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Long L, Lin Q, Wang J, Ding S. Microbial α-L-arabinofuranosidases: diversity, properties, and biotechnological applications. World J Microbiol Biotechnol 2024; 40:84. [PMID: 38294733 DOI: 10.1007/s11274-023-03882-z] [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: 11/12/2023] [Accepted: 12/28/2023] [Indexed: 02/01/2024]
Abstract
Arabinoxylans (AXs) are hemicellulosic polysaccharides consisting of a linear backbone of β-1,4-linked xylose residues branched by high content of α-L-arabinofuranosyl (Araf) residues along with other side-chain substituents, and are abundantly found in various agricultural crops especially cereals. The efficient bioconversion of AXs into monosaccharides, oligosaccharides and/or other chemicals depends on the synergism of main-chain enzymes and de-branching enzymes. Exo-α-L-arabinofuranosidases (ABFs) catalyze the hydrolysis of terminal non-reducing α-1,2-, α-1,3- or α-1,5- linked α-L-Araf residues from arabinose-substituted polysaccharides or oligosaccharides. ABFs are critically de-branching enzymes in bioconversion of agricultural biomass, and have received special attention due to their application potentials in biotechnological industries. In recent years, the researches on microbial ABFs have developed quickly in the aspects of the gene mining, properties of novel members, catalytic mechanisms, methodologies, and application technologies. In this review, we systematically summarize the latest advances in microbial ABFs, and discuss the future perspectives of the enzyme research.
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Affiliation(s)
- Liangkun Long
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, People's Republic of China.
- Jiangsu Province Key Laboratory of Green Biomass-Based Fuels and Chemicals, Nanjing, 210037, People's Republic of China.
| | - Qunying Lin
- Nanjing Institute for the Comprehensive Utilization of Wild Plants, China CO-OP, Nanjing, 211111, People's Republic of China
| | - Jing Wang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, People's Republic of China
| | - Shaojun Ding
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, People's Republic of China
- Jiangsu Province Key Laboratory of Green Biomass-Based Fuels and Chemicals, Nanjing, 210037, People's Republic of China
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Li G, Yuan Y, Jin B, Zhang Z, Murtaza B, Zhao H, Li X, Wang L, Xu Y. Feasibility insights into the application of Paenibacillus pabuli E1 in animal feed to eliminate non-starch polysaccharides. Front Microbiol 2023; 14:1205767. [PMID: 37608941 PMCID: PMC10440823 DOI: 10.3389/fmicb.2023.1205767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/25/2023] [Indexed: 08/24/2023] Open
Abstract
The goal of the research was to find alternative protein sources for animal farming that are efficient and cost-effective. The researchers focused on distillers dried grains with solubles (DDGS), a co-product of bioethanol production that is rich in protein but limited in its use as a feed ingredient due to its high non-starch polysaccharides (NSPs) content, particularly for monogastric animals. The analysis of the Paenibacillus pabuli E1 genome revealed the presence of 372 genes related to Carbohydrate-Active enzymes (CAZymes), with 98 of them associated with NSPs degrading enzymes that target cellulose, hemicellulose, and pectin. Additionally, although lignin is not an NSP, two lignin-degrading enzymes were also examined because the presence of lignin alongside NSPs can hinder the catalytic effect of enzymes on NSPs. To confirm the catalytic ability of the degrading enzymes, an in vitro enzyme activity assay was conducted. The results demonstrated that the endoglucanase activity reached 5.37 U/mL, while beta-glucosidase activity was 4.60 U/mL. The filter paper experiments did not detect any reducing sugars. The xylanase and beta-xylosidase activities were measured at 11.05 and 4.16 U/mL, respectively. Furthermore, the pectate lyase and pectin lyase activities were found to be 8.19 and 2.43 U/mL, respectively. The activities of laccase and MnP were determined as 1.87 and 4.30 U/mL, respectively. The researchers also investigated the effect of P. pabuli E1 on the degradation of NSPs through the solid-state fermentation of DDGS. After 240 h of fermentation, the results showed degradation rates of 11.86% for hemicellulose, 11.53% for cellulose, and 8.78% for lignin. Moreover, the crude protein (CP) content of DDGS increased from 26.59% to 30.59%. In conclusion, this study demonstrated that P. pabuli E1 possesses various potential NSPs degrading enzymes that can effectively eliminate NSPs in feed. This process improves the quality and availability of the feed, which is important for animal farming as it seeks alternative protein sources to replace traditional nutrients.
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Affiliation(s)
- Gen Li
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Yue Yuan
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China
| | - Bowen Jin
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Zhiqiang Zhang
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Bilal Murtaza
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Hong Zhao
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Xiaoyu Li
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Lili Wang
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Yongping Xu
- School of Bioengineering, Dalian University of Technology, Dalian, China
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Si Z, Cai Y, Zhao L, Han L, Wang F, Yang X, Gao X, Lu M, Liu W. Structure and function characterization of the α-L-arabinofuranosidase from the white-rot fungus Trametes hirsuta. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12561-w. [PMID: 37178306 DOI: 10.1007/s00253-023-12561-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023]
Abstract
α-L-Arabinofuranosidases (Abfs) play a crucial role in the degradation of hemicelluloses, especially arabinoxylans (AX). Most of the available characterized Abfs are from bacteria, while fungi, as natural decomposers, contain Abfs with little attention given. An arabinofuranosidase (ThAbf1), belonging to the glycoside hydrolase 51 (GH51) family, from the genome of the white-rot fungus Trametes hirsuta, was recombinantly expressed, characterized, and functionally determined. The general biochemical properties showed that the optimal conditions for ThAbf1 were pH 6.0 and 50°C. In substrate kinetics assays, ThAbf1 preferred small fragment arabinoxylo-oligosaccharides (AXOS) and could surprisingly hydrolyze di-substituted 23,33-di-L-arabinofuranosyl-xylotriose (A2,3XX). It also synergized with commercial xylanase (XYL) and increased the saccharification efficiency of arabinoxylan. The crystal structure of ThAbf1 indicated the presence of an adjacent cavity next to the catalytic pocket which led to the ability of ThAbf1 to degrade di-substituted AXOS. The narrow binding pocket prevents ThAbf1 from binding larger substrates. These findings have strengthened our understanding of the catalytic mechanism of GH51 family Abfs and provided a theoretical foundation for the development of more efficient and versatile Abfs to accelerate the degradation and biotransformation of hemicellulose in biomass. KEY POINTS: • ThAbf1 from Trametes hirsuta degraded di-substituted arabinoxylo-oligosaccharide. • ThAbf1 performed detailed biochemical characterization and kinetics. • ThAbf1 structure has been obtained to illustrate the substrate specificity.
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Affiliation(s)
- Zhenyuan Si
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, College of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Yang Cai
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, College of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Lang Zhao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, College of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Lu Han
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, College of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Feng Wang
- Simcere Pharmaceutical Group Limited, Nanjing, 210042, PR China
| | - Xiaobing Yang
- Biology and Medicine Department, Jiangsu Industrial Technology Research Institute, Nanjing, 210031, PR China
| | - Xiangdong Gao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, College of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, PR China.
| | - Meiling Lu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, College of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, PR China.
| | - Wei Liu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, College of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, PR China.
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The In Silico Characterization of Monocotyledonous α-l-Arabinofuranosidases on the Example of Maize. Life (Basel) 2023; 13:life13020266. [PMID: 36836625 PMCID: PMC9964162 DOI: 10.3390/life13020266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/26/2022] [Accepted: 01/14/2023] [Indexed: 01/20/2023] Open
Abstract
Plant α-l-arabinofuranosidases remove terminal arabinose from arabinose-containing substrates such as plant cell wall polysaccharides, including arabinoxylans, arabinogalactans, and arabinans. In plants, de-arabinosylation of cell wall polysaccharides accompanies different physiological processes such as fruit ripening and elongation growth. In this report, we address the diversity of plant α-l-arabinofuranosidases of the glycoside hydrolase (GH) family 51 through their phylogenetic analysis as well as their structural features. The CBM4-like domain at N-terminus was found to exist only in GH51 family proteins and was detected in almost 90% of plant sequences. This domain is similar to bacterial CBM4, but due to substitutions of key amino acid residues, it does not appear to be able to bind carbohydrates. Despite isoenzymes of GH51 being abundant, in particular in cereals, almost half of the GH51 proteins in Poales have a mutation of the acid/base residue in the catalytic site, making them potentially inactive. Open-source data on the transcription and translation of GH51 isoforms in maize were analyzed to discuss possible functions of individual isoenzymes. The results of homology modeling and molecular docking showed that the substrate binding site can accurately accommodate terminal arabinofuranose and that arabinoxylan is a more favorable ligand for all maize GH51 enzymes than arabinan.
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Leschonski KP, Kaasgaard SG, Spodsberg N, Krogh KBRM, Kabel MA. Two Subgroups within the GH43_36 α-l-Arabinofuranosidase Subfamily Hydrolyze Arabinosyl from Either Mono-or Disubstituted Xylosyl Units in Wheat Arabinoxylan. Int J Mol Sci 2022; 23:ijms232213790. [PMID: 36430284 PMCID: PMC9693073 DOI: 10.3390/ijms232213790] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
Fungal arabinofuranosidases (ABFs) catalyze the hydrolysis of arabinosyl substituents (Ara) and are key in the interplay with other glycosyl hydrolases to saccharify arabinoxylans (AXs). Most characterized ABFs belong to GH51 and GH62 and are known to hydrolyze the linkage of α-(1→2)-Ara and α-(1→3)-Ara in monosubstituted xylosyl residues (Xyl) (ABF-m2,3). Nevertheless, in AX a substantial number of Xyls have two Aras (i.e., disubstituted), which are unaffected by ABFs from GH51 and GH62. To date, only two fungal enzymes have been identified (in GH43_36) that specifically release the α-(1→3)-Ara from disubstituted Xyls (ABF-d3). In our research, phylogenetic analysis of available GH43_36 sequences revealed two major clades (GH43_36a and GH43_36b) with an expected substrate specificity difference. The characterized fungal ABF-d3 enzymes aligned with GH43_36a, including the GH43_36 from Humicola insolens (HiABF43_36a). Hereto, the first fungal GH43_36b (from Talaromyces pinophilus) was cloned, purified, and characterized (TpABF43_36b). Surprisingly, TpABF43_36b was found to be active as ABF-m2,3, albeit with a relatively low rate compared to other ABFs tested, and showed minor xylanase activity. Novel specificities were also discovered for the HiABF43_36a, as it also released α-(1→2)-Ara from a disubstitution on the non-reducing end of an arabinoxylooligosaccharide (AXOS), and it was active to a lesser extent as an ABF-m2,3 towards AXOS when the Ara was on the second xylosyl from the non-reducing end. In essence, this work adds new insights into the biorefinery of agricultural residues.
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Affiliation(s)
| | | | | | | | - Mirjam A. Kabel
- Laboratory of Food Chemistry, Wageningen University, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
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Kouzounis D, Sun P, Bakx EJ, Schols HA, Kabel MA. Strategy to identify reduced arabinoxylo-oligosaccharides by HILIC-MSn. Carbohydr Polym 2022; 289:119415. [DOI: 10.1016/j.carbpol.2022.119415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 01/03/2023]
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Baudrexl M, Fida T, Berk B, Schwarz WH, Zverlov VV, Groll M, Liebl W. Biochemical and Structural Characterization of Thermostable GH159 Glycoside Hydrolases Exhibiting α-L-Arabinofuranosidase Activity. Front Mol Biosci 2022; 9:907439. [PMID: 35847984 PMCID: PMC9278983 DOI: 10.3389/fmolb.2022.907439] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Functional, biochemical, and preliminary structural properties are reported for three glycoside hydrolases of the recently described glycoside hydrolase (GH) family 159. The genes were cloned from the genomic sequences of different Caldicellulosiruptor strains. This study extends the spectrum of functions of GH159 enzymes. The only activity previously reported for GH159 was hydrolytic activity on β-galactofuranosides. Activity screening using a set of para-nitrophenyl (pNP) glycosides suggested additional arabinosidase activity on substrates with arabinosyl residues, which has not been previously reported for members of GH159. Even though the thermophilic enzymes investigated—Cs_Gaf159A, Ch_Gaf159A, and Ck_Gaf159A—cleaved pNP-α-l-arabinofuranoside, they were only weakly active on arabinogalactan, and they did not cleave arabinose from arabinan, arabinoxylan, or gum arabic. However, the enzymes were able to hydrolyze the α-1,3-linkage in different arabinoxylan-derived oligosaccharides (AXOS) with arabinosylated xylose at the non-reducing end (A3X, A2,3XX), suggesting their role in the intracellular hydrolysis of oligosaccharides. Crystallization and structural analysis of the apo form of one of the Caldicellulosiruptor enzymes, Ch_Gaf159A, enabled the elucidation of the first 3D structure of a GH159 member. This work revealed a five-bladed β-propeller structure for GH159 enzymes. The 3D structure and its substrate-binding pocket also provides an explanation at the molecular level for the observed exo-activity of the enzyme. Furthermore, the structural data enabled the prediction of the catalytic amino acids. This was supported by the complete inactivation by mutation of residues D19, D142, and E190 of Ch_Gaf159A.
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Affiliation(s)
- Melanie Baudrexl
- Chair of Microbiology, Technical University of Munich, Freising, Germany
| | - Tarik Fida
- Chair of Microbiology, Technical University of Munich, Freising, Germany
| | - Berkay Berk
- Chair of Microbiology, Technical University of Munich, Freising, Germany
| | | | - Vladimir V. Zverlov
- Chair of Microbiology, Technical University of Munich, Freising, Germany
- Institute of Molecular Genetics, Russian Academy of Science, Moscow, Russia
| | - Michael Groll
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Garching, Germany
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, Freising, Germany
- *Correspondence: Wolfgang Liebl,
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Villa-Rivera MG, Cano-Camacho H, López-Romero E, Zavala-Páramo MG. The Role of Arabinogalactan Type II Degradation in Plant-Microbe Interactions. Front Microbiol 2021; 12:730543. [PMID: 34512607 PMCID: PMC8424115 DOI: 10.3389/fmicb.2021.730543] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/04/2021] [Indexed: 11/13/2022] Open
Abstract
Arabinogalactans (AGs) are structural polysaccharides of the plant cell wall. A small proportion of the AGs are associated with hemicellulose and pectin. Furthermore, AGs are associated with proteins forming the so-called arabinogalactan proteins (AGPs), which can be found in the plant cell wall or attached through a glycosylphosphatidylinositol (GPI) anchor to the plasma membrane. AGPs are a family of highly glycosylated proteins grouped with cell wall proteins rich in hydroxyproline. These glycoproteins have important and diverse functions in plants, such as growth, cellular differentiation, signaling, and microbe-plant interactions, and several reports suggest that carbohydrate components are crucial for AGP functions. In beneficial plant-microbe interactions, AGPs attract symbiotic species of fungi or bacteria, promote the development of infectious structures and the colonization of root tips, and furthermore, these interactions can activate plant defense mechanisms. On the other hand, plants secrete and accumulate AGPs at infection sites, creating cross-links with pectin. As part of the plant cell wall degradation machinery, beneficial and pathogenic fungi and bacteria can produce the enzymes necessary for the complete depolymerization of AGs including endo-β-(1,3), β-(1,4) and β-(1,6)-galactanases, β-(1,3/1,6) galactanases, α-L-arabinofuranosidases, β-L-arabinopyranosidases, and β-D-glucuronidases. These hydrolytic enzymes are secreted during plant-pathogen interactions and could have implications for the function of AGPs. It has been proposed that AGPs could prevent infection by pathogenic microorganisms because their degradation products generated by hydrolytic enzymes of pathogens function as damage-associated molecular patterns (DAMPs) eliciting the plant defense response. In this review, we describe the structure and function of AGs and AGPs as components of the plant cell wall. Additionally, we describe the set of enzymes secreted by microorganisms to degrade AGs from AGPs and its possible implication for plant-microbe interactions.
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Affiliation(s)
- Maria Guadalupe Villa-Rivera
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico
| | - Horacio Cano-Camacho
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Mexico
| | - Everardo López-Romero
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Guanajuato, Mexico
| | - María Guadalupe Zavala-Páramo
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Mexico
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Vuong TV, Master ER. Enzymatic upgrading of heteroxylans for added-value chemicals and polymers. Curr Opin Biotechnol 2021; 73:51-60. [PMID: 34311175 DOI: 10.1016/j.copbio.2021.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/27/2021] [Accepted: 07/02/2021] [Indexed: 02/06/2023]
Abstract
Xylan is one of the most abundant, natural polysaccharides, and much recent interest focuses on upgrading heteroxylan to make use of its unique structures and chemistries. Significant progress has been made in the discovery and application of novel enzymes for debranching and modifying heteroxylans. Debranching enzymes include acetylxylan esterases, α-l-arabinofuranosidases and α-dglucuronidases that release side groups from the xylan backbone to recover both biochemicals and less substituted xylans for polymer applications in food packaging or drug delivery systems. Besides esterases and hydrolases, many oxidoreductases including carbohydrate oxidases, lytic polysaccharide monooxygenases, laccases and peroxidases have been also applied to alter different types of xylans for improved physical and chemical properties. This review will highlight the recent discovery and application of enzymes for upgrading xylans for use as added-value chemicals and in functional polymers.
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Affiliation(s)
- Thu V Vuong
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Emma R Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada; Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland.
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Liu Y, Vanderhaeghen S, Feiler W, Angelov A, Baudrexl M, Zverlov V, Liebl W. Characterization of Two α-l-Arabinofuranosidases from Acetivibrio mesophilus and Their Synergistic Effect in Degradation of Arabinose-Containing Substrates. Microorganisms 2021; 9:microorganisms9071467. [PMID: 34361903 PMCID: PMC8307384 DOI: 10.3390/microorganisms9071467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 11/16/2022] Open
Abstract
Arabinofuranosidases are important accessory enzymes involved in the degradation of arabinose-containing poly- and oligosaccharides. Two arabinofuranosidases from the recently described novel anaerobic cellulolytic bacterium Acetivibrio mesophilus, designated AmAraf51 and AmAraf43, were heterologously expressed in Escherichia coli and biochemically characterized. AmAraf51 not only removed arabinose moieties at O-3, O-2 and terminal O-5 positions of arabinose-containing oligosaccharides, but also exhibited exo-β-xylosidase side activity. In comparison, AmAraf43 preferably cleaved 1,3-linkages from arabinosyl disubstitutions. AmAraf51 and AmAraf43 demonstrated maximum activity at 70 °C and 57 °C, respectively. Judging from the genetic context and substrate specificity, AmAraf51 may decompose internalized arabino/xylo-oligosaccharides. The embedding of the AmAraf43 gene between genes for several putative xylanolytic enzymes, along with its enzymatic properties suggests that AmAraf43 cleaves arabinose decorations from heteroxylans extracellularly. The enzymes revealed completely converse activity profiles towards arabinan/arabinoxylan: AmAraf51 displayed strong activity on arabinan, while AmAraf43 prefers arabinoxylan. AmAraf51 dramatically stimulated the saccharification level of wheat arabinoxylan (WAX-RS) and sugar beet arabinan when administered along with xylanase M_Xyn10 or arabinanase PpAbn43, respectively. For WAX-RS degradation, the yield of arabinose and xylose was boosted 13.77-fold and 4.96-fold, respectively. The bifunctional activity, thermostability and high catalytic efficiency make AmAraf51 an interesting candidate for industrial applications.
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Yan R, Wang W, Vuong TV, Xiu Y, Skarina T, Di Leo R, Gatenholm P, Toriz G, Tenkanen M, Stogios PJ, Master ER. Structural characterization of the family GH115 α-glucuronidase from Amphibacillus xylanus yields insight into its coordinated action with α-arabinofuranosidases. N Biotechnol 2021; 62:49-56. [PMID: 33486119 DOI: 10.1016/j.nbt.2021.01.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 01/11/2021] [Accepted: 01/16/2021] [Indexed: 01/01/2023]
Abstract
The coordinated action of carbohydrate-active enzymes has mainly been evaluated for the purpose of complete saccharification of plant biomass (lignocellulose) to sugars. By contrast, the coordinated action of accessory hemicellulases on xylan debranching and recovery is less well characterized. Here, the activity of two family GH115 α-glucuronidases (SdeAgu115A from Saccharophagus degradans, and AxyAgu115A from Amphibacillus xylanus) on spruce arabinoglucuronoxylan (AGX) was evaluated in combination with an α-arabinofuranosidase from families GH51 (AniAbf51A, aka E-AFASE from Aspergillus niger) and GH62 (SthAbf62A from Streptomyces thermoviolaceus). The α-arabinofuranosidases boosted (methyl)-glucuronic acid release by SdeAgu115A by approximately 50 % and 30 %, respectively. The impact of the α-arabinofuranosidases on AxyAgu115A activity was comparatively low, motivating its structural characterization. The crystal structure of AxyAgu115A revealed increased length and flexibility of the active site loop compared to SdeAgu115A. This structural difference could explain the ability of AxyAgu115A to accommodate more highly substituted arabinoglucuronoxylan, and inform enzyme selections for improved AGX recovery and use.
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Affiliation(s)
- Ruoyu Yan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | - Weijun Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | - Thu V Vuong
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | - Yang Xiu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | - Rosa Di Leo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | - Paul Gatenholm
- Department of Chemistry and Chemical Engineering, Wallenberg Wood Science Center and Biopolymer Technology, Chalmers University of Technology, Kemivägen 4, Gothenburg, 412 96, Sweden
| | - Guillermo Toriz
- Department of Wood, Cellulose and Paper Research, University of Guadalajara, Guadalajara, 44100, Mexico
| | - Maija Tenkanen
- Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 27, Helsinki, 00014, Finland
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | - Emma R Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada; Department of Bioproducts and Biosystems, Aalto University, FI-00076, Aalto, Kemistintie 1, Espoo, Finland.
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McGregor NGS, Turkenburg JP, Mørkeberg Krogh KBR, Nielsen JE, Artola M, Stubbs KA, Overkleeft HS, Davies GJ. Structure of a GH51 α-L-arabinofuranosidase from Meripilus giganteus: conserved substrate recognition from bacteria to fungi. Acta Crystallogr D Struct Biol 2020; 76:1124-1133. [PMID: 33135683 PMCID: PMC7604909 DOI: 10.1107/s205979832001253x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/14/2020] [Indexed: 03/17/2023] Open
Abstract
α-L-Arabinofuranosidases from glycoside hydrolase family 51 use a stereochemically retaining hydrolytic mechanism to liberate nonreducing terminal α-L-arabinofuranose residues from plant polysaccharides such as arabinoxylan and arabinan. To date, more than ten fungal GH51 α-L-arabinofuranosidases have been functionally characterized, yet no structure of a fungal GH51 enzyme has been solved. In contrast, seven bacterial GH51 enzyme structures, with low sequence similarity to the fungal GH51 enzymes, have been determined. Here, the crystallization and structural characterization of MgGH51, an industrially relevant GH51 α-L-arabinofuranosidase cloned from Meripilus giganteus, are reported. Three crystal forms were grown in different crystallization conditions. The unliganded structure was solved using sulfur SAD data collected from a single crystal using the I23 in vacuo diffraction beamline at Diamond Light Source. Crystal soaks with arabinose, 1,4-dideoxy-1,4-imino-L-arabinitol and two cyclophellitol-derived arabinose mimics reveal a conserved catalytic site and conformational itinerary between fungal and bacterial GH51 α-L-arabinofuranosidases.
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Affiliation(s)
- Nicholas G. S. McGregor
- York Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Johan P. Turkenburg
- York Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, United Kingdom
| | | | - Jens Erik Nielsen
- Protein Biochemistry and Stability, Novozymes A/S, Krogshøjvej 36, 2880 Bagsvaerd, Denmark
| | - Marta Artola
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Keith A. Stubbs
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Herman S. Overkleeft
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Gideon J. Davies
- York Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, United Kingdom
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Mroueh M, Aruanno M, Borne R, de Philip P, Fierobe HP, Tardif C, Pagès S. The xyl- doc gene cluster of Ruminiclostridium cellulolyticum encodes GH43- and GH62-α-l-arabinofuranosidases with complementary modes of action. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:144. [PMID: 31198441 PMCID: PMC6556953 DOI: 10.1186/s13068-019-1483-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 06/03/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND The α-l-arabinofuranosidases (α-l-ABFs) are exoenzymes involved in the hydrolysis of α-l-arabinosyl linkages in plant cell wall polysaccharides. They play a crucial role in the degradation of arabinoxylan and arabinan and they are used in many biotechnological applications. Analysis of the genome of R. cellulolyticum showed that putative cellulosomal α-l-ABFs are exclusively encoded by the xyl-doc gene cluster, a large 32-kb gene cluster. Indeed, among the 14 Xyl-Doc enzymes encoded by this gene cluster, 6 are predicted to be α-l-ABFs belonging to the CAZyme families GH43 and GH62. RESULTS The biochemical characterization of these six Xyl-Doc enzymes revealed that four of them are α-l-ABFs. GH4316-1229 (RcAbf43A) which belongs to the subfamily 16 of the GH43, encoded by the gene at locus Ccel_1229, has a low specific activity on natural substrates and can cleave off arabinose decorations located at arabinoxylan chain extremities. GH4310-1233 (RcAbf43Ad2,3), the product of the gene at locus Ccel_1233, belonging to subfamily 10 of the GH43, can convert the double arabinose decorations present on arabinoxylan into single O2- or O3-linked decorations with high velocity (k cat = 16.6 ± 0.6 s-1). This enzyme acts in synergy with GH62-1234 (RcAbf62Am2,3), the product of the gene at locus Ccel_1234, a GH62 α-l-ABF which hydrolyzes α-(1 → 3) or α-(1 → 2)-arabinosyl linkages present on polysaccharides and arabinoxylooligosaccharides monodecorated. Finally, a bifunctional enzyme, GH62-CE6-1240 (RcAbf62Bm2,3Axe6), encoded by the gene at locus Ccel_1240, which contains a GH62-α-l-ABF module and a carbohydrate esterase (CE6) module, catalyzes deacylation of plant cell wall polymers and cleavage of arabinosyl mono-substitutions. These enzymes are also active on arabinan, a component of the type I rhamnogalacturonan, showing their involvement in pectin degradation. CONCLUSION Arabinofuranosyl decorations on arabinoxylan and pectin strongly inhibit the action of xylan-degrading enzymes and pectinases. α-l-ABFs encoded by the xyl-doc gene cluster of R. cellulolyticum can remove all the decorations present in the backbone of arabinoxylan and arabinan, act synergistically, and, thus, play a crucial role in the degradation of plant cell wall polysaccharides.
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Affiliation(s)
- Mohamed Mroueh
- Aix Marseille Université, CNRS, LCB UMR7283, IMM-CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Marion Aruanno
- Institute of Microbiology, Lausanne University Hospital, Lausanne, Switzerland
| | - Romain Borne
- Aix Marseille Université, CNRS, LCB UMR7283, IMM-CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Pascale de Philip
- Aix Marseille Université, CNRS, LCB UMR7283, IMM-CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Henri-Pierre Fierobe
- Aix Marseille Université, CNRS, LCB UMR7283, IMM-CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Chantal Tardif
- Aix Marseille Université, CNRS, LCB UMR7283, IMM-CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Sandrine Pagès
- Aix Marseille Université, CNRS, LCB UMR7283, IMM-CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
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Sarch C, Suzuki H, Master ER, Wang W. Kinetics and regioselectivity of three GH62 α-L-arabinofuranosidases from plant pathogenic fungi. Biochim Biophys Acta Gen Subj 2019; 1863:1070-1078. [DOI: 10.1016/j.bbagen.2019.03.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 03/07/2019] [Accepted: 03/27/2019] [Indexed: 01/21/2023]
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15
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Highly thermostable GH51 α-arabinofuranosidase from Hungateiclostridium clariflavum DSM 19732. Appl Microbiol Biotechnol 2019; 103:3783-3793. [DOI: 10.1007/s00253-019-09753-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 02/18/2019] [Accepted: 03/06/2019] [Indexed: 10/27/2022]
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16
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Xin D, Chen X, Wen P, Zhang J. Insight into the role of α-arabinofuranosidase in biomass hydrolysis: cellulose digestibility and inhibition by xylooligomers. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:64. [PMID: 30949240 PMCID: PMC6429694 DOI: 10.1186/s13068-019-1412-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 03/15/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND α-l-Arabinofuranosidase (ARA), a debranching enzyme that can remove arabinose substituents from arabinoxylan and arabinoxylooligomers (AXOS), promotes the hydrolysis of the arabinoxylan fraction of biomass; however, the impact of ARA on the overall digestibility of cellulose is controversial. In this study, we investigated the effects of the addition of ARA on cellulase hydrolytic action. RESULTS We found that approximately 15% of the xylan was converted into AXOS during the hydrolysis of aqueous ammonia-pretreated corn stover and that this AXOS fraction was approximately 12% substituted with arabinose. The addition of ARA removes a portion of the arabinose decoration, but the resulting less-substituted AXOS inhibited cellulase action much more effectively; showing an increase of 45.7%. Kinetic experiments revealed that AXOS with a lower degree of arabinose substitution showed stronger affinity for the active site of cellobiohydrolase, which could be the mechanism of increased inhibition. CONCLUSIONS Our findings strongly suggest that the ratio of ARA and other xylanases should be carefully selected to avoid the strong inhibition caused by the less-substituted AXOS during the hydrolysis of arabinoxylan-containing biomass. This study advances our understanding of the inhibitory mechanism of xylooligomers and provides critical new insights into the relationship of ARA addition and cellulose digestibility.
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Affiliation(s)
- Donglin Xin
- College of Forestry, Northwest A&F University, 3 Taicheng Road, Yangling, 712100 Shaanxi China
| | - Xiang Chen
- College of Forestry, Northwest A&F University, 3 Taicheng Road, Yangling, 712100 Shaanxi China
| | - Peiyao Wen
- College of Forestry, Northwest A&F University, 3 Taicheng Road, Yangling, 712100 Shaanxi China
| | - Junhua Zhang
- College of Forestry, Northwest A&F University, 3 Taicheng Road, Yangling, 712100 Shaanxi China
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Ruminiclostridium josui Abf62A-Axe6A: A tri-functional xylanolytic enzyme exhibiting α-l-arabinofuranosidase, endoxylanase, and acetylxylan esterase activities. Enzyme Microb Technol 2018; 117:1-8. [DOI: 10.1016/j.enzmictec.2018.05.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 05/25/2018] [Accepted: 05/25/2018] [Indexed: 12/30/2022]
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18
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Maurício da Fonseca MJ, Jurak E, Kataja K, Master ER, Berrin JG, Stals I, Desmet T, Van Landschoot A, Briers Y. Analysis of the substrate specificity of α-L-arabinofuranosidases by DNA sequencer-aided fluorophore-assisted carbohydrate electrophoresis. Appl Microbiol Biotechnol 2018; 102:10091-10102. [PMID: 30267127 DOI: 10.1007/s00253-018-9389-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/04/2018] [Accepted: 09/09/2018] [Indexed: 01/11/2023]
Abstract
Carbohydrate-active enzyme discovery is often not accompanied by experimental validation, demonstrating the need for techniques to analyze substrate specificities of carbohydrate-active enzymes in an efficient manner. DNA sequencer-aided fluorophore-assisted carbohydrate electrophoresis (DSA-FACE) is utmost appropriate for the analysis of glycoside hydrolases that have complex substrate specificities. DSA-FACE is demonstrated here to be a highly convenient method for the precise identification of the specificity of different α-L-arabinofuranosidases for (arabino)xylo-oligosaccharides ((A)XOS). The method was validated with two α-L-arabinofuranosidases (EC 3.2.1.55) with well-known specificity, specifically a GH62 α-L-arabinofuranosidase from Aspergillus nidulans (AnAbf62A-m2,3) and a GH43 α-L-arabinofuranosidase from Bifidobacterium adolescentis (BaAXH-d3). Subsequently, application of DSA-FACE revealed the AXOS specificity of two α-L-arabinofuranosidases with previously unknown AXOS specificities. PaAbf62A, a GH62 α-L-arabinofuranosidase from Podospora anserina strain S mat+, was shown to target the O-2 and the O-3 arabinofuranosyl monomers as side chain from mono-substituted β-D-xylosyl residues, whereas a GH43 α-L-arabinofuranosidase from a metagenomic sample (AGphAbf43) only removes an arabinofuranosyl monomer from the smallest AXOS tested. DSA-FACE excels ionic chromatography in terms of detection limit for (A)XOS (picomolar sensitivity), hands-on and analysis time, and the analysis of the degree of polymerization and binding site of the arabinofuranosyl substituent.
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Affiliation(s)
| | - Edita Jurak
- Department of Biotechnology and Chemical Technology, Aalto University, Espoo, Finland
| | - Kim Kataja
- Department of Biotechnology and Chemical Technology, Aalto University, Espoo, Finland
| | - Emma R Master
- Department of Biotechnology and Chemical Technology, Aalto University, Espoo, Finland
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jean-Guy Berrin
- INRA, Aix Marseille Université, UMR1163 BBF, Marseille, France
| | - Ingeborg Stals
- Department of Materials, Textiles and Chemical Engineering, Ghent University, Ghent, Belgium
| | - Tom Desmet
- Department of Biotechnology, Ghent University, Ghent, Belgium
| | | | - Yves Briers
- Department of Biotechnology, Ghent University, Ghent, Belgium.
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19
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dos Santos CR, de Giuseppe PO, de Souza FHM, Zanphorlin LM, Domingues MN, Pirolla RAS, Honorato RV, Tonoli CCC, de Morais MAB, de Matos Martins VP, Fonseca LM, Büchli F, de Oliveira PSL, Gozzo FC, Murakami MT. The mechanism by which a distinguishing arabinofuranosidase can cope with internal di-substitutions in arabinoxylans. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:223. [PMID: 30127853 PMCID: PMC6087011 DOI: 10.1186/s13068-018-1212-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/23/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND Arabinoxylan is an abundant polysaccharide in industrially relevant biomasses such as sugarcane, corn stover and grasses. However, the arabinofuranosyl di-substitutions that decorate the xylan backbone are recalcitrant to most known arabinofuranosidases (Abfs). RESULTS In this work, we identified a novel GH51 Abf (XacAbf51) that forms trimers in solution and can cope efficiently with both mono- and di-substitutions at terminal or internal xylopyranosyl units of arabinoxylan. Using mass spectrometry, the kinetic parameters of the hydrolysis of 33-α-l-arabinofuranosyl-xylotetraose and 23,33-di-α-l-arabinofuranosyl-xylotetraose by XacAbf51 were determined, demonstrating the capacity of this enzyme to cleave arabinofuranosyl linkages of internal mono- and di-substituted xylopyranosyl units. Complementation studies of fungal enzyme cocktails with XacAbf51 revealed an increase of up to 20% in the release of reducing sugars from pretreated sugarcane bagasse, showing the biotechnological potential of a generalist GH51 in biomass saccharification. To elucidate the structural basis for the recognition of internal di-substitutions, the crystal structure of XacAbf51 was determined unveiling the existence of a pocket strategically arranged near to the - 1 subsite that can accommodate a second arabinofuranosyl decoration, a feature not described for any other GH51 Abf structurally characterized so far. CONCLUSIONS In summary, this study reports the first kinetic characterization of internal di-substitution release by a GH51 Abf, provides the structural basis for this activity and reveals a promising candidate for industrial processes involving plant cell wall depolymerization.
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Affiliation(s)
- Camila Ramos dos Santos
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Priscila Oliveira de Giuseppe
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Flávio Henrique Moreira de Souza
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Letícia Maria Zanphorlin
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Mariane Noronha Domingues
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Renan Augusto Siqueira Pirolla
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Rodrigo Vargas Honorato
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Celisa Caldana Costa Tonoli
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Mariana Abrahão Bueno de Morais
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Vanesa Peixoto de Matos Martins
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Lucas Miranda Fonseca
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Fernanda Büchli
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Paulo Sergio Lopes de Oliveira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Fábio Cesar Gozzo
- Dalton Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, Campinas, Sao Paulo 13083-861 Brazil
| | - Mário Tyago Murakami
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
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20
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Vos AM, Jurak E, de Gijsel P, Ohm RA, Henrissat B, Lugones LG, Kabel MA, Wösten HAB. Production of α-1,3-L-arabinofuranosidase active on substituted xylan does not improve compost degradation by Agaricus bisporus. PLoS One 2018; 13:e0201090. [PMID: 30040824 PMCID: PMC6057652 DOI: 10.1371/journal.pone.0201090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 07/09/2018] [Indexed: 12/02/2022] Open
Abstract
Agaricus bisporus consumes carbohydrates contained in wheat straw based compost used for commercial mushroom production. Double substituted arabinoxylan is part of the ~40% of the compost polysaccharides that are not degraded by A. bisporus during its growth and development. Genes encoding α-1,3-l-arabinofuranosidase (AXHd3) enzymes that act on xylosyl residues doubly substituted with arabinosyl residues are absent in this mushroom forming fungus. Here, the AXHd3 encoding hgh43 gene of Humicola insolens was expressed in A. bisporus with the aim to improve its substrate utilization and mushroom yield. Transformants secreted active AXHd3 in compost as shown by the degradation of double substituted arabinoxylan oligomers in an in vitro assay. However, carbohydrate composition and degree of arabinosyl substitution of arabinoxylans were not affected in compost possibly due to inaccessibility of the doubly substituted xylosyl residues.
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Affiliation(s)
- Aurin M. Vos
- Microbiology, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Edita Jurak
- Laboratory of Food Chemistry, Wageningen University and Research, Wageningen, The Netherlands
| | - Peter de Gijsel
- Laboratory of Food Chemistry, Wageningen University and Research, Wageningen, The Netherlands
| | - Robin A. Ohm
- Microbiology, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Luis G. Lugones
- Microbiology, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Mirjam A. Kabel
- Laboratory of Food Chemistry, Wageningen University and Research, Wageningen, The Netherlands
| | - Han A. B. Wösten
- Microbiology, Department of Biology, Utrecht University, Utrecht, The Netherlands
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Mechelke M, Herlet J, Benz JP, Schwarz WH, Zverlov VV, Liebl W, Kornberger P. HPAEC-PAD for oligosaccharide analysis—novel insights into analyte sensitivity and response stability. Anal Bioanal Chem 2017; 409:7169-7181. [DOI: 10.1007/s00216-017-0678-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/21/2017] [Accepted: 09/26/2017] [Indexed: 01/08/2023]
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Wang W, Andric N, Sarch C, Silva BT, Tenkanen M, Master ER. Constructing arabinofuranosidases for dual arabinoxylan debranching activity. Biotechnol Bioeng 2017; 115:41-49. [PMID: 28868788 DOI: 10.1002/bit.26445] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 08/22/2017] [Accepted: 08/28/2017] [Indexed: 11/08/2022]
Abstract
Enzymatic conversion of arabinoxylan requires α-L-arabinofuranosidases able to remove α-L-arabinofuranosyl residues (α-L-Araf) from both mono- and double-substituted D-xylopyranosyl residues (Xylp) in xylan (i.e., AXH-m and AXH-d activity). Herein, SthAbf62A (a family GH62 α-L-arabinofuranosidase with AXH-m activity) and BadAbf43A (a family GH43 α-L-arabinofuranosidase with AXH-d3 activity), were fused to create SthAbf62A_BadAbf43A and BadAbf43A_SthAbf62A. Both fusion enzymes displayed dual AXH-m,d and synergistic activity toward native, highly branched wheat arabinoxylan (WAX). When using a customized arabinoxylan substrate comprising mainly α-(1 → 3)-L-Araf and α-(1 → 2)-L-Araf substituents attached to disubstituted Xylp (d-2,3-WAX), the specific activity of the fusion enzymes was twice that of enzymes added as separate proteins. Moreover, the SthAbf62A_BadAbf43A fusion removed 83% of all α-L-Araf from WAX after a 20 hr treatment. 1 H NMR analyses further revealed differences in SthAbf62A_BadAbf43 rate of removal of specific α-L-Araf substituents from WAX, where 9.4 times higher activity was observed toward d-α-(1 → 3)-L-Araf compared to m-α-(1 → 3)-L-Araf positions.
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Affiliation(s)
- Weijun Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Nikola Andric
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Cody Sarch
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Bruno T Silva
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Maija Tenkanen
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Emma R Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.,Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
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23
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Mechelke M, Koeck DE, Broeker J, Roessler B, Krabichler F, Schwarz WH, Zverlov VV, Liebl W. Characterization of the arabinoxylan-degrading machinery of the thermophilic bacterium Herbinix hemicellulosilytica-Six new xylanases, three arabinofuranosidases and one xylosidase. J Biotechnol 2017; 257:122-130. [PMID: 28450260 DOI: 10.1016/j.jbiotec.2017.04.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 04/20/2017] [Accepted: 04/20/2017] [Indexed: 10/19/2022]
Abstract
Herbinix hemicellulosilytica is a newly isolated, gram-positive, anaerobic bacterium with extensive hemicellulose-degrading capabilities obtained from a thermophilic biogas reactor. In order to exploit its potential as a source for new industrial arabinoxylan-degrading enzymes, six new thermophilic xylanases, four from glycoside hydrolase family 10 (GH10) and two from GH11, three arabinofuranosidases (1x GH43, 2x GH51) and one β-xylosidase (GH43) were selected. The recombinantly produced enzymes were purified and characterized. All enzymes were active on different xylan-based polysaccharides and most of them showed temperature-vs-activity profiles with maxima around 55-65°C. HPAEC-PAD analysis of the hydrolysates of wheat arabinoxylan and of various purified xylooligosaccharides (XOS) and arabinoxylooligosaccharides (AXOS) was used to investigate their substrate and product specificities: among the GH10 xylanases, XynB showed a different product pattern when hydrolysing AXOS compared to XynA, XynC, and XynD. None of the GH11 xylanases was able to degrade any of the tested AXOS. All three arabinofuranosidases, ArfA, ArfB and ArfC, were classified as type AXH-m,d enzymes. None of the arabinofuranosidases was able to degrade the double-arabinosylated xylooligosaccharides XA2+3XX. β-Xylosidase XylA (GH43) was able to degrade unsubstituted XOS, but showed limited activity to degrade AXOS.
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Affiliation(s)
- M Mechelke
- Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - D E Koeck
- Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - J Broeker
- Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - B Roessler
- Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - F Krabichler
- Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - W H Schwarz
- Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - V V Zverlov
- Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany; Institute of Molecular Genetics, Russian Academy of Science, Kurchatov Sq. 2, 123182 Moscow Russia
| | - W Liebl
- Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany.
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Towards enzymatic breakdown of complex plant xylan structures: State of the art. Biotechnol Adv 2016; 34:1260-1274. [PMID: 27620948 DOI: 10.1016/j.biotechadv.2016.09.001] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/02/2016] [Accepted: 09/07/2016] [Indexed: 02/07/2023]
Abstract
Significant progress over the past few years has been achieved in the enzymology of microbial degradation and saccharification of plant xylan, after cellulose being the most abundant natural renewable polysaccharide. Several new types of xylan depolymerizing and debranching enzymes have been described in microorganisms. Despite the increasing variety of known glycoside hydrolases and carbohydrate esterases, some xylan structures still appear quite recalcitrant. This review focuses on the mode of action of different types of depolymerizing endoxylanases and their cooperation with β-xylosidase and accessory enzymes in breakdown of complex highly branched xylan structures. Emphasis is placed on the enzymatic hydrolysis of alkali-extracted deesterified polysaccharide as well as acetylated xylan isolated from plant cell walls under non-alkaline conditions. It is also shown how the combination of selected endoxylanases and debranching enzymes can determine the nature of prebiotic xylooligosaccharides or lead to complete hydrolysis of the polysaccharide. The article also highlights the possibility for discovery of novel xylanolytic enzymes, construction of multifunctional chimeric enzymes and xylanosomes in parallel with increasing knowledge on the fine structure of the polysaccharide.
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