,4-imino-L-arabinitol and two cyclophellitol-derived arabinose mimics reveal a conserved catalytic site and conformational itinerary between fungal and bacterial GH51 α-L-arabinofuranosidases.
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Affiliation(s)
- Nicholas G. S. McGregor
- York Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Johan P. Turkenburg
- York Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, United Kingdom
| | | | - Jens Erik Nielsen
- Protein Biochemistry and Stability, Novozymes A/S, Krogshøjvej 36, 2880 Bagsvaerd, Denmark
| | - Marta Artola
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Keith A. Stubbs
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Herman S. Overkleeft
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Gideon J. Davies
- York Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, United Kingdom
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2
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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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3
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Blake AD, Beri NR, Guttman HS, Cheng R, Gardner JG. The complex physiology of
Cellvibrio japonicus
xylan degradation relies on a single cytoplasmic β‐xylosidase for xylo‐oligosaccharide utilization. Mol Microbiol 2018; 107:610-622. [DOI: 10.1111/mmi.13903] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 12/15/2017] [Accepted: 12/18/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Andrew D. Blake
- Department of Biological SciencesUniversity of Maryland ‐ Baltimore CountyBaltimore Maryland USA
| | - Nina R. Beri
- Department of Biological SciencesUniversity of Maryland ‐ Baltimore CountyBaltimore Maryland USA
| | - Hadassa S. Guttman
- Department of Biological SciencesUniversity of Maryland ‐ Baltimore CountyBaltimore Maryland USA
| | - Raymond Cheng
- Department of Biological SciencesUniversity of Maryland ‐ Baltimore CountyBaltimore Maryland USA
| | - Jeffrey G. Gardner
- Department of Biological SciencesUniversity of Maryland ‐ Baltimore CountyBaltimore Maryland USA
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4
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Gardner JG. Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus. World J Microbiol Biotechnol 2016; 32:121. [PMID: 27263016 DOI: 10.1007/s11274-016-2068-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 04/07/2016] [Indexed: 01/10/2023]
Abstract
Study of recalcitrant polysaccharide degradation by bacterial systems is critical for understanding biological processes such as global carbon cycling, nutritional contributions of the human gut microbiome, and the production of renewable fuels and chemicals. One bacterium that has a robust ability to degrade polysaccharides is the Gram-negative saprophyte Cellvibrio japonicus. A bacterium with a circuitous history, C. japonicus underwent several taxonomy changes from an initially described Pseudomonas sp. Most of the enzymes described in the pre-genomics era have also been renamed. This review aims to consolidate the biochemical, structural, and genetic data published on C. japonicus and its remarkable ability to degrade cellulose, xylan, and pectin substrates. Initially, C. japonicus carbohydrate-active enzymes were studied biochemically and structurally for their novel polysaccharide binding and degradation characteristics, while more recent systems biology approaches have begun to unravel the complex regulation required for lignocellulose degradation in an environmental context. Also included is a discussion for the future of C. japonicus as a model system, with emphasis on current areas unexplored in terms of polysaccharide degradation and emerging directions for C. japonicus in both environmental and biotechnological applications.
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Affiliation(s)
- Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, MD, USA.
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5
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In-Frame Deletions Allow Functional Characterization of Complex Cellulose Degradation Phenotypes in Cellvibrio japonicus. Appl Environ Microbiol 2015; 81:5968-75. [PMID: 26116676 DOI: 10.1128/aem.00847-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 06/16/2015] [Indexed: 12/31/2022] Open
Abstract
The depolymerization of the recalcitrant polysaccharides found in lignocellulose has become an area of intense interest due to the role of this process in global carbon cycling, human gut microbiome nutritional contributions, and bioenergy production. However, underdeveloped genetic tools have hampered study of bacterial lignocellulose degradation, especially outside model organisms. In this report, we describe an in-frame deletion strategy for the Gram-negative lignocellulose-degrading bacterium Cellvibrio japonicus. This method leverages optimized growth conditions for conjugation and sacB counterselection for the generation of markerless in-frame deletions. This method produces mutants in as few as 8 days and allows for the ability to make multiple gene deletions per strain. It is also possible to remove large sections of the genome, as shown in this report with the deletion of the nine-gene (9.4-kb) gsp operon in C. japonicus. We applied this system to study the complex phenotypes of cellulose degradation in C. japonicus. Our data indicated that a Δcel5B Δcel6A double mutant is crippled for cellulose utilization, more so than by either single mutation alone. Additionally, we deleted individual genes in the two-gene cbp2ED operon and showed that both genes contribute to cellulose degradation in C. japonicus. Overall, these described techniques substantially enhance the utility of C. japonicus as a model system to study lignocellulose degradation.
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Larsbrink J, Thompson AJ, Lundqvist M, Gardner JG, Davies GJ, Brumer H. A complex gene locus enables xyloglucan utilization in the model saprophyte Cellvibrio japonicus. Mol Microbiol 2014; 94:418-33. [PMID: 25171165 PMCID: PMC4285296 DOI: 10.1111/mmi.12776] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2014] [Indexed: 12/17/2022]
Abstract
The degradation of plant biomass by saprophytes is an ecologically important part of the global carbon cycle, which has also inspired a vast diversity of industrial enzyme applications. The xyloglucans (XyGs) constitute a family of ubiquitous and abundant plant cell wall polysaccharides, yet the enzymology of XyG saccharification is poorly studied. Here, we present the identification and molecular characterization of a complex genetic locus that is required for xyloglucan utilization by the model saprophyte Cellvibrio japonicus. In harness, transcriptomics, reverse genetics, enzyme kinetics, and structural biology indicate that the encoded cohort of an α-xylosidase, a β-galactosidase, and an α-l-fucosidase is specifically adapted for efficient, concerted saccharification of dicot (fucogalacto)xyloglucan oligosaccharides following import into the periplasm via an associated TonB-dependent receptor. The data support a biological model of xyloglucan degradation by C. japonicus with striking similarities – and notable differences – to the complex polysaccharide utilization loci of the Bacteroidetes.
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Affiliation(s)
- Johan Larsbrink
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91, Stockholm, Sweden
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7
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Gardner JG, Keating DH. Genetic and Functional Genomic Approaches for the Study of Plant Cell Wall Degradation in Cellvibrio japonicus. Methods Enzymol 2012; 510:331-47. [DOI: 10.1016/b978-0-12-415931-0.00018-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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8
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Cartmell A, McKee LS, Peña MJ, Larsbrink J, Brumer H, Kaneko S, Ichinose H, Lewis RJ, Viksø-Nielsen A, Gilbert HJ, Marles-Wright J. The structure and function of an arabinan-specific alpha-1,2-arabinofuranosidase identified from screening the activities of bacterial GH43 glycoside hydrolases. J Biol Chem 2011; 286:15483-95. [PMID: 21339299 PMCID: PMC3083193 DOI: 10.1074/jbc.m110.215962] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Revised: 02/16/2011] [Indexed: 11/06/2022] Open
Abstract
Reflecting the diverse chemistry of plant cell walls, microorganisms that degrade these composite structures synthesize an array of glycoside hydrolases. These enzymes are organized into sequence-, mechanism-, and structure-based families. Genomic data have shown that several organisms that degrade the plant cell wall contain a large number of genes encoding family 43 (GH43) glycoside hydrolases. Here we report the biochemical properties of the GH43 enzymes of a saprophytic soil bacterium, Cellvibrio japonicus, and a human colonic symbiont, Bacteroides thetaiotaomicron. The data show that C. japonicus uses predominantly exo-acting enzymes to degrade arabinan into arabinose, whereas B. thetaiotaomicron deploys a combination of endo- and side chain-cleaving glycoside hydrolases. Both organisms, however, utilize an arabinan-specific α-1,2-arabinofuranosidase in the degradative process, an activity that has not previously been reported. The enzyme can cleave α-1,2-arabinofuranose decorations in single or double substitutions, the latter being recalcitrant to the action of other arabinofuranosidases. The crystal structure of the C. japonicus arabinan-specific α-1,2-arabinofuranosidase, CjAbf43A, displays a five-bladed β-propeller fold. The specificity of the enzyme for arabinan is conferred by a surface cleft that is complementary to the helical backbone of the polysaccharide. The specificity of CjAbf43A for α-1,2-l-arabinofuranose side chains is conferred by a polar residue that orientates the arabinan backbone such that O2 arabinose decorations are directed into the active site pocket. A shelflike structure adjacent to the active site pocket accommodates O3 arabinose side chains, explaining how the enzyme can target O2 linkages that are components of single or double substitutions.
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Affiliation(s)
- Alan Cartmell
- From the Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom
- the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Lauren S. McKee
- From the Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom
- the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Maria J. Peña
- the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Johan Larsbrink
- the School of Biotechnology, Royal Institute of Technology, AlbaNova University Centre, 10691 Stockholm, Sweden
| | - Harry Brumer
- the School of Biotechnology, Royal Institute of Technology, AlbaNova University Centre, 10691 Stockholm, Sweden
| | - Satoshi Kaneko
- the Food Biotechnology Division, National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan, and
| | - Hitomi Ichinose
- the Food Biotechnology Division, National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan, and
| | - Richard J. Lewis
- From the Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom
| | | | - Harry J. Gilbert
- From the Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom
- the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Jon Marles-Wright
- From the Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom
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9
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Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus. J Bacteriol 2008; 190:5455-63. [PMID: 18556790 DOI: 10.1128/jb.01701-07] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The plant cell wall, which consists of a highly complex array of interconnecting polysaccharides, is the most abundant source of organic carbon in the biosphere. Microorganisms that degrade the plant cell wall synthesize an extensive portfolio of hydrolytic enzymes that display highly complex molecular architectures. To unravel the intricate repertoire of plant cell wall-degrading enzymes synthesized by the saprophytic soil bacterium Cellvibrio japonicus, we sequenced and analyzed its genome, which predicts that the bacterium contains the complete repertoire of enzymes required to degrade plant cell wall and storage polysaccharides. Approximately one-third of these putative proteins (57) are predicted to contain carbohydrate binding modules derived from 13 of the 49 known families. Sequence analysis reveals approximately 130 predicted glycoside hydrolases that target the major structural and storage plant polysaccharides. In common with that of the colonic prokaryote Bacteroides thetaiotaomicron, the genome of C. japonicus is predicted to encode a large number of GH43 enzymes, suggesting that the extensive arabinose decorations appended to pectins and xylans may represent a major nutrient source, not just for intestinal bacteria but also for microorganisms that occupy terrestrial ecosystems. The results presented here predict that C. japonicus possesses an extensive range of glycoside hydrolases, lyases, and esterases. Most importantly, the genome of C. japonicus is remarkably similar to that of the gram-negative marine bacterium, Saccharophagus degradans 2-40(T). Approximately 50% of the predicted C. japonicus plant-degradative apparatus appears to be shared with S. degradans, consistent with the utilization of plant-derived complex carbohydrates as a major substrate by both organisms.
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10
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Shulami S, Zaide G, Zolotnitsky G, Langut Y, Feld G, Sonenshein AL, Shoham Y. A two-component system regulates the expression of an ABC transporter for xylo-oligosaccharides in Geobacillus stearothermophilus. Appl Environ Microbiol 2006; 73:874-84. [PMID: 17142383 PMCID: PMC1800775 DOI: 10.1128/aem.02367-06] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Geobacillus stearothermophilus T-6 utilizes an extensive and highly regulated hemicellulolytic system. The genes comprising the xylanolytic system are clustered in a 39.7-kb chromosomal segment. This segment contains a 6-kb transcriptional unit (xynDCEFG) coding for a potential two-component system (xynDC) and an ATP-binding cassette (ABC) transport system (xynEFG). The xynD promoter region contains a 16-bp inverted repeat resembling the operator site for the xylose repressor, XylR. XylR was found to bind specifically to this sequence, and binding was efficiently prevented in vitro in the presence of xylose. The ABC transport system was shown to comprise an operon of three genes (xynEFG) that is transcribed from its own promoter. The nonphosphorylated fused response regulator, His6-XynC, bound to a 220-bp fragment corresponding to the xynE operator. DNase I footprinting analysis showed four protected zones that cover the -53 and the +34 regions and revealed direct repeat sequences of a GAAA-like motif. In vitro transcriptional assays and quantitative reverse transcription-PCR demonstrated that xynE transcription is activated 140-fold in the presence of 1.5 microM XynC. The His6-tagged sugar-binding lipoprotein (XynE) of the ABC transporter interacted with different xylosaccharides, as demonstrated by isothermal titration calorimetry. The change in the heat capacity of binding (DeltaCp) for XynE with xylotriose suggests a stacking interaction in the binding site that can be provided by a single Trp residue and a sugar moiety. Taken together, our data show that XynEFG constitutes an ABC transport system for xylo-oligosaccharides and that its transcription is negatively regulated by XylR and activated by the response regulator XynC, which is part of a two-component sensing system.
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Affiliation(s)
- Smadar Shulami
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel
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11
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Taylor E, Smith N, Turkenburg J, D'Souza S, Gilbert H, Davies G. Structural insight into the ligand specificity of a thermostable family 51 arabinofuranosidase, Araf51, from Clostridium thermocellum. Biochem J 2006; 395:31-7. [PMID: 16336192 PMCID: PMC1409695 DOI: 10.1042/bj20051780] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The digestion of the plant cell wall requires the concerted action of a diverse repertoire of enzyme activities. An important component of these hydrolase consortia are arabinofuranosidases, which release L-arabinofuranose moieties from a range of plant structural polysaccharides. The anaerobic bacterium Clostridium thermocellum, a highly efficient plant cell wall degrader, possesses a single alpha-L-arabinofuranosidase (EC 3.2.1.55), CtAraf51A, located in GH51 (glycoside hydrolase family 51). The crystal structure of the enzyme has been solved in native form and in 'Michaelis' complexes with both alpha-1,5-linked arabinotriose and alpha-1,3 arabinoxylobiose, both forming a hexamer in the asymmetric unit. Kinetic studies reveal that CtAraf51A, in contrast with well-characterized GH51 enzymes including the Cellvibrio japonicus enzyme [Beylot, McKie, Voragen, Doeswijk-Voragen and Gilbert (2001) Biochem. J. 358, 607-614], catalyses the hydrolysis of alpha-1,5-linked arabino-oligosaccharides and the alpha-1,3 arabinosyl side chain decorations of xylan with equal efficiency. The paucity of direct hydrogen bonds with the aglycone moiety and the flexible conformation adopted by Trp(178), which stacks against the sugar at the +1 subsite, provide a structural explanation for the plasticity in substrate specificity displayed by the clostridial arabinofuranosidase.
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Affiliation(s)
- Edward J. Taylor
- *York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, U.K
| | - Nicola L. Smith
- †Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, U.K
| | - Johan P. Turkenburg
- *York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, U.K
| | - Simone D'Souza
- *York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, U.K
| | - Harry J. Gilbert
- †Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, U.K
| | - Gideon J. Davies
- *York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, U.K
- To whom correspondence should be addressed (email )
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Abstract
Hemicellulases are a diverse group of enzymes that hydrolyze hemicelluloses--one of the most abundant groups of polysaccharide in nature. These enzymes have many biotechnological applications and their structure/function relationships are a subject of intense research. During the past year, new high-resolution structures of catalytic and non-catalytic domains of hemicellulases have been elucidated, and, together with biochemical studies, they reveal the principles of catalysis and specificity for these enzymes.
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Affiliation(s)
- Dalia Shallom
- Department of Food Engineering and Biotechnology and Institute of Catalysis, Science and Technology, Technion, Haifa 32000, Israel
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13
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Sakamoto T, Kawasaki H. Purification and properties of two type-B alpha-L-arabinofuranosidases produced by Penicillium chrysogenum. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1621:204-10. [PMID: 12726996 DOI: 10.1016/s0304-4165(03)00058-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two distinct extracellular alpha-L-arabinofuranosidases (AFases; EC 3.2.1.55) were purified from the culture filtrate of Penicillium chrysogenum 31B. The molecular masses of the enzymes were estimated to be 79 kDa (AFQ1) and 52 kDa (AFS1) by SDS-PAGE. Both enzymes had their highest activities at 50 degrees C and were stable up to 50 degrees C. Enzyme activities of AFQ1 and AFS1 were highest at pH 4.0 to 6.5 and pH 3.3 to 5.0, respectively. Addition of 10 mg/ml arabinose to the reaction mixture decreased the AFS1 activity but hardly affected AFQ1. Both enzymes displayed broad substrate specificities; they released arabinose from branched arabinan, debranched arabinan, arabinoxylan, arabinogalactan, and arabino-oligosaccharides. AFS1 also showed low activity towards p-nitrophenyl-beta-D-xylopyranoside. An exo-arabinanase, which catalyzes the release of arabinobiose from linear arabinan at the nonreducing terminus, acted synergistically with both enzymes to produce L-arabinose from branched arabinan.
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Affiliation(s)
- T Sakamoto
- Division of Applied Biochemistry, Graduate School of Agriculture and Biological Sciences, Osaka Prefecture University, Osaka 599-8531, Japan.
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14
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Nagy T, Emami K, Fontes CMGA, Ferreira LMA, Humphry DR, Gilbert HJ. The membrane-bound alpha-glucuronidase from Pseudomonas cellulosa hydrolyzes 4-O-methyl-D-glucuronoxylooligosaccharides but not 4-O-methyl-D-glucuronoxylan. J Bacteriol 2002; 184:4925-9. [PMID: 12169619 PMCID: PMC135289 DOI: 10.1128/jb.184.17.4925-4929.2002] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The microbial degradation of xylan is a key biological process. Hardwood 4-O-methyl-D-glucuronoxylans are extensively decorated with 4-O-methyl-D-glucuronic acid, which is cleaved from the polysaccharides by alpha-glucuronidases. In this report we describe the primary structures of the alpha-glucuronidase from Cellvibrio mixtus (C. mixtus GlcA67A) and the alpha-glucuronidase from Pseudomonas cellulosa (P. cellulosa GlcA67A) and characterize P. cellulosa GlcA67A. The primary structures of C. mixtus GlcA67A and P. cellulosa GlcA67A, which are 76% identical, exhibit similarities with alpha-glucuronidases in glycoside hydrolase family 67. The membrane-associated pseudomonad alpha-glucuronidase released 4-O-methyl-D-glucuronic acid from 4-O-methyl-D-glucuronoxylooligosaccharides but not from 4-O-methyl-D-glucuronoxylan. We propose that the role of the glucuronidase, in combination with cell-associated xylanases, is to hydrolyze decorated xylooligosaccharides, generated by extracellular hemicellulases, to xylose and 4-O-methyl-D-glucuronic acid, enabling the pseudomonad to preferentially utilize the sugars derived from these polymers.
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Affiliation(s)
- Tibor Nagy
- Department of Biological and Nutritional Sciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, United Kingdom
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15
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Emami K, Nagy T, Fontes CMGA, Ferreira LMA, Gilbert HJ. Evidence for temporal regulation of the two Pseudomonas cellulosa xylanases belonging to glycoside hydrolase family 11. J Bacteriol 2002; 184:4124-33. [PMID: 12107129 PMCID: PMC135193 DOI: 10.1128/jb.184.15.4124-4133.2002] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas cellulosa is a highly efficient xylan-degrading bacterium. Genes encoding five xylanases, and several accessory enzymes, which remove the various side chains that decorate the xylan backbone, have been isolated from the pseudomonad and characterized. The xylanase genes consist of xyn10A, xyn10B, xyn10C, xyn10D, and xyn11A, which encode Xyn10A, Xyn10B, Xyn10C, Xyn10D, and Xyn11A, respectively. In this study a sixth xylanase gene, xyn11B, was isolated which encodes a 357-residue modular enzyme, designated Xyn11B, comprising a glycoside hydrolase family 11 catalytic domain appended to a C-terminal X-14 module, a homologue of which binds to xylan. Localization studies showed that the two xylanases with glycoside hydrolase family (GH) 11 catalytic modules, Xyn11A and Xyn11B, are secreted into the culture medium, whereas Xyn10C is membrane bound. xyn10C, xyn10D, xyn11A, and xyn11B were all abundantly expressed when the bacterium was cultured on xylan or beta-glucan but not on medium containing mannan, whereas glucose repressed transcription of these genes. Although all of the xylanase genes were induced by the same polysaccharides, temporal regulation of xyn11A and xyn11B was apparent on xylan-containing media. Transcription of xyn11A occurred earlier than transcription of xyn11B, which is consistent with the predicted mode of action of the encoded enzymes. Xyn11A, but not Xyn11B, exhibits xylan esterase activity, and the removal of acetate side chains is required for xylanases to hydrolyze the xylan backbone. A transposon mutant of P. cellulosa in which xyn11A and xyn11B were inactive displayed greatly reduced extracellular but normal cell-associated xylanase activity, and its growth rate on medium containing xylan was indistinguishable from wild-type P. cellulosa. Based on the data presented here, we propose a model for xylan degradation by P. cellulosa in which the GH11 enzymes convert decorated xylans into substituted xylooligosaccharides, which are then hydrolyzed to their constituent sugars by the combined action of cell-associated GH10 xylanases and side chain-cleaving enzymes.
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Affiliation(s)
- Kaveh Emami
- Department of Biological and Nutritional Sciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, United Kingdom, CIISA-Faculdade de Medicina Veterinaria, 1199 Lisboa Codex, Portugal
| | - Tibor Nagy
- Department of Biological and Nutritional Sciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, United Kingdom, CIISA-Faculdade de Medicina Veterinaria, 1199 Lisboa Codex, Portugal
| | - Carlos M. G. A. Fontes
- Department of Biological and Nutritional Sciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, United Kingdom, CIISA-Faculdade de Medicina Veterinaria, 1199 Lisboa Codex, Portugal
| | - Luis M. A. Ferreira
- Department of Biological and Nutritional Sciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, United Kingdom, CIISA-Faculdade de Medicina Veterinaria, 1199 Lisboa Codex, Portugal
| | - Harry J. Gilbert
- Department of Biological and Nutritional Sciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, United Kingdom, CIISA-Faculdade de Medicina Veterinaria, 1199 Lisboa Codex, Portugal
- Corresponding author. Mailing address: Department of Biological and Nutritional Sciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, United Kingdom. Phone: 44(191)2226962. Fax: 44(191)2228684. E-mail:
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Nurizzo D, Nagy T, Gilbert HJ, Davies GJ. The structural basis for catalysis and specificity of the Pseudomonas cellulosa alpha-glucuronidase, GlcA67A. Structure 2002; 10:547-56. [PMID: 11937059 DOI: 10.1016/s0969-2126(02)00742-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Alpha-glucuronidases, components of an ensemble of enzymes central to the recycling of photosynthetic biomass, remove the alpha-1,2 linked 4-O-methyl glucuronic acid from xylans. The structure of the alpha-glucuronidase, GlcA67A, from Pseudomonas cellulosa reveals three domains, the central of which is a (beta/alpha)(8) barrel housing the catalytic apparatus. Complexes of the enzyme with the individual reaction products, either xylobiose or glucuronic acid, and the ternary complex of both glucuronic acid and xylotriose reveal a "blind" pocket which selects for short decorated xylooligosaccharides substituted with the uronic acid at their nonreducing end, consistent with kinetic data. The catalytic center reveals a constellation of carboxylates; Glu292 is poised to provide protonic assistance to leaving group departure with Glu393 and Asp365 both appropriately positioned to provide base-catalyzed assistance for inverting nucleophilic attack by water.
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Affiliation(s)
- Didier Nurizzo
- Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, United Kingdom
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Beylot MH, McKie VA, Voragen AG, Doeswijk-Voragen CH, Gilbert HJ. The Pseudomonas cellulosa glycoside hydrolase family 51 arabinofuranosidase exhibits wide substrate specificity. Biochem J 2001; 358:607-14. [PMID: 11535122 PMCID: PMC1222095 DOI: 10.1042/0264-6021:3580607] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
To investigate the mechanism by which Pseudomonas cellulosa releases arabinose from polysaccharides and oligosaccharides, a gene library of P. cellulosa genomic DNA was screened for 4-methylumbelliferyl-alpha-L-arabinofuranosidase (MUAase) activity. A single MUAase gene (abf51A) was isolated, which encoded a non-modular glycoside hydrolase family (GH) 51 arabinofuranosidase (Abf51A) of 57000 Da. The substrate specificity of the Abf51A showed that it preferentially removed alpha1,2- and alpha1,3-linked arabinofuranose side chains from either arabinan or arabinoxylan, and hydrolysed alpha1,5-linked arabino-oligosaccharides, although at a much lower rate. The activity of Abf51A against arabinoxylan was similar to a GH62 arabinofuranosidase encoded by a P. cellulosa gene. Glu-194 and Glu-321 of Abf51A are conserved in GH51 enzymes, and it has been suggested that these amino acids comprise the key catalytic acid/base and nucleophile residues, respectively. To evaluate this hypothesis the biochemical properties of E194A and E321A mutants of Abf51A were evaluated. The data were consistent with the view that Glu-194 and Glu-321 comprise the key catalytic residues of Abf51A. These data, in conjunction with the results presented in the accompanying paper [Beylot, Emami, McKie, Gilbert and Pell (2001) Biochem. J. 358, 599-605], indicate that P. cellulosa expresses a membrane-bound GH51 arabinofuranosidase that plays a pivotal role in releasing arabinose from a range of polysaccharides and oligosaccharides.
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Affiliation(s)
- M H Beylot
- Department of Biological and Nutritional Sciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, UK
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