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Leys S, De Bondt Y, Schreurs L, Courtin CM. Sensitivity of the Bacillus subtilis Xyn A Xylanase and Its Mutants to Different Xylanase Inhibitors Determines Their Activity Profile and Functionality during Bread Making. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:11198-11209. [PMID: 31532988 DOI: 10.1021/acs.jafc.9b04712] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The importance of inhibition sensitivity for xylanase functionality in bread making was investigated using mutants of the wild-type Bacillus subtilis xylanase (XBSTAXI), sensitive to Triticum aestivum xylanase inhibitor (TAXI). XBSNI, a mutant with reduced sensitivity to TAXI, and XBSTI, a mutant sensitive to all wheat endogenous proteinaceous inhibitors (TAXI, Xylanase Inhibiting Protein and Thaumatin-like Xylanase Inhibitor) were used. The higher inhibition sensitivity of XBSTAXI and XBSTI compared to XBSNI was associated with a respective 7- and 53-fold increase in enzyme dosage required for a maximal increase in bread loaf volume. XBSTI and XBSTAXI were only active during the mixing phase and the beginning of fermentation, while XBSNI was able to hydrolyze arabinoxylan until the end of fermentation. In spite of this difference in activity profile, no differences in loaf volume were observed for the different xylanases at optimal concentrations. Dough extensional viscosity analysis suggests that increased water availability as a result of xylanase activity favors starch-starch and starch-gluten interactions and drives the improvement in bread loaf volume.
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Affiliation(s)
- Sofie Leys
- Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe) , KU Leuven , Kasteelpark Arenberg 20 , 3001 Leuven , Belgium
| | - Yamina De Bondt
- Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe) , KU Leuven , Kasteelpark Arenberg 20 , 3001 Leuven , Belgium
| | - Linde Schreurs
- Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe) , KU Leuven , Kasteelpark Arenberg 20 , 3001 Leuven , Belgium
| | - Christophe M Courtin
- Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe) , KU Leuven , Kasteelpark Arenberg 20 , 3001 Leuven , Belgium
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Denisenko YA, Gusakov AV, Rozhkova AM, Zorov IN, Bashirova AV, Matys VY, Nemashkalov VA, Sinitsyn AP. Protein engineering of GH10 family xylanases for gaining a resistance to cereal proteinaceous inhibitors. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.01.042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Abstract
SUMMARY Biomass is constructed of dense recalcitrant polymeric materials: proteins, lignin, and holocellulose, a fraction constituting fibrous cellulose wrapped in hemicellulose-pectin. Bacteria and fungi are abundant in soil and forest floors, actively recycling biomass mainly by extracting sugars from holocellulose degradation. Here we review the genome-wide contents of seven Aspergillus species and unravel hundreds of gene models encoding holocellulose-degrading enzymes. Numerous apparent gene duplications followed functional evolution, grouping similar genes into smaller coherent functional families according to specialized structural features, domain organization, biochemical activity, and genus genome distribution. Aspergilli contain about 37 cellulase gene models, clustered in two mechanistic categories: 27 hydrolyze and 10 oxidize glycosidic bonds. Within the oxidative enzymes, we found two cellobiose dehydrogenases that produce oxygen radicals utilized by eight lytic polysaccharide monooxygenases that oxidize glycosidic linkages, breaking crystalline cellulose chains and making them accessible to hydrolytic enzymes. Among the hydrolases, six cellobiohydrolases with a tunnel-like structural fold embrace single crystalline cellulose chains and cooperate at nonreducing or reducing end termini, splitting off cellobiose. Five endoglucanases group into four structural families and interact randomly and internally with cellulose through an open cleft catalytic domain, and finally, seven extracellular β-glucosidases cleave cellobiose and related oligomers into glucose. Aspergilli contain, on average, 30 hemicellulase and 7 accessory gene models, distributed among 9 distinct functional categories: the backbone-attacking enzymes xylanase, mannosidase, arabinase, and xyloglucanase, the short-side-chain-removing enzymes xylan α-1,2-glucuronidase, arabinofuranosidase, and xylosidase, and the accessory enzymes acetyl xylan and feruloyl esterases.
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Kushwaha R, Payne CM, Downie AB. Uses of phage display in agriculture: a review of food-related protein-protein interactions discovered by biopanning over diverse baits. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2013; 2013:653759. [PMID: 23710253 PMCID: PMC3655605 DOI: 10.1155/2013/653759] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 04/02/2013] [Indexed: 12/24/2022]
Abstract
This review highlights discoveries made using phage display that impact the use of agricultural products. The contribution phage display made to our fundamental understanding of how various protective molecules serve to safeguard plants and seeds from herbivores and microbes is discussed. The utility of phage display for directed evolution of enzymes with enhanced capacities to degrade the complex polymers of the cell wall into molecules useful for biofuel production is surveyed. Food allergies are often directed against components of seeds; this review emphasizes how phage display has been employed to determine the seed component(s) contributing most to the allergenic reaction and how it has played a central role in novel approaches to mitigate patient response. Finally, an overview of the use of phage display in identifying the mature seed proteome protection and repair mechanisms is provided. The identification of specific classes of proteins preferentially bound by such protection and repair proteins leads to hypotheses concerning the importance of safeguarding the translational apparatus from damage during seed quiescence and environmental perturbations during germination. These examples, it is hoped, will spur the use of phage display in future plant science examining protein-ligand interactions.
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Affiliation(s)
- Rekha Kushwaha
- Department of Horticulture, Agricultural Science Center North, University of Kentucky, Room 308J, Lexington, KY 40546, USA
- Seed Biology Group, University of Kentucky, Lexington, KY 40546, USA
| | - Christina M. Payne
- Department of Chemical and Materials Engineering, University of Kentucky, Room 159, F. Paul Anderson Tower, Lexington, KY 40546, USA
- Center for Computational Sciences, University of Kentucky, Lexington, KY 40506, USA
| | - A. Bruce Downie
- Seed Biology Group, University of Kentucky, Lexington, KY 40546, USA
- Department of Horticulture, University of Kentucky, Room 401A, Plant Science Building, Lexington, KY 40546, USA
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Paës G, Berrin JG, Beaugrand J. GH11 xylanases: Structure/function/properties relationships and applications. Biotechnol Adv 2011; 30:564-92. [PMID: 22067746 DOI: 10.1016/j.biotechadv.2011.10.003] [Citation(s) in RCA: 287] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 10/06/2011] [Accepted: 10/13/2011] [Indexed: 01/02/2023]
Abstract
For technical, environmental and economical reasons, industrial demands for process-fitted enzymes have evolved drastically in the last decade. Therefore, continuous efforts are made in order to get insights into enzyme structure/function relationships to create improved biocatalysts. Xylanases are hemicellulolytic enzymes, which are responsible for the degradation of the heteroxylans constituting the lignocellulosic plant cell wall. Due to their variety, xylanases have been classified in glycoside hydrolase families GH5, GH8, GH10, GH11, GH30 and GH43 in the CAZy database. In this review, we focus on GH11 family, which is one of the best characterized GH families with bacterial and fungal members considered as true xylanases compared to the other families because of their high substrate specificity. Based on an exhaustive analysis of the sequences and 3D structures available so far, in relation with biochemical properties, we assess biochemical aspects of GH11 xylanases: structure, catalytic machinery, focus on their "thumb" loop of major importance in catalytic efficiency and substrate selectivity, inhibition, stability to pH and temperature. GH11 xylanases have for a long time been used as biotechnological tools in various industrial applications and represent in addition promising candidates for future other uses.
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Affiliation(s)
- Gabriel Paës
- INRA, UMR614 FARE, 2 esplanade Roland-Garros, F-51686 Reims, France.
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6
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Gusakov AV. Proteinaceous inhibitors of microbial xylanases. BIOCHEMISTRY (MOSCOW) 2010; 75:1185-99. [DOI: 10.1134/s0006297910100019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Reitinger S, Yu Y, Wicki J, Ludwiczek M, D’Angelo I, Baturin S, Okon M, Strynadka NCJ, Lutz S, Withers SG, McIntosh LP. Circular Permutation of Bacillus circulans Xylanase: A Kinetic and Structural Study. Biochemistry 2010; 49:2464-74. [DOI: 10.1021/bi100036f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stephan Reitinger
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
- Centre for High Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
| | - Ying Yu
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322
| | - Jacqueline Wicki
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
- Centre for High Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
| | - Martin Ludwiczek
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Igor D’Angelo
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Simon Baturin
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Mark Okon
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Natalie C. J. Strynadka
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
- Michael Smith Laboratory, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
- Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Stefan Lutz
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322
| | - Stephen G. Withers
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
- Centre for High Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Lawrence P. McIntosh
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
- Centre for High Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
- Michael Smith Laboratory, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
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Lagaert S, Beliën T, Volckaert G. Plant cell walls: Protecting the barrier from degradation by microbial enzymes. Semin Cell Dev Biol 2009; 20:1064-73. [DOI: 10.1016/j.semcdb.2009.05.008] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Accepted: 05/25/2009] [Indexed: 10/20/2022]
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Cervera Tison M, André-Leroux G, Lafond M, Georis J, Juge N, Berrin JG. Molecular determinants of substrate and inhibitor specificities of the Penicillium griseofulvum family 11 xylanases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1794:438-45. [PMID: 19118652 DOI: 10.1016/j.bbapap.2008.11.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2008] [Revised: 11/21/2008] [Accepted: 11/24/2008] [Indexed: 11/18/2022]
Abstract
Penicillium griseofulvum possesses two endo-(1,4)-beta-xylanase genes, PgXynA and PgXynB, belonging to family 11 glycoside hydrolases. The enzymes share 69% identity, a similar hydrolysis profile i.e. the predominant production of xylobiose and xylotriose as end products from wheat arabinoxylan and a specificity region of six potential xylose subsites, but differ in terms of catalytic efficiency which can be explained by subtle structural differences in the positioning of xylohexaose in the PgXynB model. Site-directed mutagenesis of the "thumb" region revealed structural basis of PgXynB substrate and inhibitor specificities. We produced variants displaying increased catalytic efficiency towards wheat arabinoxylan and xylo-oligosaccharides and identified specific determinants in PgXynB "thumb" region responsible for resistance to the wheat xylanase inhibitor XIP-I. Based on kinetic analysis and homology modeling, we suggested that Pro130(PgXynB), Lys131(PgXynB) and Lys132(PgXynB) hamper flexibility of the loop forming the "thumb" and interfere by steric hindrance with the inhibitor.
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Affiliation(s)
- Marine Cervera Tison
- Biosciences ISM(2) UMR-CNRS-6263, Université Paul Cézanne Aix Marseille III, Av. Escadrille Normandie-Niemen, 13397 Marseille Cedex 20, France
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André-Leroux G, Berrin JG, Georis J, Arnaut F, Juge N. Structure-based mutagenesis of Penicillium griseofulvum xylanase using computational design. Proteins 2008; 72:1298-307. [DOI: 10.1002/prot.22029] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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11
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Factors affecting xylanase functionality in the degradation of arabinoxylans. Biotechnol Lett 2008; 30:1139-50. [DOI: 10.1007/s10529-008-9669-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 02/04/2008] [Accepted: 02/07/2008] [Indexed: 10/22/2022]
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12
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Beliën T, Verjans P, Courtin CM, Delcour JA. Phage display based identification of novel stabilizing mutations in glycosyl hydrolase family 11 B. subtilis endoxylanase XynA. Biochem Biophys Res Commun 2008; 368:74-80. [DOI: 10.1016/j.bbrc.2008.01.047] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2008] [Accepted: 01/07/2008] [Indexed: 10/22/2022]
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13
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Understanding the structural basis for substrate and inhibitor recognition in eukaryotic GH11 xylanases. J Mol Biol 2007; 375:1293-305. [PMID: 18078955 DOI: 10.1016/j.jmb.2007.11.007] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2007] [Revised: 11/01/2007] [Accepted: 11/02/2007] [Indexed: 11/21/2022]
Abstract
Endo-beta1,4-xylanases (xylanases) hydrolyse the beta1,4 glycosidic bonds in the backbone of xylan. Although xylanases from glycoside hydrolase family 11 (GH11) have been extensively studied, several issues remain unresolved. Thus, the mechanism by which these enzymes hydrolyse decorated xylans is unclear and the structural basis for the variation in catalytic activity within this family is unknown. Furthermore, the mechanism for the differences in the inhibition of fungal GH11 enzymes by the wheat protein XIP-I remains opaque. To address these issues we report the crystal structure and biochemical properties of the Neocallimastix patriciarum xylanase NpXyn11A, which displays unusually high catalytic activity and is one of the few fungal GH11 proteins not inhibited by XIP-I. Although the structure of NpXyn11A could not be determined in complex with substrates, we have been able to investigate how GH11 enzymes hydrolyse decorated substrates by solving the crystal structure of a second GH11 xylanase, EnXyn11A (encoded by an environmental DNA sample), bound to ferulic acid-1,5-arabinofuranose-alpha1,3-xylotriose (FAX(3)). The crystal structure of the EnXyn11A-FAX(3) complex shows that solvent exposure of the backbone xylose O2 and O3 groups at subsites -3 and +2 allow accommodation of alpha1,2-linked 4-methyl-D-glucuronic acid and L-arabinofuranose side chains. Furthermore, the ferulated arabinofuranose side chain makes hydrogen bonds and hydrophobic interactions at the +2 subsite, indicating that the decoration may represent a specificity determinant at this aglycone subsite. The structure of NpXyn11A reveals potential -3 and +3 subsites that are kinetically significant. The extended substrate-binding cleft of NpXyn11A, compared to other GH11 xylanases, may explain why the Neocallimastix enzyme displays unusually high catalytic activity. Finally, the crystal structure of NpXyn11A shows that the resistance of the enzyme to XIP-I is not due solely to insertions in the loop connecting beta strands 11 and 12, as suggested previously, but is highly complex.
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Beliën T, Van Campenhout S, Van Acker M, Robben J, Courtin CM, Delcour JA, Volckaert G. Mutational analysis of endoxylanases XylA and XylB from the phytopathogen Fusarium graminearum reveals comprehensive insights into their inhibitor insensitivity. Appl Environ Microbiol 2007; 73:4602-8. [PMID: 17513587 PMCID: PMC1932832 DOI: 10.1128/aem.00442-07] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Endo-beta-1,4-xylanases (EC 3.2.1.8; endoxylanases), key enzymes in the degradation of xylan, are considered to play an important role in phytopathogenesis, as they occupy a prominent position in the arsenal of hydrolytic enzymes secreted by phytopathogens to breach the cell wall and invade the plant tissue. Plant endoxylanase inhibitors are increasingly being pinpointed as part of a counterattack mechanism. To understand the surprising XIP-type endoxylanase inhibitor insensitivity of endoxylanases XylA and XylB from the phytopathogen Fusarium graminearum, an extensive mutational study of these enzymes was performed. Using combinatorial and site-directed mutagenesis, the XIP insensitivity of XylA as well as XylB was proven to be solely due to amino acid sequence adaptations in the "thumb" structural region. While XylB residues Cys141, Asp148, and Cys149 were shown to prevent XIP interaction, the XIP insensitivity of XylA could be ascribed to the occurrence of only one aberrant residue, i.e., Val151. This study, in addition to providing a thorough explanation for the XIP insensitivity of both F. graminearum endoxylanases at the molecular level, generated XylA and XylB mutants with altered inhibition specificities and pH optima. As this is the first experimental elucidation of the molecular determinants dictating the specificity of the interaction between endoxylanases of phytopathogenic origin and a plant inhibitor, this work sheds more light on the ongoing evolutionary arms race between plants and phytopathogenic fungi involving recognition of endoxylanases.
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Affiliation(s)
- Tim Beliën
- Laboratory of Gene Technology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium.
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