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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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Tundo S, Mandalà G, Sella L, Favaron F, Bedre R, Kalunke RM. Xylanase Inhibitors: Defense Players in Plant Immunity with Implications in Agro-Industrial Processing. Int J Mol Sci 2022; 23:ijms232314994. [PMID: 36499321 PMCID: PMC9739030 DOI: 10.3390/ijms232314994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022] Open
Abstract
Xylanase inhibitors (XIs) are plant cell wall proteins largely distributed in monocots that inhibit the hemicellulose degrading activity of microbial xylanases. XIs have been classified into three classes with different structures and inhibition specificities, namely Triticum aestivum xylanase inhibitors (TAXI), xylanase inhibitor proteins (XIP), and thaumatin-like xylanase inhibitors (TLXI). Their involvement in plant defense has been established by several reports. Additionally, these inhibitors have considerable economic relevance because they interfere with the activity of xylanases applied in several agro-industrial processes. Previous reviews highlighted the structural and biochemical properties of XIs and hypothesized their role in plant defense. Here, we aimed to update the information on the genomic organization of XI encoding genes, the inhibition properties of XIs against microbial xylanases, and the structural properties of xylanase-XI interaction. We also deepened the knowledge of XI regulation mechanisms in planta and their involvement in plant defense. Finally, we reported the recently studied strategies to reduce the negative impact of XIs in agro-industrial processes and mentioned their allergenicity potential.
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Affiliation(s)
- Silvio Tundo
- Department of Land, Environment, Agriculture, and Forestry (TESAF), University of Padova, 35020 Legnaro, Italy
- Correspondence:
| | - Giulia Mandalà
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Luca Sella
- Department of Land, Environment, Agriculture, and Forestry (TESAF), University of Padova, 35020 Legnaro, Italy
| | - Francesco Favaron
- Department of Land, Environment, Agriculture, and Forestry (TESAF), University of Padova, 35020 Legnaro, Italy
| | - Renesh Bedre
- Texas A&M AgriLife Research and Extension Center, Texas A&M University System, Weslaco, TX 78596, USA
| | - Raviraj M. Kalunke
- Donald Danforth Plant Science Center, 975 N Warson Rd, 7 Olivette, St. Louis, MO 63132, USA
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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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Yang G, Peng S, Wang T, Gao X, Li D, Li M, Chen S, Xu Z. Walnut ethylene response factor JrERF2-2 interact with JrWRKY7 to regulate the GSTs in plant drought tolerance. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 228:112945. [PMID: 34737155 DOI: 10.1016/j.ecoenv.2021.112945] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/04/2021] [Accepted: 10/21/2021] [Indexed: 06/13/2023]
Abstract
Juglans regia is a world-famous woody oil plant, whose yield and quality are affected by drought stress. Ethylene-responsive factors (ERFs) play vital role in plant stress response. In current study, to comprehend the walnut molecular mechanism of drought stress response, an ERF transcription factor was clarified from J. regia (JrERF2-2) and its potential function mechanism to drought was clarified. The results showed that JrERF2-2 could be induced significantly by drought. The transgenic Arabidopsis over-expression of JrERF2-2 displayed enhanced growth, antioxidant enzyme vitalities, reactive oxygen species scavenging and proline produce under drought stress. Especial the glutathione-S-transferase (GST) activity and most GST genes' transcription were elevated obviously. Yeast one-hybrid (Y1H) and co-transient expression (CTE) methods revealed that JrERF2-2 could recognize JrGST4, JrGST6, JrGST7, JrGST8, and JrGSTF8 by binding to GCC-box, and recognize JrGST11, JrGST12, and JrGSTN2 by binding to DRE motif. Meanwhile, the binding activity was strengthened by drought stress. Moreover, JrERF2-2 could interact with JrWRKY7 to promote plant drought tolerance; JrWRKY7 could also distinguish JrGST4, JrGST7, JrGST8, JrGST11, JrGST12, and JrGSTF8 via binding to W-Box motif. These results suggested that JrERF2-2 could effectively improve plant drought tolerance through interacting with JrWRKY7 to control the expression of GSTs. JrERF2-2 is a useful plant representative gene for drought response in molecular breeding.
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Affiliation(s)
- Guiyan Yang
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100 Shaanxi, China; Key Laboratory of Economic Plant Resources Development and Utilization in Shaanxi Province, College of Forestry, Northwest A & F University, Yangling, 712100 Shaanxi, China
| | - Shaobing Peng
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100 Shaanxi, China
| | - Tianyu Wang
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100 Shaanxi, China; Key Laboratory of Economic Plant Resources Development and Utilization in Shaanxi Province, College of Forestry, Northwest A & F University, Yangling, 712100 Shaanxi, China
| | - Xiangqian Gao
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100 Shaanxi, China; Key Laboratory of Economic Plant Resources Development and Utilization in Shaanxi Province, College of Forestry, Northwest A & F University, Yangling, 712100 Shaanxi, China
| | - Dapei Li
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100 Shaanxi, China; Key Laboratory of Economic Plant Resources Development and Utilization in Shaanxi Province, College of Forestry, Northwest A & F University, Yangling, 712100 Shaanxi, China
| | - Mengge Li
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100 Shaanxi, China; Key Laboratory of Economic Plant Resources Development and Utilization in Shaanxi Province, College of Forestry, Northwest A & F University, Yangling, 712100 Shaanxi, China
| | - Shuwen Chen
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100 Shaanxi, China; Key Laboratory of Economic Plant Resources Development and Utilization in Shaanxi Province, College of Forestry, Northwest A & F University, Yangling, 712100 Shaanxi, China
| | - Zhenggang Xu
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100 Shaanxi, China.
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Liu F, Xu WF, Mu H, Lv ZR, Peng J, Guo C, Zhou HM, Ye ZM, Li XH. Inhibition kinetics of acetosyringone on xylanase in hydrolysis of hemicellulose. Biosci Biotechnol Biochem 2020; 84:1788-1798. [PMID: 32448038 DOI: 10.1080/09168451.2020.1767499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Many phenolic compounds, derived from lignin during the pretreatment of lignocellulosic biomass, could obviously inhibit the activity of cellulolytic and hemicellulolytic enzymes. Acetosyringone (AS) is one of the phenolic compounds produced from lignin degradation. In this study, we investigated the inhibitory effects of AS on xylanase activity through kinetic experiments. The results showed that AS could obviously inhibit the activity of xylanase in a reversible and noncompetitive binding manner (up to 50% activity loss). Inhibitory kinetics and constants of xylanase on AS were conducted by the HCH-1 model (β = 0.0090 ± 0.0009 mM-1). Furthermore, intrinsic and 8-anilino-1-naphthalenesulfonic (ANS)-binding fluorescence results showed that the tertiary structure of AS-mediated xylanase was altered. These findings provide new insights into the role of AS in xylanase activity. Our results also suggest that AS was an inhibitor of xylanase and targeting AS was a potential strategy to increase xylose production.
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Affiliation(s)
- Feng Liu
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University , Guangdong, China.,Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University , Zhejiang, China
| | - Wen-Fei Xu
- Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University , Zhejiang, China
| | - Hang Mu
- Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University , Zhejiang, China
| | - Zhi-Rong Lv
- Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University , Zhejiang, China
| | - Jie Peng
- Women's Hospital, School of Medicine, Zhejiang University , Hangzhou, China
| | - Chao Guo
- Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University , Zhejiang, China
| | - Hai-Meng Zhou
- Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University , Zhejiang, China
| | - Zhuo-Ming Ye
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University , Guangdong, China
| | - Xu-Hui Li
- Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University , Zhejiang, China
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Liu MQ, Li JY, Rehman AU, Xu X, Gu ZJ, Wu RC. Laboratory Evolution of GH11 Endoxylanase Through DNA Shuffling: Effects of Distal Residue Substitution on Catalytic Activity and Active Site Architecture. Front Bioeng Biotechnol 2019; 7:350. [PMID: 31824938 PMCID: PMC6883096 DOI: 10.3389/fbioe.2019.00350] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 11/06/2019] [Indexed: 11/15/2022] Open
Abstract
Endoxylanase with high specific activity, thermostability, and broad pH adaptability is in huge demand. The mutant library of GH11 endoxylanase was constructed via DNA shuffling by using the catalytic domain of Bacillus amyloliquefaciens xylanase A (BaxA) and Thermomonospora fusca TF xylanase A (TfxA) as parents. A total of 2,250 colonies were collected and 756 of them were sequenced. Three novel mutants (DS153: N29S, DS241: S31R and DS428: I51V) were identified and characterized in detail. For these mutants, three residues of BaxA were substituted by the corresponding one of TfxA_CD. The specific activity of DS153, DS241, and DS428 in the optimal condition was 4.54, 4.35, and 3.9 times compared with the recombinant BaxA (reBaxA), respectively. The optimum temperature of the three mutants was 50°C. The optimum pH for DS153, DS241, and DS428 was 6.0, 7.0, and 6.0, respectively. The catalytic efficiency of DS153, DS241, and DS428 enhanced as well, while their sensitivity to recombinant rice xylanase inhibitor (RIXI) was lower than that of reBaxA. Three mutants have identical hydrolytic function as reBaxA, which released xylobiose–xylopentaose from oat spelt, birchwood, and beechwood xylan. Furthermore, molecular dynamics simulations were performed on BaxA and three mutants to explore the precise impact of gain-of-function on xylanase activity. The tertiary structure of BaxA was not altered under the substitution of distal residues (N29S, S31R, and I51V); it induced slightly changes in active site architecture. The distal impact rescued the BaxA from native conformation (“closed state”) through weakening interactions between “gate” residues (R112, N35 in DS241 and DS428; W9, P116 in DS153) and active site residues (E78, E172, Y69, and Y80), favoring conformations with an “open state” and providing improved activity. The current findings would provide a better and more in-depth understanding of how distal single residue substitution improved the catalytic activity of xylanase at the atomic level.
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Affiliation(s)
- Ming-Qi Liu
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Jia-Yi Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ashfaq Ur Rehman
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Xu
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Zhu-Jun Gu
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Ruo-Chen Wu
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
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