1
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Saberi M, Chikunova A, Ben Bdira F, Cramer-Blok A, Timmer M, Voskamp P, Ubbink M. Bimodal substrate binding in the active site of the glycosidase BcX. FEBS J 2024. [PMID: 39185686 DOI: 10.1111/febs.17251] [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: 03/04/2024] [Revised: 05/02/2024] [Accepted: 08/13/2024] [Indexed: 08/27/2024]
Abstract
Bacillus circulans xylanase (BcX) from the glycoside hydrolase family 11 degrades xylan through a retaining, double-displacement mechanism. The enzyme is thought to hydrolyze glycosidic bonds in a processive manner and has a large, active site cleft, with six subsites allowing the binding of six xylose units. Such an active site architecture suggests that oligomeric xylose substrates can bind in multiple ways. In the crystal structure of the catalytically inactive variant BcX E78Q, the substrate xylotriose is observed in the active site, as well as bound to the known secondary binding site and a third site on the protein surface. Nuclear magnetic resonance (NMR) titrations with xylose oligomers of different lengths yield nonlinear chemical shift trajectories for active site nuclei resonances, indicative of multiple binding orientations for these substrates for which binding and dissociation are in fast exchange on the NMR timescale, exchanging on the micro- to millisecond timescale. Active site binding can be modeled with a 2 : 1 model with dissociation constants in the low and high millimolar range. Extensive mutagenesis of active site residues indicates that tight binding occurs in the glycon binding site and is stabilized by Trp9 and the thumb region. Mutations F125A and W71A lead to large structural rearrangements. Binding at the glycon site is sensed throughout the active site, whereas the weak binding mostly affects the aglycon site. The interactions with the two active site locations are largely independent of each other and of binding at the secondary binding site.
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Affiliation(s)
- Mahin Saberi
- Leiden Institute of Chemistry, Leiden University, The Netherlands
| | | | - Fredj Ben Bdira
- Leiden Institute of Chemistry, Leiden University, The Netherlands
| | | | - Monika Timmer
- Leiden Institute of Chemistry, Leiden University, The Netherlands
| | - Patrick Voskamp
- Leiden Institute of Chemistry, Leiden University, The Netherlands
| | - Marcellus Ubbink
- Leiden Institute of Chemistry, Leiden University, The Netherlands
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2
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Huang J, Zhang D, Omedi JO, Lei Y, Su X, Wu M, Huang W. Improving the inhibitory resistance of xylanase FgXyn11C from Fusarium graminearum to SyXIP-I by site-directed mutagenesis. Int J Biol Macromol 2024; 271:132434. [PMID: 38788879 DOI: 10.1016/j.ijbiomac.2024.132434] [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: 03/04/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024]
Abstract
The aim of this study was to improve the inhibitory resistance of xylanase FgXyn11C from Fusarium graminearum to XIP in cereal flour. Site saturation mutagenesis was performed using computer-aided redesign. Firstly, based on multiple primary structure alignments, the amino acid residues in the active site architecture were identified, and specific residue T144 in the thumb region of FgXyn11C was selected for site-saturation mutagenesis. After screening, FgXyn11CT144F was selected as the best mutant, as it displayed the highest enzymatic activity and resistance simultaneously compared to other mutants. The specific activity of FgXyn11CT144F was 208.8 U/mg and it exhibited complete resistance to SyXIP-I. Compared with the wild-type, FgXyn11CT144F displayed similar activity and the most resistant against SyXIP-I. The optimal temperature and pH of the wild-type and purified FgXyn11CT144F were similar at pH 5.0 and 30 °C. Our findings provided preliminary insight into how the specific residue at position 144 in the thumb region of FgXyn11C influenced the enzymatic properties and interacted with SyXIP-I. The inhibition sensitivity of FgXyn11C was reduced through directed evolution, leading to creation of the mutant enzyme FgXyn11CT144F. The FgXyn11CT144F resistance to SyXIP-I has potential application and can also provide references for engineering other resistant xylanases of the GHF11.
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Affiliation(s)
- Jing Huang
- State Key Laboratory of Food Science and Technology, the Laboratory of Baking and Fermentation Science, Cereals/Sourdough and Ingredient Functionality Research, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Dong Zhang
- School of Biotechnology, Jiangnan University, Wuxi 214122, China; Wuxi School of Medicine, Jiangnan University, Wuxi 214122, China
| | - Jacob Ojobi Omedi
- State Key Laboratory of Food Science and Technology, the Laboratory of Baking and Fermentation Science, Cereals/Sourdough and Ingredient Functionality Research, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yuqing Lei
- School of Biotechnology, Jiangnan University, Wuxi 214122, China; Wuxi School of Medicine, Jiangnan University, Wuxi 214122, China
| | - Xiaoya Su
- School of Biotechnology, Jiangnan University, Wuxi 214122, China; Wuxi School of Medicine, Jiangnan University, Wuxi 214122, China
| | - Minchen Wu
- Wuxi School of Medicine, Jiangnan University, Wuxi 214122, China.
| | - Weining Huang
- State Key Laboratory of Food Science and Technology, the Laboratory of Baking and Fermentation Science, Cereals/Sourdough and Ingredient Functionality Research, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
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3
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Mendonça M, Barroca M, Collins T. Endo-1,4-β-xylanase-containing glycoside hydrolase families: Characteristics, singularities and similarities. Biotechnol Adv 2023; 65:108148. [PMID: 37030552 DOI: 10.1016/j.biotechadv.2023.108148] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 04/02/2023] [Accepted: 04/04/2023] [Indexed: 04/09/2023]
Abstract
Endo-1,4-β-xylanases (EC 3.2.1.8) are O-glycoside hydrolases that cleave the internal β-1,4-D-xylosidic linkages of the complex plant polysaccharide xylan. They are produced by a vast array of organisms where they play critical roles in xylan saccharification and plant cell wall hydrolysis. They are also important industrial biocatalysts with widespread application. A large and ever growing number of xylanases with wildly different properties and functionalites are known and a better understanding of these would enable a more effective use in various applications. The Carbohydrate-Active enZYmes database (CAZy), which classifies evolutionarily related proteins into a glycoside hydrolase family-subfamily organisational scheme has proven powerful in understanding these enzymes. Nevertheless, ambiguity currently exists as to the number of glycoside hydrolase families and subfamilies harbouring catalytic domains with true endoxylanase activity and as to the specific characteristics of each of these families/subfamilies. This review seeks to clarify this, identifying 9 glycoside hydrolase families containing enzymes with endo-1,4-β-xylanase activity and discussing their properties, similarities, differences and biotechnological perspectives. In particular, substrate specificities and hydrolysis patterns and the structural determinants of these are detailed, with taxonomic aspects of source organisms being also presented. Shortcomings in current knowledge and research areas that require further clarification are highlighted and suggestions for future directions provided. This review seeks to motivate further research on these enzymes and especially of the lesser known endo-1,4-β-xylanase containing families. A better understanding of these enzymes will serve as a foundation for the knowledge-based development of process-fitted endo-1,4-β-xylanases and will accelerate their development for use with even the most recalcitrant of substrates in the biobased industries of the future.
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Exploring competitive inhibition of a family 10 xylanase derived from Hu sheep rumen microbiota by Oryza sativa xylanase inhibitor protein: In vitro and in silico perspectives. Enzyme Microb Technol 2022; 160:110082. [PMID: 35709658 DOI: 10.1016/j.enzmictec.2022.110082] [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: 04/13/2022] [Revised: 05/20/2022] [Accepted: 06/09/2022] [Indexed: 01/18/2023]
Abstract
The catalytic domain of family GH10 xylanase, XYN-LXY_CD derived from Hu sheep rumen microbiota was expressed in Pichia pastoris X33. The special activity of reXYN-LXY_CD in the culture supernatant was 232.56 U/mg. The optima of reXYN-LXY_CD were 53 °C and pH 7.0. Recombinant Oryza sativa xylanase inhibitor protein (rePOsXIP) competitively inhibited reXYN-LXY_CD with an inhibition constant (Ki) value of 237.37 nM. The concentration of hydrolysates released from beechwood xylan by reXYN-LXY_CD reduced when rePOsXIP was added into the hydrolytic system. Fluorescence of reXYN-LXY_CD was statically quenched by rePOsXIP in a dose-dependent manner. The details in intermolecular interaction between XYN-LXY_CD and OsXIP were investigated by using molecular dynamics (MD) simulations, binding free energy computation and non-covalent interactions (NCI) analysis. Hydrogen bonding and van der Waals played indispensable roles in the XYN-LXY_CD/OsXIP interaction. The α-7 helix of OsXIP tightly occupied the catalytic pocket of XYN-LXY_CD with hydrogen bonding such as K239OsXIP-N261/Q292/E197XYN-LXY_CD (E197, the acid-base catalytic residue), D236OsXIP-K327XYN-LXY_CD and Q242OsXIP-E211/Q212XYN-LXY_CD. Based on the quantum theory of atoms in molecules (QTAIM), the Laplacian of electron density and core-valence bifurcation index of HZ3K239-OE2E197 were 0.1025 a.u. and 0.002218, respectively. Elucidating the mechanism underlying xylanase-inhibitor interactions might help construct XYN-LXY_CD mutants that gain resistance to XIPs and high catalytic activity, which would be more efficient in feed additives in livestock.
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5
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Sensitivity of family GH11 Bacillus amyloliquefaciens xylanase A (BaxA) and the T33I mutant to Oryza sativa xylanase inhibitor protein (OsXIP): An experimental and computational study. Enzyme Microb Technol 2022; 156:109998. [DOI: 10.1016/j.enzmictec.2022.109998] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 01/17/2022] [Accepted: 01/27/2022] [Indexed: 11/22/2022]
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6
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Wang Y, Liu M, Li J, Wei H, Zhang K. Experimental and in silico studies of competitive inhibition of family GH10 Aspergillus fumigatus xylanase A by Oryza sativa xylanase inhibitor protein. Int J Biol Macromol 2021; 193:1391-1399. [PMID: 34742846 DOI: 10.1016/j.ijbiomac.2021.10.201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 10/07/2021] [Accepted: 10/26/2021] [Indexed: 11/25/2022]
Abstract
The family GH10 Aspergillus fumigatus xylanase A (AfXylA10) gene, afxyla10 was cloned and recombinantly expressed in Pichia pastoris X33. The optimum temperature and pH of reAfXylA10 was 53 °C and 7.0, and Mn2+ remarkably activated the catalytic activity. The recombinant Oryza sativa xylanase inhibitor protein, rePOsXIP significantly inhibited reAfXylA10 with inhibition constant (Ki) of 177.94 nM via competitive inhibition and decreased the concentration of hydrolysate from beechwood xylan. Optimal inhibition of rePOsXIP on reAfXylA10 occurred at 45 °C for 40 min. The fluorescence of reAfXylA10 was statically quenched by rePOsXIP, indicating the formation of reAfXylA10-rePOsXIP complex during their interaction. Furthermore, molecular dynamics (MD) simulations were performed to obtain the detailed information on enzyme-inhibitor interaction. The binding free energy (ΔG) of AfXylA10-OsXIP complex was -30 ± 9 kcal/mol by MM-PBSA calculation, and the α-7 helix of OsXIP anchored in the catalytic cleft of AfXylA10 by competition with the xylan substrate. K239OsXIP stably interacted with the catalytic site E140AfXylA10 through hydrogen bond and vdW interaction. Intermolecular hydrogen bonds T104AfXylA10/V99AfXylA10-Q5OsXIP, R256AfXylA10-E235OsXIP, D155AfXylA10-Y243OsXIP and D145AfXylA10-R194OsXIP on the upper of the TIM barrel were essential for strengthening the stability of complex. Therefore, these non-covalent interactions (NCI) played key role in the interaction between AfXylA10 and OsXIP.
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Affiliation(s)
- Yuting Wang
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Mingqi Liu
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China.
| | - Jiayi Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huiwen Wei
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Keer Zhang
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
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7
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Endo-xylanases from Cohnella sp. AR92 aimed at xylan and arabinoxylan conversion into value-added products. Appl Microbiol Biotechnol 2021; 105:6759-6778. [PMID: 34458936 DOI: 10.1007/s00253-021-11495-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/29/2021] [Accepted: 08/03/2021] [Indexed: 10/20/2022]
Abstract
The genus Cohnella belongs to a group of Gram-positive endospore-forming bacteria within the Paenibacillaceae family. Although most species were described as xylanolytic bacteria, the literature still lacks some key information regarding their repertoire of xylan-degrading enzymes. The whole genome sequence of an isolated xylan-degrading bacterium Cohnella sp. strain AR92 was found to contain five genes encoding putative endo-1,4-β-xylanases, of which four were cloned, expressed, and characterized to better understand the contribution of the individual endo-xylanases to the overall xylanolytic properties of strain AR92. Three of the enzymes, CoXyn10A, CoXyn10C, and CoXyn11A, were shown to be effective at hydrolyzing xylans-derived from agro-industrial, producing oligosaccharides with substrate conversion values of 32.5%, 24.7%, and 10.6%, respectively, using sugarcane bagasse glucuronoarabinoxylan and of 29.9%, 19.1%, and 8.0%, respectively, using wheat bran-derived arabinoxylan. The main reaction products from GH10 enzymes were xylobiose and xylotriose, whereas CoXyn11A produced mostly xylooligosaccharides (XOS) with 2 to 5 units of xylose, often substituted, resulting in potentially prebiotic arabinoxylooligosaccharides (AXOS). The endo-xylanases assay displayed operational features (temperature optima from 49.9 to 50.4 °C and pH optima from 6.01 to 6.31) fitting simultaneous xylan utilization. Homology modeling confirmed the typical folds of the GH10 and GH11 enzymes, substrate docking studies allowed the prediction of subsites (- 2 to + 1 in GH10 and - 3 to + 1 in GH11) and identification of residues involved in ligand interactions, supporting the experimental data. Overall, the Cohnella sp. AR92 endo-xylanases presented significant potential for enzymatic conversion of agro-industrial by-products into high-value products.Key points• Cohnella sp. AR92 genome encoded five potential endo-xylanases.• Cohnella sp. AR92 enzymes produced xylooligosaccharides from xylan, with high yields.• GH10 enzymes from Cohnella sp. AR92 are responsible for the production of X2 and X3 oligosaccharides.• GH11 from Cohnella sp. AR92 contributes to the overall xylan degradation by producing substituted oligosaccharides.
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Vucinic J, Novikov G, Montanier CY, Dumon C, Schiex T, Barbe S. A Comparative Study to Decipher the Structural and Dynamics Determinants Underlying the Activity and Thermal Stability of GH-11 Xylanases. Int J Mol Sci 2021; 22:ijms22115961. [PMID: 34073139 PMCID: PMC8199483 DOI: 10.3390/ijms22115961] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 11/23/2022] Open
Abstract
With the growing need for renewable sources of energy, the interest for enzymes capable of biomass degradation has been increasing. In this paper, we consider two different xylanases from the GH-11 family: the particularly active GH-11 xylanase from Neocallimastix patriciarum, NpXyn11A, and the hyper-thermostable mutant of the environmentally isolated GH-11 xylanase, EvXyn11TS. Our aim is to identify the molecular determinants underlying the enhanced capacities of these two enzymes to ultimately graft the abilities of one on the other. Molecular dynamics simulations of the respective free-enzymes and enzyme–xylohexaose complexes were carried out at temperatures of 300, 340, and 500 K. An in-depth analysis of these MD simulations showed how differences in dynamics influence the activity and stability of these two enzymes and allowed us to study and understand in greater depth the molecular and structural basis of these two systems. In light of the results presented in this paper, the thumb region and the larger substrate binding cleft of NpXyn11A seem to play a major role on the activity of this enzyme. Its lower thermal stability may instead be caused by the higher flexibility of certain regions located further from the active site. Regions such as the N-ter, the loops located in the fingers region, the palm loop, and the helix loop seem to be less stable than in the hyper-thermostable EvXyn11TS. By identifying molecular regions that are critical for the stability of these enzymes, this study allowed us to identify promising targets for engineering GH-11 xylanases. Eventually, we identify NpXyn11A as the ideal host for grafting the thermostabilizing traits of EvXyn11TS.
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Affiliation(s)
- Jelena Vucinic
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, ANITI, 31400 Toulouse, France; (J.V.); (G.N.); (C.Y.M.); (C.D.)
- Université Fédérale de Toulouse, ANITI, INRAE, UR 875, 31326 Toulouse, France;
| | - Gleb Novikov
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, ANITI, 31400 Toulouse, France; (J.V.); (G.N.); (C.Y.M.); (C.D.)
| | - Cédric Y. Montanier
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, ANITI, 31400 Toulouse, France; (J.V.); (G.N.); (C.Y.M.); (C.D.)
| | - Claire Dumon
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, ANITI, 31400 Toulouse, France; (J.V.); (G.N.); (C.Y.M.); (C.D.)
| | - Thomas Schiex
- Université Fédérale de Toulouse, ANITI, INRAE, UR 875, 31326 Toulouse, France;
| | - Sophie Barbe
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, ANITI, 31400 Toulouse, France; (J.V.); (G.N.); (C.Y.M.); (C.D.)
- Correspondence:
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Zhu D, Liu X, Xie X, Yang S, Lin H, Chen H. Characteristics of a
XIP
‐resistant xylanase from
Neocallimastix
sp.
GMLF
1 and its advantage in barley malt saccharification. Int J Food Sci Technol 2020. [DOI: 10.1111/ijfs.14341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dongdong Zhu
- College of Life Sciences Henan Agricultural University 95 Wenhua Road Zhengzhou 450002 China
| | - Xinyu Liu
- College of Life Sciences Henan Agricultural University 95 Wenhua Road Zhengzhou 450002 China
| | - Xia Xie
- College of Life Sciences Henan Agricultural University 95 Wenhua Road Zhengzhou 450002 China
| | - Sen Yang
- College of Life Sciences Henan Agricultural University 95 Wenhua Road Zhengzhou 450002 China
| | - Hui Lin
- College of Life Sciences Henan Agricultural University 95 Wenhua Road Zhengzhou 450002 China
| | - Hongge Chen
- College of Life Sciences Henan Agricultural University 95 Wenhua Road Zhengzhou 450002 China
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Differential inhibition of GH family 11 endo-xylanase by rice xylanase inhibitor and verification by a modified yeast two-hybrid system. Int J Biol Macromol 2019; 132:514-523. [PMID: 30951774 DOI: 10.1016/j.ijbiomac.2019.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/30/2019] [Accepted: 04/01/2019] [Indexed: 11/22/2022]
Abstract
Rice xylanase inhibitor (RIXI) is a XIP-type xylanase inhibitor protein that protects rice cells from pathogenic organisms. RIXI inhibits most microbial xylanases and thus decreases their practical application. The recombinant RIXI (rePRIXI) showed evident inhibitory activities against several family 11 endo-xylanases. After interaction with rePRIXI at 50 °C for 40 min, the residual activities of reBaxA50, reBaxA, TfxA_CD214, and TfxA_CD were 55.6%, 30.3%, 30.09%, and 11.20%, respectively. Intrinsic fluorescence of reBaxA50 and TfxA_CD214 was statically quenched after interaction with rePRIXI. rePRIXI decreased hydrolysis of beechwood xylan by reBaxA50 and TfxA_CD214. Molecular dynamics simulations revealed the long loop (residues 144-153) of RIXI inserts into the catalytic cleft of family 11 xylanases. Native PAGE results revealed the formation of RIXI-xylanase complex after their interaction in the test tube. Interactions were also observed between RIXI and xylanases in living yeast cells. The results of inhibitory activity assay and modified yeast two-hybrid revealed that the inhibitory activity of RIXI on family 11 xylanase improved with the interaction strength of the RIXI-xylanase complex, indicating their positive correlation. The modified yeast two-hybrid system is relatively simple and has low cost, and its use may be extended to other studies on protein-protein interactions.
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11
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Dang Y, Liu M, Wu X. Recombinant rice xylanase-inhibiting protein inhibits GH11 endo-xylanases through competitive inhibition. Protein Expr Purif 2019; 156:17-24. [DOI: 10.1016/j.pep.2018.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 11/23/2018] [Accepted: 12/28/2018] [Indexed: 12/22/2022]
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12
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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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13
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Inhibiting the Catalytic Activity of Family GH11 Xylanases by Recombinant Rice Xylanase-Inhibiting Protein. Catal Letters 2018. [DOI: 10.1007/s10562-018-2431-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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14
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Bai W, Cao Y, Liu J, Wang Q, Jia Z. Improvement of alkalophilicity of an alkaline xylanase Xyn11A-LC from Bacillus sp. SN5 by random mutation and Glu135 saturation mutagenesis. BMC Biotechnol 2016; 16:77. [PMID: 27825339 PMCID: PMC5101721 DOI: 10.1186/s12896-016-0310-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 10/21/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Family 11 alkaline xylanases have great potential economic applications in the pulp and paper industry. In this study, we would improve the alkalophilicity of family 11 alkaline xylanase Xyn11A-LC from Bacillus sp. SN5, for the better application in this field. RESULTS A random mutation library of Xyn11A-LC with about 10,000 clones was constructed by error-prone PCR. One mutant, M52-C10 (V116A and E135V), with improved alkalophilicity was obtained from the library. Site-directed mutation showed that the mutation E135V was responsible for the alkalophilicity of the mutant. The variant E135V shifted the optimum pH of the wild-type enzyme from 7.5 to 8.0. Compared to the relative activities of the wild type enzyme, those of the mutant E135V increased by 17.5, 18.9, 14.3 and 9.5 % at pH 8.5, 9.0, 9.5 and 10.0, respectively. Furthermore, Glu135 saturation mutagenesis showed that the only mutant to have better alkalophilicity than E135V was E135R. The optimal pH of the mutant E135R was 8.5, 1.0 pH units higher than that of the wild-type. In addition, compared to the wild-type enzyme, the mutations E135V and E135R increased the catalytic efficiency (k cat/K m) by 57 and 37 %, respectively. Structural analysis showed that the residue at position 135, located in the eight-residue loop on the protein surface, might improve the alkalophilicity and catalytic activity by the elimination of the negative charge and the formation of salt-bridge. CONCLUSIONS Mutants E135V and E135R with improved alkalophilicity were obtained by directed evolution and site saturation mutagenesis. The residue at position 135 in the eight-residue loop on the protein surface was found to play an important role in the pH activity profile of family 11 xylanases. This study provided alkalophilic mutants for application in bleaching process, and it was also helpful to understand the alkaline adaptation mechanism of family 11 xylanases.
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Affiliation(s)
- Wenqin Bai
- Department of Strategic and Integrative Research, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China. .,College of Life Science, Shanxi Normal University, Linfen, 041004, China.
| | - Yufan Cao
- Department of Strategic and Integrative Research, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China.,College of Life Science, Shanxi Normal University, Linfen, 041004, China
| | - Jun Liu
- Department of Strategic and Integrative Research, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China.,College of Life Science, Shanxi Normal University, Linfen, 041004, China
| | - Qinhong Wang
- Department of Strategic and Integrative Research, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
| | - Zhenhu Jia
- College of Life Science, Shanxi Normal University, Linfen, 041004, China.
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15
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Driss D, Berrin JG, Juge N, Bhiri F, Ghorbel R, Chaabouni SE. Functional characterization of Penicillium occitanis Pol6 and Penicillium funiculosum GH11 xylanases. Protein Expr Purif 2013; 90:195-201. [DOI: 10.1016/j.pep.2013.06.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 06/05/2013] [Accepted: 06/07/2013] [Indexed: 10/26/2022]
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16
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Probing the role of sigma π interaction and energetics in the catalytic efficiency of endo-1,4-β-xylanase. Appl Environ Microbiol 2012; 78:8817-21. [PMID: 23023743 DOI: 10.1128/aem.02261-12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chaetomium globosum endo-1,4-β-xylanase (XylCg) is distinguished from other xylanases by its high turnover rate (1,860 s(-1)), the highest ever reported for fungal xylanases. One conserved amino acid, W48, in the substrate binding pocket of wild-type XylCg was identified as an important residue affecting XylCg's catalytic efficiency.
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17
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Andersen MR, Giese M, de Vries RP, Nielsen J. Mapping the polysaccharide degradation potential of Aspergillus niger. BMC Genomics 2012; 13:313. [PMID: 22799883 PMCID: PMC3542576 DOI: 10.1186/1471-2164-13-313] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 06/08/2012] [Indexed: 11/10/2022] Open
Abstract
Background The degradation of plant materials by enzymes is an industry of increasing importance. For sustainable production of second generation biofuels and other products of industrial biotechnology, efficient degradation of non-edible plant polysaccharides such as hemicellulose is required. For each type of hemicellulose, a complex mixture of enzymes is required for complete conversion to fermentable monosaccharides. In plant-biomass degrading fungi, these enzymes are regulated and released by complex regulatory structures. In this study, we present a methodology for evaluating the potential of a given fungus for polysaccharide degradation. Results Through the compilation of information from 203 articles, we have systematized knowledge on the structure and degradation of 16 major types of plant polysaccharides to form a graphical overview. As a case example, we have combined this with a list of 188 genes coding for carbohydrate-active enzymes from Aspergillus niger, thus forming an analysis framework, which can be queried. Combination of this information network with gene expression analysis on mono- and polysaccharide substrates has allowed elucidation of concerted gene expression from this organism. One such example is the identification of a full set of extracellular polysaccharide-acting genes for the degradation of oat spelt xylan. Conclusions The mapping of plant polysaccharide structures along with the corresponding enzymatic activities is a powerful framework for expression analysis of carbohydrate-active enzymes. Applying this network-based approach, we provide the first genome-scale characterization of all genes coding for carbohydrate-active enzymes identified in A. niger.
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Affiliation(s)
- Mikael R Andersen
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
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Paës G, Cortés J, Siméon T, O'Donohue MJ, Tran V. Thumb-loops up for catalysis: a structure/function investigation of a functional loop movement in a GH11 xylanase. Comput Struct Biotechnol J 2012; 1:e201207001. [PMID: 24688637 PMCID: PMC3962102 DOI: 10.5936/csbj.201207001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 05/23/2012] [Accepted: 05/27/2012] [Indexed: 12/17/2022] Open
Abstract
Dynamics is a key feature of enzyme catalysis. Unfortunately, current experimental and computational techniques do not yet provide a comprehensive understanding and description of functional macromolecular motions. In this work, we have extended a novel computational technique, which combines molecular modeling methods and robotics algorithms, to investigate functional motions of protein loops. This new approach has been applied to study the functional importance of the so-called thumb-loop in the glycoside hydrolase family 11 xylanase from Thermobacillus xylanilyticus (Tx-xyl). The results obtained provide new insight into the role of the loop in the glycosylation/deglycosylation catalytic cycle, and underline the key importance of the nature of the residue located at the tip of the thumb-loop. The effect of mutations predicted in silico has been validated by in vitro site-directed mutagenesis experiments. Overall, we propose a comprehensive model of Tx-xyl catalysis in terms of substrate and product dynamics by identifying the action of the thumb-loop motion during catalysis.
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Affiliation(s)
- Gabriel Paës
- CNRS, FRE3478 UFIP, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, F-44322 Nantes, France ; University of Nantes, FRE3478 UFIP, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, F-44322 Nantes, France ; INRA, UMR614 FARE, 2 esplanade Roland Garros, F-51686 Reims, France ; University of Reims Champagne-Ardenne, UMR614 FARE, 2 esplanade Roland Garros, F-51686 Reims, France
| | - Juan Cortés
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France ; University of Toulouse, LAAS, F-31400 Toulouse, France
| | - Thierry Siméon
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France ; University of Toulouse, LAAS, F-31400 Toulouse, France
| | - Michael J O'Donohue
- INRA, UMR614 FARE, 2 esplanade Roland Garros, F-51686 Reims, France ; University of Reims Champagne-Ardenne, UMR614 FARE, 2 esplanade Roland Garros, F-51686 Reims, France ; INRA, UMR792 LISBP, 137 avenue de Rangueil, F-31077 Toulouse, France ; INSA, UMR792 LISBP, 137 avenue de Rangueil, F-31077 Toulouse, France
| | - Vinh Tran
- CNRS, FRE3478 UFIP, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, F-44322 Nantes, France ; University of Nantes, FRE3478 UFIP, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, F-44322 Nantes, France
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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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20
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Driss D, Bhiri F, Elleuch L, Bouly N, Stals I, Miled N, Blibech M, Ghorbel R, Chaabouni SE. Purification and properties of an extracellular acidophilic endo-1,4-β-xylanase, naturally deleted in the “thumb”, from Penicillium occitanis Pol6. Process Biochem 2011. [DOI: 10.1016/j.procbio.2011.02.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Fushinobu S, Uno T, Kitaoka M, Hayashi K, Matsuzawa H, Wakagi T. Mutational Analysis of Fungal Family 11 Xylanases on pH Optimum Determination. J Appl Glycosci (1999) 2011. [DOI: 10.5458/jag.jag.jag-2011_001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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22
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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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23
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Yi X, Shi Y, Xu H, Li W, Xie J, Yu R, Zhu J, Cao Y, Qiao D. Hyperexpression of two Aspergillus Niger Xylanase Genes in Escherichia Coli and Characterization of the Gene Products. Braz J Microbiol 2010; 41:778-86. [PMID: 24031555 PMCID: PMC3768633 DOI: 10.1590/s1517-83822010000300030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Revised: 10/07/2009] [Accepted: 02/18/2010] [Indexed: 11/22/2022] Open
Abstract
The analysis of individual gene product should enable to clarify the role of a particular enzyme in a complex xylanase system of A. niger. The two genes encoding precursors of co-produced endo-1,4-β-D-xylanases, xynA1 and xynB, were isolated from Aspergillus niger SCTCC 400264 (SCTCC, China) by using RT-PCR technique and then successfully expressed in Escherichia coli BL21. The nucleotide sequences of the xynA1 and xynB genes revealed that they were only 52.5% homology to each other. Characterization of the recombinant enzymes revealed the different properties: the specific activity of recombinant XYNA1 was 16.58 U/mg compared to 1201.7 U/mg for recombinant XYNB; The optimum temperature and pH of the recombinant XYNA1 were 35 °C and 3.0, respectively, whereas the corresponding values for the recombinant XYNB were 55 °C and 5.0, respectively; The recombinant XYNB showed much more thermostability than recombinant XYNA1; The recombinant XYNB showed 94% of maximal activity after incubating in water for 60 min at 60 °C compared to no activity for recombinant XYNA1. Various metal ions had different effects on activity between the two recombinant xylanases.
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Affiliation(s)
- Xiuli Yi
- College of Life Science , Sichuan University, Chengdu 610064 , China ; Microbiology and Metabolic Engineering key Laboratory of Sichuan Province , Chengdu 610064 , China
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Mutagenesis and subsite mapping underpin the importance for substrate specificity of the aglycon subsites of glycoside hydrolase family 11 xylanases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:977-85. [DOI: 10.1016/j.bbapap.2010.01.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Revised: 01/04/2010] [Accepted: 01/12/2010] [Indexed: 11/18/2022]
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25
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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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26
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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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27
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Al Balaa B, Brijs K, Gebruers K, Vandenhaute J, Wouters J, Housen I. Xylanase XYL1p from Scytalidium acidophilum: site-directed mutagenesis and acidophilic adaptation. BIORESOURCE TECHNOLOGY 2009; 100:6465-6471. [PMID: 19640703 DOI: 10.1016/j.biortech.2009.06.111] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Revised: 06/23/2009] [Accepted: 06/24/2009] [Indexed: 05/28/2023]
Abstract
The role of residues Asp60, Tyr35 and Glu141 in the pH-dependent activity of xylanase XYL1p from Scytalidium acidophilum was investigated by site-directed mutagenesis. These amino acids are highly conserved among the acidophilic family 11 xylanases and located near the catalytic site. XYL1p and its single mutants D60N, Y35W and E141A and three combined mutants DN/YW, DN/EA and YW/EA were over-expressed in Pichia pastoris and purified. Xylanase activities at different pH's and temperatures were determined. All mutations increased the pH optimum by 0.5-1.5 pH units. All mutants have lower specific activities except the E141A mutant that exhibited a 50% increase in specific activity at pH 4.0 and had an overall catalytic efficiency higher than the wild-type enzyme. Thermal unfolding experiments show that both the wild-type and E141A mutant proteins have a T(m) maximum at pH 3.5, the E141A mutant being slightly less stable than the wild-type enzyme. These mutations confirm the importance of these amino acids in the pH adaptation. Mutant E141A with its enhanced specific activity at pH 4.0 and improved overall catalytic efficiency is of possible interest for biotechnological applications.
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Affiliation(s)
- Bassam Al Balaa
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria, Damascus, P.O. Box 6091, Syria
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28
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29
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Gebruers K, Mokrane H, Nadjemi B, Beaugrand J, Fierens K, Proost P, Courtin CM, Delcour JA. Sorghum (Sorghum bicolor L. Moench) contains a XIP-type xylanase inhibitor but none of the TAXI- and TLXI-types. J Cereal Sci 2008. [DOI: 10.1016/j.jcs.2007.09.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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30
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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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31
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Crystallographic analysis shows substrate binding at the -3 to +1 active-site subsites and at the surface of glycoside hydrolase family 11 endo-1,4-beta-xylanases. Biochem J 2008; 410:71-9. [PMID: 17983355 DOI: 10.1042/bj20071128] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
GH 11 (glycoside hydrolase family 11) xylanases are predominant enzymes in the hydrolysis of heteroxylan, an abundant structural polysaccharide in the plant cell wall. To gain more insight into the protein-ligand interactions of the glycone as well as the aglycone subsites of these enzymes, catalytically incompetent mutants of the Bacillus subtilis and Aspergillus niger xylanases were crystallized, soaked with xylo-oligosaccharides and subjected to X-ray analysis. For both xylanases, there was clear density for xylose residues in the -1 and -2 subsites. In addition, for the B. subtilis xylanase, there was also density for xylose residues in the -3 and +1 subsite showing the spanning of the -1/+1 subsites. These results, together with the observation that some residues in the aglycone subsites clearly adopt a different conformation upon substrate binding, allowed us to identify the residues important for substrate binding in the aglycone subsites. In addition to substrate binding in the active site of the enzymes, the existence of an unproductive second ligand-binding site located on the surface of both the B. subtilis and A. niger xylanases was observed. This extra binding site may have a function similar to the separate carbohydrate-binding modules of other glycoside hydrolase families.
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32
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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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33
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Importance of C-Terminal Region for Thermostability of GH11 Xylanase from Streptomyces lividans. Appl Biochem Biotechnol 2007; 144:273-82. [DOI: 10.1007/s12010-007-8016-z] [Citation(s) in RCA: 9] [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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34
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Beliën T, Van Campenhout S, Vanden Bosch A, Bourgois TM, Rombouts S, Robben J, Courtin CM, Delcour JA, Volckaert G. Engineering molecular recognition of endoxylanase enzymes and their inhibitors through phage display. J Mol Recognit 2007; 20:103-12. [PMID: 17393541 DOI: 10.1002/jmr.818] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Specific binding of interacting proteins generally depends on a limited set of amino acid residues located at the contact interface. We have applied a phage-display-based screening method to simultaneously evaluate the role of multiple residues of endo-beta-1,4-xylanase enzymes in conferring binding specificity towards two different endoxylanase inhibitors. Seven residues of the two beta-strand 'thumb' region of Trichoderma longibrachiatum endo-beta-1,4-xylanase XynII were targeted for randomization. The generated combinatorial library representing 62,208 site-directed variants was displayed on the surface of filamentous phage and selected against xylanase inhibitor protein (XIP) and Triticum aestivum xylanase inhibitor (TAXI). DNA sequence analysis of phagemid panning isolates provided information on the occurrence of particular amino acids at distinct positions. In particular, residues at positions 124 (Asn) and 131 (Thr) were found to be critical for specific inhibitor binding. These residue predictions derived from the combinatorial exploration of the thumb region and accompanying sequence analyses were experimentally confirmed by testing the inhibitor sensitivity of a limited set of recombinantly expressed XynII mutants. In addition, we successfully altered the inhibition susceptibility of the bacterial Bacillus subtilis endoxylanase XynA from XIP-insensitive to XIP-sensitive.
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Affiliation(s)
- Tim Beliën
- Laboratory of Gene Technology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, B-3001 Leuven, Belgium.
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35
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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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Berrin JG, Ajandouz EH, Georis J, Arnaut F, Juge N. Substrate and product hydrolysis specificity in family 11 glycoside hydrolases: an analysis of Penicillium funiculosum and Penicillium griseofulvum xylanases. Appl Microbiol Biotechnol 2007; 74:1001-10. [PMID: 17216454 DOI: 10.1007/s00253-006-0764-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2006] [Revised: 11/06/2006] [Accepted: 11/14/2006] [Indexed: 10/23/2022]
Abstract
Two genes encoding family 11 endo-(1,4)-beta-xylanases from Penicillium griseofulvum (PgXynA) and Penicillium funiculosum (PfXynC) were heterologously expressed in Escherichia coli as glutathione S-transferase fusion proteins, and the recombinant enzymes were purified after affinity chromatography and proteolysis. PgXynA and PfXynC were identical to their native counterparts in terms of molecular mass, pI, N-terminal sequence, optimum pH, and enzymatic activity towards arabinoxylan. Further investigation of the rate and pattern of hydrolysis of PgXynA and PfXynC on wheat soluble arabinoxylan showed the predominant production of xylotriose and xylobiose as end products. The initial rate data from the hydrolysis of short xylo-oligosaccharides indicated that the catalytic efficiency increased with increasing chain length (n) of oligomer up to n = 6, suggesting that the specificity region of both Penicillium xylanases spans about six xylose units. In contrast to PfXynC, PgXynA was found insensitive to the wheat xylanase inhibitor protein XIP-I.
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Affiliation(s)
- Jean-Guy Berrin
- Biosciences FRE-3005-CNRS, Université Paul Cézanne Aix Marseille III, Av. Escadrille Normandie-Niemen, 13397 Marseille Cedex 20, France
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Paës G, Tran V, Takahashi M, Boukari I, O'Donohue MJ. New insights into the role of the thumb-like loop in GH-11 xylanases. Protein Eng Des Sel 2007; 20:15-23. [PMID: 17218335 DOI: 10.1093/protein/gzl049] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
GH-11 xylanases are highly specific and possess a thumb-shaped loop, a unique structure among enzymes with a jelly-roll scaffold. To investigate this structure, in vitro mutagenesis was performed on a GH-11 xylanase (Tx-Xyl) from Thermobacillus xylanilyticus. Targets were the conserved amino acids Pro(114)-Ser(115)-Ile(116) that are located at the thumb's tip and Thr(121) and Tyr(111), linker residues that connect the thumb to the main enzyme scaffold. Site-saturation mutagenesis provided an active variant that possesses a new triplet (Pro(114)-Gly(115)-Cys(116)), not found in naturally occurring GH-11 xylanases. The k(cat) value for xylan hydrolysis catalysed by this mutant was increased by 20%. Re-positioning of the thumb through the deletion of the linker residues produced different effects. As predicted by in silico analyses, deletion of Thr(121) had drastic consequences on activity, whereas deletion of Tyr(111) only affected (4-fold decrease) k(cat). Finally, deletion mutagenesis was used to create a thumbless variant that was almost catalytically inactive. Fluorescence titration with xylotetraose and xylopentaose revealed that this thumb-deleted xylanase retained the ability to bind substrates. This binding was comparable to that of the wild-type enzyme. Additionally, unlike wild-type Tx-Xyl, the thumb-deleted xylanase efficiently bound cellotetraose, although no cellulose hydrolysing activity was detected. Overall, these data show that the thumb is a key determinant for substrate selection and support previous data that suggest that it plays a role in the catalytic process.
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Affiliation(s)
- Gabriel Paës
- Institut National de la Recherche Agronomique, UMR FARE 614, 8 rue Gabriel Voisin, BP 316, 51688 Reims Cedex 2, France
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Ge Y, Antoulinakis EG, Gee KR, Johnson I. An ultrasensitive, continuous assay for xylanase using the fluorogenic substrate 6,8-difluoro-4-methylumbelliferyl beta-D-xylobioside. Anal Biochem 2006; 362:63-8. [PMID: 17241608 DOI: 10.1016/j.ab.2006.11.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2006] [Revised: 11/17/2006] [Accepted: 11/22/2006] [Indexed: 12/01/2022]
Abstract
We describe a fluorescence-based assay for the analysis of xylanase activity using a novel fluorogenic substrate, 6,8-difluoro-4-methylumbelliferyl beta-D-xylobioside (DiFMUX(2)). Generation of fluorescent 6,8-difluoro-4-methylumbelliferone (DiFMU) from the substrate corresponded directly to xylanase activity. High-performance liquid chromatography analysis of the digestion products showed that xylanase hydrolyzed DiFMUX(2) directly to DiFMU and xylobiose. The assay provides the speed, sensitivity, and convenience required for measuring xylanase activity or for screening xylanase inhibitors in a high-throughput format and is suitable for the kinetic assay of xylanases from a variety of sources.
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Affiliation(s)
- Yue Ge
- Invitrogen Corp., 29851 Willow Creek Road, Eugene, OR 97402, USA
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Beliën T, Van Campenhout S, Robben J, Volckaert G. Microbial endoxylanases: effective weapons to breach the plant cell-wall barrier or, rather, triggers of plant defense systems? MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2006; 19:1072-81. [PMID: 17022171 DOI: 10.1094/mpmi-19-1072] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Endo-beta-1,4-xylanases (EC 3.2.1.8) are key enzymes in the degradation of xylan, the predominant hemicellulose in the cell walls of plants and the second most abundant polysaccharide on earth. A number of endoxylanases are produced by microbial phytopathogens responsible for severe crop losses. These enzymes are considered to play an important role in phytopathogenesis, as they provide essential means to the attacking organism to break through the plant cell wall. Plants have evolved numerous defense mechanisms to protect themselves against invading pathogens, amongst which are proteinaceous inhibitors of cell wall-degrading enzymes. These defense mechanisms are triggered when a pathogen-derived elicitor is recognized by the plant. In this review, the diverse aspects of endoxylanases in promoting virulence and in eliciting plant defense systems are highlighted. Furthermore, the role of the relatively recently discovered cereal endoxylanase inhibitor families TAXI (Triticum aestivum xylanase inhibitor) and XIP (xylanase inhibitor protein) in plant defense is discussed.
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Affiliation(s)
- Tim Beliën
- Katholieke Universiteit Leuven, Laboratory of Gene Technology, Kasteelpark Arenberg 21, B-3001 Leuven, Belgium.
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40
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Juge N. Plant protein inhibitors of cell wall degrading enzymes. TRENDS IN PLANT SCIENCE 2006; 11:359-67. [PMID: 16774842 DOI: 10.1016/j.tplants.2006.05.006] [Citation(s) in RCA: 153] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2006] [Revised: 05/04/2006] [Accepted: 05/25/2006] [Indexed: 05/10/2023]
Abstract
Plant cell walls, which consist mainly of polysaccharides (i.e. cellulose, hemicelluloses and pectins), play an important role in defending plants against pathogens. Most phytopathogenic microorganisms secrete an array of cell wall degrading enzymes (CWDEs) capable of depolymerizing the polysaccharides in the plant host wall. In response, plants have evolved a diverse battery of defence responses including protein inhibitors of these enzymes. These include inhibitors of pectin degrading enzymes such as polygalacturonases, pectinmethyl esterases and pectin lyases, and hemicellulose degrading enzymes such as endoxylanases and xyloglucan endoglucanases. The discovery of these plant inhibitors and the recent resolution of their three-dimensional structures, free or in complex with their target enzymes, provide new lines of evidence regarding their function and evolution in plant-pathogen interactions.
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Affiliation(s)
- Nathalie Juge
- Institut Méditerranéen de Recherche en Nutrition, Faculté des Sciences de St Jérôme, F-13397 Marseilles Cedex 20, France.
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Zhang C, Liu S, Zhou Y. Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function. Proteins 2006; 60:314-8. [PMID: 15981255 DOI: 10.1002/prot.20576] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We entered the CAPRI experiment during the middle of Round 4 and have submitted predictions for all 6 targets released since then. We used the following procedures for docking prediction: (1) the identification of possible binding region(s) of a target based on known biological information, (2) rigid-body sampling around the binding region(s) by using the docking program ZDOCK, (3) ranking of the sampled complex conformations by employing the DFIRE-based statistical energy function, (4) clustering based on pairwise root-mean-square distance and the DFIRE energy, and (5) manual inspection and relaxation of the side-chain conformations of the top-ranked structures by geometric constraint. Reasonable predictions were made for 4 of the 6 targets. The best fraction of native contacts within the top 10 models are 89.1% for Target 12, 54.3% for Target 13, 29.3% for Target 14, and 94.1% for Target 18. The origin of successes and failures is discussed. .
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Affiliation(s)
- Chi Zhang
- Howard Hughes Medical Institute Center for Single Molecule Biophysics, Department of Physiology and Biophysics, State University of New York at Buffalo, 14214, USA
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Inbar Y, Schneidman-Duhovny D, Halperin I, Oron A, Nussinov R, Wolfson HJ. Approaching the CAPRI challenge with an efficient geometry-based docking. Proteins 2006; 60:217-23. [PMID: 15981251 DOI: 10.1002/prot.20561] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The last 3 rounds (3-5) of CAPRI included a wide range of docking targets. Several targets were especially challenging, since they involved large-scale movements and symmetric rearrangement, while others were based on homology models. We have approached the targets with a variety of geometry-based docking algorithms that include rigid docking, symmetric docking, and flexible docking with symmetry constraints. For all but 1 docking target, we were able to submit at least 1 acceptable quality prediction. Here, we detail for each target the prediction methods used and the specific biological data employed, and supply a retrospective analysis of the results. We highlight the advantages of our techniques, which efficiently exploit the geometric shape complementarity properties of the interaction. These enable them to run only few minutes on a standard PC even for flexible docking, thus proving their scalability toward computational genomic scale experiments. We also outline the major required enhancements, such as the introduction of side-chain position refinement and the introduction of flexibility for both docking partners.
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Affiliation(s)
- Yuval Inbar
- School of Computer Science, Beverly and Raymond Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
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43
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Daily MD, Masica D, Sivasubramanian A, Somarouthu S, Gray JJ. CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock. Proteins 2006; 60:181-6. [PMID: 15981262 DOI: 10.1002/prot.20555] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
CAPRI Rounds 3, 4, and 5 are the first public test of the published RosettaDock algorithm. The targets cover a wide range of sizes and shapes. For most targets, published biological information indicated the region of the binding site on at least one docking partner. The RosettaDock algorithm produced high accuracy predictions for three targets, medium-accuracy predictions for two targets, and an acceptable prediction for one target. RosettaDock predicted all five targets with less than 450 residues to high or medium accuracy, but it predicted only one of seven targets with above 450 residues to acceptable accuracy. RosettaDock's high-accuracy predictions for small to moderately large targets reveal the predictive power and fidelity of the algorithm, especially the high-resolution refinement and scoring protocol. In addition, RosettaDock can predict complexes from at least one homology-modeled docking partner with comparable accuracy to unbound cases of similar size. Larger targets present a more intensive sampling problem, and some large targets present repulsive barriers to entering the binding site. Ongoing improvements to RosettaDock's low-resolution search may alleviate this problem. This first public test suggests that RosettaDock can be useful in a significant range of applications in biochemistry and cell biology.
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Affiliation(s)
- Michael D Daily
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
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Sørensen JF, Sibbesen O. Mapping of residues involved in the interaction between the Bacillus subtilis xylanase A and proteinaceous wheat xylanase inhibitors. Protein Eng Des Sel 2006; 19:205-10. [PMID: 16517552 DOI: 10.1093/protein/gzl002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Bacillus subtilis xylanase A was subjected to site-directed mutagenesis, aimed at changing the interaction with Triticum aestivum xylanase inhibitor, the only wheat endogenous proteinaceous xylanase inhibitor interacting with this xylanase. The published structure of Bacillus circulans XynA was used to target amino acids surrounding the active site cleft of B.subtilis XynA for mutation. Twenty-two residues were mutated, resulting in 62 different variants. The catalytic activity of active mutants ranged from 563 to 5635 XU/mg and the interaction with T.aestivum xylanase inhibitor showed a similar variation. The results indicate that T.aestivum xylanase inhibitor interacts with several amino acid residues surrounding the active site of the enzyme. Three different amino acid substitutions in one particular residue (D11) completely abolished the interaction between T.aestivum xylanase inhibitor and B.subtilis xylanase A.
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Affiliation(s)
- J F Sørensen
- Danisco, Edwin Rahrs Vej 38, DK-8220 Brabrand and Danisco, Langebrogade 1, DK-1001 Copenhagen C, Denmark.
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Krisana A, Rutchadaporn S, Jarupan G, Lily E, Sutipa T, Kanyawim K. Endo-1,4-beta-xylanase B from Aspergillus cf. niger BCC14405 isolated in Thailand: purification, characterization and gene isolation. BMB Rep 2005; 38:17-23. [PMID: 15715941 DOI: 10.5483/bmbrep.2005.38.1.017] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During the screening of xylanolytic enzymes from locally isolated fungi, one strain BCC14405, exhibited high enzyme activity with thermostability. This fugal strain was identified as Aspergillus cf. niger based on its morphological characteristics and internal transcribed spacer (ITS) sequences. An enzyme with xylanolytic activity from BCC14405 was later purified and characterized. It was found to have a molecular mass of ca. 21 kDa, an optimal pH of 5.0, and an optimal temperature of 55 degrees C. When tested using xylan from birchwood, it showed K(m) and V(max) values of 8.9 mg/ml and 11,100 U/mg, respectively. The enzyme was inhibited by CuSO(4) EDTA, and by FeSO(4) The homology of the 20-residue N-terminal protein sequence showed that the enzyme was an endo-1,4-beta-xylanase. The full-length gene encoding endo-1,4-beta-xylanase from BCC14405 was obtained by PCR amplification of its cDNA. The gene contained an open reading frame of 678 bp, encoding a 225 amino acid protein, which was identical to the endo-1,4-a-xylanase B previously identified in A. niger.
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Affiliation(s)
- Asano Krisana
- National Center for Genetic Engineering and Biotechnology,113 Thailand Science Park, Paholyothin Rd., Klong 1, Klong Luang, Pathumthani 12120, Thailand.
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Abstract
Transforming growth factor-beta is a pleiotropic growth factor that has enthralled many investigators for approximately two decades. In addition to many reports that have clarified the basic mechanism of transforming growth factor-beta signal transduction, numerous laboratories have published on the clinical implication/application of transforming growth factor-beta . To name a few, dysregulation of transforming growth factor-beta signaling plays a role in carcinogenesis, autoimmunity, angiogenesis, and wound healing. In this report, we will review these clinical implications of transforming growth factor-beta .
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Affiliation(s)
- Isaac Yi Kim
- Department of Urology, University of California at Irvine, Orange, CA 92868, USA
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Ma XH, Li CH, Shen LZ, Gong XQ, Chen WZ, Wang CX. Biologically enhanced sampling geometric docking and backbone flexibility treatment with multiconformational superposition. Proteins 2005; 60:319-23. [PMID: 15981260 DOI: 10.1002/prot.20577] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An efficient biologically enhanced sampling geometric docking method is presented based on the FTDock algorithm to predict the protein-protein binding modes. The active site data from different sources, such as biochemical and biophysical experiments or theoretical analyses of sequence data, can be incorporated in the rotation-translation scan. When discretizing a protein onto a 3-dimensional (3D) grid, a zero value is given to grid points outside a sphere centered on the geometric center of specified residues. In this way, docking solutions are biased toward modes where the interface region is inside the sphere. We also adopt a multiconformational superposition scheme to represent backbone flexibility in the proteins. When these procedures were applied to the targets of CAPRI, a larger number of hits and smaller ligand root-mean-square deviations (RMSDs) were obtained at the conformational search stage in all cases, and especially Target 19. With Target 18, only 1 near-native structure was retained by the biologically enhanced sampling geometric docking method, but this number increased to 53 and the least ligand RMSD decreased from 8.1 A to 2.9 A after performing multiconformational superposition. These results were obtained after the CAPRI prediction deadlines.
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Affiliation(s)
- Xiao Hui Ma
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, China
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48
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Smith GR, Fitzjohn PW, Page CS, Bates PA. Incorporation of flexibility into rigid-body docking: Applications in rounds 3-5 of CAPRI. Proteins 2005; 60:263-8. [PMID: 15981258 DOI: 10.1002/prot.20568] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We have submitted models for all 9 targets in Rounds 3-5 of CAPRI and have predicted at least 30% of the correct contacts for 4 of the targets and at least 10% of the correct contacts for another 4 targets. We have employed a variety of techniques but have had the greatest success by combining established rigid-body docking with a variety of initial conformations generated by molecular dynamics.
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Affiliation(s)
- Graham R Smith
- Biomolecular Modelling Laboratory, Cancer Research U.K. London Research Institute, Lincoln's Inn Fields Laboratories, London, United Kingdom
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Ben-Zeev E, Kowalsman N, Ben-Shimon A, Segal D, Atarot T, Noivirt O, Shay T, Eisenstein M. Docking to single-domain and multiple-domain proteins: Old and new challenges. Proteins 2005; 60:195-201. [PMID: 15981268 DOI: 10.1002/prot.20557] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The diverse selection of targets in the CAPRI experiments provides grounds for determining the limits of our rigid-body docking program MolFit, and for extending it. We find that the sensitivity of MolFit is high, enabling it to produce reasonably accurate docking solutions when the structures undergo moderate local conformation changes upon complex formation or when the docked molecules are modeled. Yet the ranks of these solutions are sometimes too low to meet the requirements of CAPRI assessment. This indicates that the selectivity of MolFit, which was optimized for docking of unbound X-ray structures, and which relies on the availability of external data from biochemical and bioinformatic sources, needs readjustment in order to meet the challenges presented by NMR or modeled structures. A different challenge is presented by large global conformation changes such as movements of domains. We show that such changes can be accommodated within the rigid-body approximation by employing rigid multibody multistage docking procedures. We also address the difficulty of ranking results from 2-body and multibody docking scans in cases in which there are no external data favoring one option over the other.
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Affiliation(s)
- E Ben-Zeev
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
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Durand A, Hughes R, Roussel A, Flatman R, Henrissat B, Juge N. Emergence of a subfamily of xylanase inhibitors within glycoside hydrolase family 18. FEBS J 2005; 272:1745-55. [PMID: 15794761 DOI: 10.1111/j.1742-4658.2005.04606.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The xylanase inhibitor protein I (XIP-I), recently identified in wheat, inhibits xylanases belonging to glycoside hydrolase families 10 (GH10) and 11 (GH11). Sequence and structural similarities indicate that XIP-I is related to chitinases of family GH18, despite its lack of enzymatic activity. Here we report the identification and biochemical characterization of a XIP-type inhibitor from rice. Despite its initial classification as a chitinase, the rice inhibitor does not exhibit chitinolytic activity but shows specificities towards fungal GH11 xylanases similar to that of its wheat counterpart. This, together, with an analysis of approximately 150 plant members of glycosidase family GH18 provides compelling evidence that xylanase inhibitors are largely represented in this family, and that this novel function has recently emerged based on a common scaffold. The plurifunctionality of GH18 members has major implications for genomic annotations and predicted gene function. This study provides new information which will lead to a better understanding of the biological significance of a number of GH18 'inactivated' chitinases.
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Affiliation(s)
- Anne Durand
- Institute of Food Research (IFR), Norwich, UK
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