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Akram F, Fatima T, Ibrar R, Shabbir I, Shah FI, Haq IU. Trends in the development and current perspective of thermostable bacterial hemicellulases with their industrial endeavors: A review. Int J Biol Macromol 2024; 265:130993. [PMID: 38508567 DOI: 10.1016/j.ijbiomac.2024.130993] [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: 07/15/2023] [Revised: 03/12/2024] [Accepted: 03/17/2024] [Indexed: 03/22/2024]
Abstract
Hemicellulases are enzymes that hydrolyze hemicelluloses, common polysaccharides in nature. Thermophilic hemicellulases, derived from microbial strains, are extensively studied as natural biofuel sources due to the complex structure of hemicelluloses. Recent research aims to elucidate the catalytic principles, mechanisms and specificity of hemicellulases through investigations into their high-temperature stability and structural features, which have applications in biotechnology and industry. This review article targets to serve as a comprehensive resource, highlighting the significant progress in the field and emphasizing the vital role of thermophilic hemicellulases in eco-friendly catalysis. The primary goal is to improve the reliability of hemicellulase enzymes obtained from thermophilic bacterial strains. Additionally, with their ability to break down lignocellulosic materials, hemicellulases hold immense potential for biofuel production. Despite their potential, the commercial viability is hindered by their high enzyme costs, necessitating the development of efficient bioprocesses involving waste pretreatment with microbial consortia to overcome this challenge.
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Affiliation(s)
- Fatima Akram
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan.
| | - Taseer Fatima
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Ramesha Ibrar
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Ifrah Shabbir
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | | | - Ikram Ul Haq
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan; Pakistan Academy of Sciences, Islamabad, Pakistan
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2
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Paesani C, Lammers TCGL, Sciarini LS, Moiraghi M, Pérez GT, Fabi JP. Effect of chemical, thermal, and enzymatic processing of wheat bran on the solubilization, technological and biological properties of non-starch polysaccharides. Carbohydr Polym 2024; 328:121747. [PMID: 38220355 DOI: 10.1016/j.carbpol.2023.121747] [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: 10/04/2023] [Revised: 12/20/2023] [Accepted: 12/26/2023] [Indexed: 01/16/2024]
Abstract
Wheat bran is a low-cost by-product with significant nutritional value, but it is primarily utilized in animal feed applications. This study sought to investigate chemical methodologies for modifying the wheat bran's structure, enhancing non-starch polysaccharides solubility in water, and assessing alterations in functional and biological attributes. Chemical modifications were conducted under aqueous, alkaline, acid, and oxidizing conditions. Parameters such as yield, monosaccharides, arabinoxylans, β-glucan and phenolic content, molecular weight, functional properties, and prebiotic in vitro capacity were examined. The samples exhibited higher yields than the control, particularly in alkaline and acidic extractions. Notably, all soluble polysaccharide fractions (SPF) displayed a reduced molecular weight (<25KDa). β-glucan contents were raised in alkaline and acid extractions compared to the control, despite only in alkaline extraction were observed increase in arabinoxylans, confirmed by enzymatic-driven linkage analyses. Phenolic compounds and their antioxidant activities were low across all SPF. The samples showed heightened solubility, minimal foaming, and reduced water absorption properties. An alkaline extraction demonstrated a potential high prebiotic effect. Most samples showed positive relative growth and prebiotic activity for Lactobacillus and Bifidobacterium. This study suggests that an alkaline extraction of wheat by-product could enhance its value by increasing β-glucan content, arabinoxylans release, and prebiotic potential.
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Affiliation(s)
- Candela Paesani
- University of São Paulo, Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Av. Prof. Lineu Prestes 580, São Paulo, SP, Brazil; ICYTA (Instituto de Ciencia y Tecnología de los alimentos Córdoba), UNC-CONICET, Av. Filloy s/n, Cuidad Universitaria, Córdoba, Argentina.
| | - Tamy C G L Lammers
- University of São Paulo, Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Av. Prof. Lineu Prestes 580, São Paulo, SP, Brazil
| | - Lorena S Sciarini
- ICYTA (Instituto de Ciencia y Tecnología de los alimentos Córdoba), UNC-CONICET, Av. Filloy s/n, Cuidad Universitaria, Córdoba, Argentina.
| | - Malena Moiraghi
- ICYTA (Instituto de Ciencia y Tecnología de los alimentos Córdoba), UNC-CONICET, Av. Filloy s/n, Cuidad Universitaria, Córdoba, Argentina.
| | - Gabriela T Pérez
- ICYTA (Instituto de Ciencia y Tecnología de los alimentos Córdoba), UNC-CONICET, Av. Filloy s/n, Cuidad Universitaria, Córdoba, Argentina.
| | - João Paulo Fabi
- University of São Paulo, Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Av. Prof. Lineu Prestes 580, São Paulo, SP, Brazil; Food Research Center (FoRC), CEPID-FAPESP, Research Innovation and Dissemination Centers, São Paulo Research Foundation, Rua do Lago, 250, São Paulo, SP, Brazil; Food and Nutrition Research Center (NAPAN), University of São Paulo, São Paulo, SP, Brazil.
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3
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Martins M, Dos Santos AM, da Costa CHS, Canner SW, Chungyoun M, Gray JJ, Skaf MS, Ostermeier M, Goldbeck R. Thermostability Enhancement of GH 62 α-l-Arabinofuranosidase by Directed Evolution and Rational Design. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4225-4236. [PMID: 38354215 DOI: 10.1021/acs.jafc.3c08019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
GH 62 arabinofuranosidases are known for their excellent specificity for arabinoxylan of agroindustrial residues and their synergism with endoxylanases and other hemicellulases. However, the low thermostability of some GH enzymes hampers potential industrial applications. Protein engineering research highly desires mutations that can enhance thermostability. Therefore, we employed directed evolution using one round of error-prone PCR and site-saturation mutagenesis for thermostability enhancement of GH 62 arabinofuranosidase from Aspergillus fumigatus. Single mutants with enhanced thermostability showed significant ΔΔG changes (<-2.5 kcal/mol) and improvements in perplexity scores from evolutionary scale modeling inverse folding. The best mutant, G205K, increased the melting temperature by 5 °C and the energy of denaturation by 41.3%. We discussed the functional mechanisms for improved stability. Analyzing the adjustments in α-helices, β-sheets, and loops resulting from point mutations, we have obtained significant knowledge regarding the potential impacts on protein stability, folding, and overall structural integrity.
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Affiliation(s)
- Manoela Martins
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, 3400 N Charles Street, Baltimore, Maryland 21218, United States
- Department of Food Engineering, State University of Campinas, Monteiro Lobato, 80, Cidade Universitária, Campinas, São Paulo 13083-862, Brazil
| | - Alberto M Dos Santos
- Department of Chemistry, State University of Campinas, 336, R. Josué de Castro, 126-Cidade Universitária, Campinas, São Paulo 13083-861, Brazil
| | - Clauber H S da Costa
- Department of Chemistry, State University of Campinas, 336, R. Josué de Castro, 126-Cidade Universitária, Campinas, São Paulo 13083-861, Brazil
| | - Samuel W Canner
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, 3400 N Charles Street, Baltimore, Maryland 21218, United States
| | - Michael Chungyoun
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, 3400 N Charles Street, Baltimore, Maryland 21218, United States
| | - Jeffrey J Gray
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, 3400 N Charles Street, Baltimore, Maryland 21218, United States
| | - Munir S Skaf
- Department of Chemistry, State University of Campinas, 336, R. Josué de Castro, 126-Cidade Universitária, Campinas, São Paulo 13083-861, Brazil
| | - Marc Ostermeier
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, 3400 N Charles Street, Baltimore, Maryland 21218, United States
| | - Rosana Goldbeck
- Department of Food Engineering, State University of Campinas, Monteiro Lobato, 80, Cidade Universitária, Campinas, São Paulo 13083-862, Brazil
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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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Wen J, Miao T, Basit A, Li Q, Tan S, Chen S, Ablimit N, Wang H, Wang Y, Zheng F, Jiang W. Highly efficient synergistic activity of an α-L-arabinofuranosidase for degradation of arabinoxylan in barley/wheat. Front Microbiol 2023; 14:1230738. [PMID: 38029111 PMCID: PMC10655120 DOI: 10.3389/fmicb.2023.1230738] [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: 05/29/2023] [Accepted: 09/13/2023] [Indexed: 12/01/2023] Open
Abstract
Here, an α-L-arabinofuranosidase (termed TtAbf62) from Thermothelomyces thermophilus is described, which efficiently removes arabinofuranosyl side chains and facilitates arabinoxylan digestion. The specific activity of TtAbf62 (179.07 U/mg) toward wheat arabinoxylan was the highest among all characterized glycoside hydrolase family 62 enzymes. TtAbf62 in combination with endoxylanase and β-xylosidase strongly promoted hydrolysis of barley and wheat. The release of reducing sugars was significantly higher for the three-enzyme combination relative to the sum of single-enzyme treatments: 85.71% for barley hydrolysis and 33.33% for wheat hydrolysis. HPLC analysis showed that TtAbf62 acted selectively on monosubstituted (C-2 or C-3) xylopyranosyl residues rather than double-substituted residues. Site-directed mutagenesis and interactional analyses of enzyme-substrate binding structures revealed the catalytic sites of TtAbf62 formed different polysaccharide-catalytic binding modes with arabinoxylo-oligosaccharides. Our findings demonstrate a "multienzyme cocktail" formed by TtAbf62 with other hydrolases strongly improves the efficiency of hemicellulose conversion and increases biomass hydrolysis through synergistic interaction.
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Affiliation(s)
- Jiaqi Wen
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ting Miao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Abdul Basit
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
- Department of Microbiology, University of Jhang, Jhang, Punjab, Pakistan
| | - Qunhong Li
- Little Tiger Biotechnology Company Limited, Hangzhou, Zhejiang, China
| | - Shenglin Tan
- Little Tiger Biotechnology Company Limited, Hangzhou, Zhejiang, China
| | - Shuqing Chen
- Little Tiger Biotechnology Company Limited, Hangzhou, Zhejiang, China
| | - Nuraliya Ablimit
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Hui Wang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yan Wang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Fengzhen Zheng
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou, China
| | - Wei Jiang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
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Tõlgo M, Hegnar OA, Larsbrink J, Vilaplana F, Eijsink VGH, Olsson L. Enzymatic debranching is a key determinant of the xylan-degrading activity of family AA9 lytic polysaccharide monooxygenases. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:2. [PMID: 36604763 PMCID: PMC9814446 DOI: 10.1186/s13068-022-02255-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/26/2022] [Indexed: 01/07/2023]
Abstract
BACKGROUND Previous studies have revealed that some Auxiliary Activity family 9 (AA9) lytic polysaccharide monooxygenases (LPMOs) oxidize and degrade certain types of xylans when incubated with mixtures of xylan and cellulose. Here, we demonstrate that the xylanolytic activities of two xylan-active LPMOs, TtLPMO9E and TtLPMO9G from Thermothielavioides terrestris, strongly depend on the presence of xylan substitutions. RESULTS Using mixtures of phosphoric acid-swollen cellulose (PASC) and wheat arabinoxylan (WAX), we show that removal of arabinosyl substitutions with a GH62 arabinofuranosidase resulted in better adsorption of xylan to cellulose, and enabled LPMO-catalyzed cleavage of this xylan. Furthermore, experiments with mixtures of PASC and arabinoglucuronoxylan from spruce showed that debranching of xylan with the GH62 arabinofuranosidase and a GH115 glucuronidase promoted LPMO activity. Analyses of mixtures with PASC and (non-arabinosylated) beechwood glucuronoxylan showed that GH115 action promoted LPMO activity also on this xylan. Remarkably, when WAX was incubated with Avicel instead of PASC in the presence of the GH62, both xylan and cellulose degradation by the LPMO9 were impaired, showing that the formation of cellulose-xylan complexes and their susceptibility to LPMO action also depend on the properties of the cellulose. These debranching effects not only relate to modulation of the cellulose-xylan interaction, which influences the conformation and rigidity of the xylan, but likely also affect the LPMO-xylan interaction, because debranching changes the architecture of the xylan surface. CONCLUSIONS Our results shed new light on xylanolytic LPMO9 activity and on the functional interplay and possible synergies between the members of complex lignocellulolytic enzyme cocktails. These findings will be relevant for the development of future lignocellulolytic cocktails and biomaterials.
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Affiliation(s)
- Monika Tõlgo
- grid.5371.00000 0001 0775 6028Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden ,grid.5371.00000 0001 0775 6028Wallenberg Wood Science Centre, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Olav A. Hegnar
- grid.19477.3c0000 0004 0607 975XFaculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Johan Larsbrink
- grid.5371.00000 0001 0775 6028Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden ,grid.5371.00000 0001 0775 6028Wallenberg Wood Science Centre, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Francisco Vilaplana
- grid.5037.10000000121581746Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, 106 91 Stockholm, Sweden ,grid.5037.10000000121581746Wallenberg Wood Science Centre, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden
| | - Vincent G. H. Eijsink
- grid.19477.3c0000 0004 0607 975XFaculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Lisbeth Olsson
- grid.5371.00000 0001 0775 6028Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden ,grid.5371.00000 0001 0775 6028Wallenberg Wood Science Centre, Chalmers University of Technology, 412 96 Gothenburg, Sweden
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Martins M, Tramontina R, Squina FM, Dinamarco TM, Goldbeck R. Synergism for xylo-oligosaccharides, ρ-coumaric and ferulic acid production, and thermostability modulation of GH 62 α-l-arabinofuranosidase. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Garrido MM, Piccinni FE, Landoni M, Peña MJ, Topalian J, Couto A, Wirth SA, Urbanowicz BR, Campos E. Insights into the xylan degradation system of Cellulomonas sp. B6: biochemical characterization of rCsXyn10A and rCsAbf62A. Appl Microbiol Biotechnol 2022; 106:5035-5049. [PMID: 35799069 DOI: 10.1007/s00253-022-12061-3] [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: 04/28/2022] [Revised: 06/21/2022] [Accepted: 06/26/2022] [Indexed: 11/29/2022]
Abstract
Valorization of the hemicellulose fraction of plant biomass is crucial for the sustainability of lignocellulosic biorefineries. The Cellulomonas genus comprises Gram-positive Actinobacteria that degrade cellulose and other polysaccharides by secreting a complex array of enzymes. In this work, we studied the specificity and synergy of two enzymes, CsXyn10A and CsAbf62A, which were identified as highly abundant in the extracellular proteome of Cellulomonas sp. B6 when grown on wheat bran. To explore their potential for bioprocessing, the recombinant enzymes were expressed and their activities were thoroughly characterized. rCsXyn10A is a GH10 endo-xylanase (EC 3.2.1.8), active across a broad pH range (5 to 9), at temperatures up to 55 °C. rCsAbf62A is an α-L-arabinofuranosidase (ABF) (EC 3.2.1.55) that specifically removes α-1,2 and α-1,3-L-arabinosyl substituents from arabino-xylo-oligosaccharides (AXOS), xylan, and arabinan backbones, but it cannot act on double-substituted residues. It also has activity on pNPA. No differences were observed regarding activity when CsAbf62A was expressed with its appended CBM13 module or only the catalytic domain. The amount of xylobiose released from either wheat arabinoxylan or arabino-xylo-oligosaccharides increased significantly when rCsXyn10A was supplemented with rCsAbf62A, indicating that the removal of arabinosyl residues by rCsAbf62A improved rCsXyn10A accessibility to β-1,4-xylose linkages, but no synergism was observed in the deconstruction of wheat bran. These results contribute to designing tailor-made, substrate-specific, enzymatic cocktails for xylan valorization. KEY POINTS: • rCsAbf62A removes α-1,2 and α-1,3-L-arabinosyl substituents from arabino-xylo-oligosaccharides, xylan, and arabinan backbones. • The appended CBM13 of rCsAbf62A did not affect the specific activity of the enzyme. • Supplementation of rCsXyn10A with rCsAbf62A improves the degradation of AXOS and xylan.
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Affiliation(s)
- Mercedes María Garrido
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA)- CONICET, Los Reseros y Nicolás Repetto S/N (1686), Hurlingham, Buenos Aires, Argentina.,Laboratorio de Agrobiotecnología, DFBMC- FCEN and Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA) CONICET- Universidad de Buenos Aires (UBA), Pab. II, Ciudad Universitaria, C1428EG, Buenos Aires, Argentina
| | - Florencia Elizabeth Piccinni
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA)- CONICET, Los Reseros y Nicolás Repetto S/N (1686), Hurlingham, Buenos Aires, Argentina.,Laboratorio de Agrobiotecnología, DFBMC- FCEN and Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA) CONICET- Universidad de Buenos Aires (UBA), Pab. II, Ciudad Universitaria, C1428EG, Buenos Aires, Argentina
| | - Malena Landoni
- Centro de Investigación en Hidratos de Carbono (CIHIDECAR)- CONICET, Departamento de Química Orgánica, FCEN- Universidad de Buenos Aires (UBA), Pab. II, Ciudad Universitaria, C1428EG, Buenos Aires, Argentina
| | - María Jesús Peña
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, USA
| | - Juliana Topalian
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA)- CONICET, Los Reseros y Nicolás Repetto S/N (1686), Hurlingham, Buenos Aires, Argentina
| | - Alicia Couto
- Centro de Investigación en Hidratos de Carbono (CIHIDECAR)- CONICET, Departamento de Química Orgánica, FCEN- Universidad de Buenos Aires (UBA), Pab. II, Ciudad Universitaria, C1428EG, Buenos Aires, Argentina
| | - Sonia Alejandra Wirth
- Laboratorio de Agrobiotecnología, DFBMC- FCEN and Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA) CONICET- Universidad de Buenos Aires (UBA), Pab. II, Ciudad Universitaria, C1428EG, Buenos Aires, Argentina
| | - Breeanna Rae Urbanowicz
- Department of Biochemistry and Molecular Biology, University of Georgia, 315 Riverbend Road, Athens, GA, USA
| | - Eleonora Campos
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA)- CONICET, Los Reseros y Nicolás Repetto S/N (1686), Hurlingham, Buenos Aires, Argentina.
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9
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Li X, Dilokpimol A, Kabel MA, de Vries RP. Fungal xylanolytic enzymes: Diversity and applications. BIORESOURCE TECHNOLOGY 2022; 344:126290. [PMID: 34748977 DOI: 10.1016/j.biortech.2021.126290] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 05/26/2023]
Abstract
As important polysaccharide degraders in nature, fungi can diversify their extensive set of carbohydrate-active enzymes to survive in ecological habitats of various composition. Among these enzymes, xylanolytic ones can efficiently and sustainably degrade xylans into (fermentable) monosaccharides to produce valuable chemicals or fuels from, for example relevant for upgrading agro-food industrial side streams. Moreover, xylanolytic enzymes are being used in various industrial applications beyond biomass saccharification, e.g. food, animal feed, biofuel, pulp and paper. As a reference for researchers working in related areas, this review summarized the current knowledge on substrate specificity of xylanolytic enzymes from different families of the Carbohydrate-Active enZyme database. Additionally, the diversity of enzyme sets in fungi were discussed by comparing the number of genes encoding xylanolytic enzymes in selected fungal genomes. Finally, to support bio-economy, the current applications of fungal xylanolytic enzymes in industry were reviewed.
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Affiliation(s)
- Xinxin Li
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Adiphol Dilokpimol
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Mirjam A Kabel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
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Long L, Sun L, Liu Z, Lin Q, Wang J, Ding S. Functional characterization of a GH62 family α-L-arabinofuranosidase from Eupenicillium parvum suitable for monosaccharification of corncob arabinoxylan in combination with key enzymes. Enzyme Microb Technol 2021; 154:109965. [PMID: 34933174 DOI: 10.1016/j.enzmictec.2021.109965] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/20/2021] [Accepted: 12/06/2021] [Indexed: 11/30/2022]
Abstract
Corncob rich in arabinoxylan is an important raw material widely used in bio-refinery. Complete saccharification of arabinoxylan depends on the synergism of different enzymes including α-L-arabinofuranosidase (ABF). This study aimed to investigate the functional characteristics of a new ABF EpABF62A belonging to glycoside hydrolase (GH) 62 family from the fungus Eupenicillium parvum, and to explore its potential in the saccharification of corncob arabinoxylan. The recombinant EpABF62A showed high activity against wheat arabinoxylan and rye arabinoxylan, with the optimal temperature of 55 °C and pH of 4.5. The protein contains an N-terminal cellulose-binding domain family 1 (CBM_1) domain, and displayed a 59.5% absorption rate to phosphoric acid swollen cellulose. Regioselectivity analysis indicated that the enzyme selectively removed α-1,2 or α-1,3 linked arabinofuranosyl residues on mono-substituted xylose residues on arabinoxylan. Corncob arabinoxylans (CAX1 or CAX2) with different (low or high) branching degrees were extracted from the raw material by alkaline hydrogen peroxide pretreatment and graded ethanol precipitation. Single EpABF62A removed 69.5% or 67.1% arabinose from CAX1 or CAX2, respectively. EpABF62A combined with a GH10 xylanase, a GH43 β-D-xylosidase and a GH67 α-glucuronidase released 75.0% or 64.5% xylose from CAX1 or CAX2, respectively. The addition of the four hemicellulases enhanced the saccharification the solid fraction of the pretreated corncob by the commercial cellulase Cellic® CTec2, and the conversion ratios of glucose, xylose and arabinose were up to 94.0%, 91.8% and 82.6%, respectively.
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Affiliation(s)
- Liangkun Long
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, Nanjing 210037, China
| | - Lu Sun
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Zhen Liu
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Qunying Lin
- Nanjing Institute for the Comprehensive Utilization of Wild Plants, Nanjing 211111, China
| | - Jing Wang
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Shaojun Ding
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, Nanjing 210037, China.
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11
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Identification of difructose dianhydride I synthase/hydrolase from an oral bacterium establishes a novel glycoside hydrolase family. J Biol Chem 2021; 297:101324. [PMID: 34688653 PMCID: PMC8605356 DOI: 10.1016/j.jbc.2021.101324] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/07/2021] [Accepted: 10/07/2021] [Indexed: 11/30/2022] Open
Abstract
Fructooligosaccharides and their anhydrides are widely used as health-promoting foods and prebiotics. Various enzymes acting on β-D-fructofuranosyl linkages of natural fructan polymers have been used to produce functional compounds. However, enzymes that hydrolyze and form α-D-fructofuranosyl linkages have been less studied. Here, we identified the BBDE_2040 gene product from Bifidobacterium dentium (α-D-fructofuranosidase and difructose dianhydride I synthase/hydrolase from Bifidobacterium dentium [αFFase1]) as an enzyme with α-D-fructofuranosidase and α-D-arabinofuranosidase activities and an anomer-retaining manner. αFFase1 is not homologous with any known enzymes, suggesting that it is a member of a novel glycoside hydrolase family. When caramelized fructose sugar was incubated with αFFase1, conversions of β-D-Frup-(2→1)-α-D-Fruf to α-D-Fruf-1,2′:2,1′-β-D-Frup (diheterolevulosan II) and β-D-Fruf-(2→1)-α-D-Fruf (inulobiose) to α-D-Fruf-1,2′:2,1′-β-D-Fruf (difructose dianhydride I [DFA I]) were observed. The reaction equilibrium between inulobiose and DFA I was biased toward the latter (1:9) to promote the intramolecular dehydrating condensation reaction. Thus, we named this enzyme DFA I synthase/hydrolase. The crystal structures of αFFase1 in complex with β-D-Fruf and β-D-Araf were determined at the resolutions of up to 1.76 Å. Modeling of a DFA I molecule in the active site and mutational analysis also identified critical residues for catalysis and substrate binding. The hexameric structure of αFFase1 revealed the connection of the catalytic pocket to a large internal cavity via a channel. Molecular dynamics analysis implied stable binding of DFA I and inulobiose to the active site with surrounding water molecules. Taken together, these results establish DFA I synthase/hydrolase as a member of a new glycoside hydrolase family (GH172).
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12
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Paesani C, Degano AL, Zalosnik MI, Fabi JP, Pérez GT. Enzymatic modification of arabinoxylans from soft and hard Argentinian wheat inhibits the viability of HCT-116 cells. Food Res Int 2021; 147:110466. [DOI: 10.1016/j.foodres.2021.110466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 05/06/2021] [Accepted: 05/23/2021] [Indexed: 02/07/2023]
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13
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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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14
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Functional and structural characterization of an α-ʟ-arabinofuranosidase from Thermothielavioides terrestris and its exquisite domain-swapped β-propeller fold crystal packing. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140533. [DOI: 10.1016/j.bbapap.2020.140533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 07/25/2020] [Accepted: 08/12/2020] [Indexed: 12/24/2022]
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15
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Long L, Sun L, Lin Q, Ding S, St John FJ. Characterization and functional analysis of two novel thermotolerant α-L-arabinofuranosidases belonging to glycoside hydrolase family 51 from Thielavia terrestris and family 62 from Eupenicillium parvum. Appl Microbiol Biotechnol 2020; 104:8719-8733. [PMID: 32880690 PMCID: PMC7502447 DOI: 10.1007/s00253-020-10867-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 08/06/2020] [Accepted: 08/26/2020] [Indexed: 11/26/2022]
Abstract
Abstract Arabinofuranose substitutions on xylan are known to interfere with enzymatic hydrolysis of this primary hemicellulose. In this work, two novel α-l-arabinofuranosidases (ABFs), TtABF51A from Thielavia terrestris and EpABF62C from Eupenicillium parvum, were characterized and functionally analyzed. From sequences analyses, TtABF51A and EpABF62C belong to glycoside hydrolase (GH) families 51 and 62, respectively. Recombinant TtABF51A showed high activity on 4-nitrophenyl-α-l-arabinofuranoside (83.39 U/mg), low-viscosity wheat arabinoxylan (WAX, 39.66 U/mg), high-viscosity rye arabinoxylan (RAX, 32.24 U/mg), and sugarbeet arabinan (25.69 U/mg), while EpABF62C preferred to degrade arabinoxylan. For EpABF62C, the rate of hydrolysis of RAX (94.10 U/mg) was 2.1 times that of WAX (45.46 U/mg). The optimal pH and reaction temperature for the two enzymes was between 4.0 and 4.5 and 65 °C, respectively. Calcium played an important role in the thermal stability of EpABF62C. TtABF51A and EpABF62C showed the highest thermal stabilities at pH 4.5 or 5.0, respectively. At their optimal pHs, TtABF51A and EpABF62C retained greater than 80% of their initial activities after incubation at 55 °C for 96 h or 144 h, respectively. 1H NMR analysis indicated that the two enzymes selectively removed arabinose linked to C-3 of mono-substituted xylose residues in WAX. Compared with the singular application of the GH10 xylanase EpXYN1 from E. parvum, co-digestions of WAX including TtABF51A and/or EpABF62C released 2.49, 3.38, and 4.81 times xylose or 3.38, 1.65, and 2.57 times of xylobiose, respectively. Meanwhile, the amount of arabinose released from WAX by TtABF51A with EpXYN1 was 2.11 times the amount with TtABF51A alone. Key points • Two novel α-l-arabinofuranosidases (ABFs) displayed high thermal stability. • The thermal stability of GH62 family EpABF62C was dependent on calcium. • Buffer pH affects the thermal stability of the two ABFs. • Both ABFs enhance the hydrolysis of WAX by a GH10 xylanase. Electronic supplementary material The online version of this article (10.1007/s00253-020-10867-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Liangkun Long
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
- Institute for Microbial and Biochemical Technology, Forest Products Laboratory, USDA Forest Service, One Gifford Pinchot Drive, Madison, WI, 53726, USA
| | - Lu Sun
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Qunying Lin
- Nanjing Institute for the Comprehensive Utilization of Wild Plants, Nanjing, 211111, China
| | - Shaojun Ding
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China.
| | - Franz J St John
- Institute for Microbial and Biochemical Technology, Forest Products Laboratory, USDA Forest Service, One Gifford Pinchot Drive, Madison, WI, 53726, USA.
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16
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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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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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Moroz OV, Sobala LF, Blagova E, Coyle T, Peng W, Mørkeberg Krogh KBR, Stubbs KA, Wilson KS, Davies GJ. Structure of a Talaromyces pinophilus GH62 arabinofuranosidase in complex with AraDNJ at 1.25 Å resolution. Acta Crystallogr F Struct Biol Commun 2018; 74:490-495. [PMID: 30084398 PMCID: PMC6096477 DOI: 10.1107/s2053230x18000250] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 01/04/2018] [Indexed: 01/09/2023] Open
Abstract
The enzymatic hydrolysis of complex plant biomass is a major societal goal of the 21st century in order to deliver renewable energy from nonpetroleum and nonfood sources. One of the major problems in many industrial processes, including the production of second-generation biofuels from lignocellulose, is the presence of `hemicelluloses' such as xylans which block access to the cellulosic biomass. Xylans, with a polymeric β-1,4-xylose backbone, are frequently decorated with acetyl, glucuronyl and arabinofuranosyl `side-chain' substituents, all of which need to be removed for complete degradation of the xylan. As such, there is interest in side-chain-cleaving enzymes and their action on polymeric substrates. Here, the 1.25 Å resolution structure of the Talaromyces pinophilus arabinofuranosidase in complex with the inhibitor AraDNJ, which binds with a Kd of 24 ± 0.4 µM, is reported. Positively charged iminosugars are generally considered to be potent inhibitors of retaining glycosidases by virtue of their ability to interact with both acid/base and nucleophilic carboxylates. Here, AraDNJ shows good inhibition of an inverting enzyme, allowing further insight into the structural basis for arabinoxylan recognition and degradation.
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Affiliation(s)
- Olga V. Moroz
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Lukasz F. Sobala
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Elena Blagova
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Travis Coyle
- School of Molecular Sciences, The University of Western Australia (M313), 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Wei Peng
- Fungal Diversity, Novozymes A/S, China Headquarters, 14 Xinxi Road, Shangdi Zone, Haidian District, Beijing 100085, People’s Republic of China
| | | | - Keith A. Stubbs
- School of Molecular Sciences, The University of Western Australia (M313), 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Keith S. Wilson
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Gideon J. Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
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Identification and characterization of GH62 bacterial α-l-arabinofuranosidase from thermotolerant Streptomyces sp. SWU10 that preferentially degrades branched l-arabinofuranoses in wheat arabinoxylan. Enzyme Microb Technol 2018; 112:22-28. [DOI: 10.1016/j.enzmictec.2018.01.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/27/2018] [Accepted: 01/27/2018] [Indexed: 11/21/2022]
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21
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Hu Y, Yan X, Zhang H, Liu J, Luo F, Cui Y, Wang W, Zhou Y. Cloning and expression of a novel α-1,3-arabinofuranosidase from Penicillium oxalicum sp. 68. AMB Express 2018; 8:51. [PMID: 29611040 PMCID: PMC5880795 DOI: 10.1186/s13568-018-0577-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 03/24/2018] [Indexed: 01/11/2023] Open
Abstract
The discovery and creation of biocatalysts for plant biomass conversion are essential for industrial demand and scientific research of the plant cell wall. α-1,2 and α-1,3-L-arabinofuranosidases are debranching enzymes that catalyzing hydrolytic release of α-L-arabinofuranosyl residues in plant cell wall. Gene database analyses shows that GH62 family only contains specific α-L-arabinofuranosidases that play an important role in the degradation and structure of the plant cell wall. At present, there are only 22 enzymes in this group has been characterized. In this study, we cloned a novel α-1,3-arabinofuranosidase gene (poabf62a) belonging to glycoside hydrolase family 62 from Penicillium oxalicum sp. 68 and expressed it in Pichia pastoris. The molecular mass of recombinant PoAbf62A was estimated to be 32.9 kDa. Using p-nitrophenyl-α-l-arabinofuranoside (pNPαAbf) as substrate, purified PoAbf62A exhibited an optimal pH of 4.5 and temperature of 35 °C. Results of methylation and 13C NMR analyses showed that PoAbf62A was exclusively α-1,3-arabinofuranosidase, specific for cleavage of α-1,3-arabinofuranosyl residues, and with the absence of activity towards α-1,2-arabinofuranose and α-1,5-arabinofuranose. Therefore, PoAbf62A exhibits high activity on sugar beet arabinan and wheat arabinoxylan, because their branched side chain are decorated with α-1,3-arabinofuranose. On the other hand, there is a lack of activity with linear-α-L-1,5-arabinan and xylan that only contained α-L-1,5-arabinofuranose or β-1,4-xylose. The α-1,3-arabinofuranosidase activity identified here provides a new biocatalytic tool to degrade hemicellulose and analyze the structure of plant cell walls.
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22
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GH62 arabinofuranosidases: Structure, function and applications. Biotechnol Adv 2017; 35:792-804. [DOI: 10.1016/j.biotechadv.2017.06.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 06/17/2017] [Accepted: 06/23/2017] [Indexed: 01/03/2023]
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23
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Olczak A, Cianci M. The signal-to-noise ratio in SAD experiments. CRYSTALLOGR REV 2017. [DOI: 10.1080/0889311x.2017.1386182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Andrzej Olczak
- Institute of General and Ecological Chemistry, Lodz University of Technology, Lodz, Poland
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
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24
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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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25
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Contesini FJ, Liberato MV, Rubio MV, Calzado F, Zubieta MP, Riaño-Pachón DM, Squina FM, Bracht F, Skaf MS, Damasio AR. Structural and functional characterization of a highly secreted α-l-arabinofuranosidase (GH62) from Aspergillus nidulans grown on sugarcane bagasse. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1758-1769. [PMID: 28890404 DOI: 10.1016/j.bbapap.2017.09.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 08/31/2017] [Accepted: 09/04/2017] [Indexed: 12/30/2022]
Abstract
Carbohydrate-Active Enzymes are key enzymes for biomass-to-bioproducts conversion. α-l-Arabinofuranosidases that belong to the Glycoside Hydrolase family 62 (GH62) have important applications in biofuel production from plant biomass by hydrolyzing arabinoxylans, found in both the primary and secondary cell walls of plants. In this work, we identified a GH62 α-l-arabinofuranosidase (AnAbf62Awt) that was highly secreted when Aspergillus nidulans was cultivated on sugarcane bagasse. The gene AN7908 was cloned and transformed in A. nidulans for homologous production of AnAbf62Awt, and we confirmed that the enzyme is N-glycosylated at asparagine 83 by mass spectrometry analysis. The enzyme was also expressed in Escherichia coli and the studies of circular dichroism showed that the melting temperature and structural profile of AnAbf62Awt and the non-glycosylated enzyme from E. coli (AnAbf62Adeglyc) were highly similar. In addition, the designed glycomutant AnAbf62AN83Q presented similar patterns of secretion and activity to the AnAbf62Awt, indicating that the N-glycan does not influence the properties of this enzyme. The crystallographic structure of AnAbf62Adeglyc was obtained and the 1.7Å resolution model showed a five-bladed β-propeller fold, which is conserved in family GH62. Mutants AnAbf62AY312F and AnAbf62AY312S showed that Y312 was an important substrate-binding residue. Molecular dynamics simulations indicated that the loop containing Y312 could access different conformations separated by moderately low energy barriers. One of these conformations, comprising a local minimum, is responsible for placing Y312 in the vicinity of the arabinose glycosidic bond, and thus, may be important for catalytic efficiency.
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Affiliation(s)
- Fabiano Jares Contesini
- Institute of Biology, University of Campinas - UNICAMP, Campinas, SP CEP 13083-862, Brazil; Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Caixa Postal 6192, 13083-970, Brazil
| | - Marcelo Vizoná Liberato
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Caixa Postal 6192, 13083-970, Brazil
| | - Marcelo Ventura Rubio
- Institute of Biology, University of Campinas - UNICAMP, Campinas, SP CEP 13083-862, Brazil
| | - Felipe Calzado
- Institute of Biology, University of Campinas - UNICAMP, Campinas, SP CEP 13083-862, Brazil
| | | | - Diego Mauricio Riaño-Pachón
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Caixa Postal 6192, 13083-970, Brazil; Laboratory of Regulatory Systems Biology, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, CEP: 05508-000, Brazil
| | - Fabio Marcio Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, (UNISO), Sorocaba, SP, CEP 18023-000, Brazil
| | - Fabricio Bracht
- Institute of Chemistry, University of Campinas - UNICAMP, Campinas, SP CEP: 13084-862, Brazil
| | - Munir S Skaf
- Institute of Chemistry, University of Campinas - UNICAMP, Campinas, SP CEP: 13084-862, Brazil
| | - André Ricardo Damasio
- Institute of Biology, University of Campinas - UNICAMP, Campinas, SP CEP 13083-862, Brazil.
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26
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Sato M, Liebschner D, Yamada Y, Matsugaki N, Arakawa T, Wills SS, Hattie M, Stubbs KA, Ito T, Senda T, Ashida H, Fushinobu S. The first crystal structure of a family 129 glycoside hydrolase from a probiotic bacterium reveals critical residues and metal cofactors. J Biol Chem 2017; 292:12126-12138. [PMID: 28546425 DOI: 10.1074/jbc.m117.777391] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 05/22/2017] [Indexed: 11/06/2022] Open
Abstract
The α-N-acetylgalactosaminidase from the probiotic bacterium Bifidobacterium bifidum (NagBb) belongs to the glycoside hydrolase family 129 and hydrolyzes the glycosidic bond of Tn-antigen (GalNAcα1-Ser/Thr). NagBb is involved in assimilation of O-glycans on mucin glycoproteins by B. bifidum in the human gastrointestinal tract, but its catalytic mechanism has remained elusive because of a lack of sequence homology around putative catalytic residues and of other structural information. Here we report the X-ray crystal structure of NagBb, representing the first GH129 family structure, solved by the single-wavelength anomalous dispersion method based on sulfur atoms of the native protein. We determined ligand-free, GalNAc, and inhibitor complex forms of NagBb and found that Asp-435 and Glu-478 are located in the catalytic domain at appropriate positions for direct nucleophilic attack at the anomeric carbon and proton donation for the glycosidic bond oxygen, respectively. A highly conserved Asp-330 forms a hydrogen bond with the O4 hydroxyl of GalNAc in the -1 subsite, and Trp-398 provides a stacking platform for the GalNAc pyranose ring. Interestingly, a metal ion, presumably Ca2+, is involved in the recognition of the GalNAc N-acetyl group. Mutations at Asp-435, Glu-478, Asp-330, and Trp-398 and residues involved in metal coordination (including an all-Ala quadruple mutant) significantly reduced the activity, indicating that these residues and the metal ion play important roles in substrate recognition and catalysis. Interestingly, NagBb exhibited some structural similarities to the GH101 endo-α-N-acetylgalactosaminidases, but several critical differences in substrate recognition and reaction mechanism account for the different activities of these two enzymes.
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Affiliation(s)
- Mayo Sato
- Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Dorothee Liebschner
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba 305-0801, Japan
| | - Yusuke Yamada
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba 305-0801, Japan
| | - Naohiro Matsugaki
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba 305-0801, Japan
| | - Takatoshi Arakawa
- Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Siobhán S Wills
- School of Molecular Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Mitchell Hattie
- School of Molecular Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Keith A Stubbs
- School of Molecular Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Tasuku Ito
- Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba 305-0801, Japan
| | - Hisashi Ashida
- Faculty of Biology-Oriented Science and Technology, Kindai University, 930 Nishimitani, Kinokawa-shi, Wakayama 649-6493, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
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27
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Littunen K, Mai-Gisondi G, Seppälä J, Master ER. Enzymatically Debranched Xylans in Graft Copolymerization. Biomacromolecules 2017; 18:1634-1641. [DOI: 10.1021/acs.biomac.7b00229] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | - Emma R. Master
- Department
of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
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28
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Structure of the Catalytic Domain of α-l-Arabinofuranosidase from Coprinopsis cinerea, CcAbf62A, Provides Insights into Structure–Function Relationships in Glycoside Hydrolase Family 62. Appl Biochem Biotechnol 2016; 181:511-525. [DOI: 10.1007/s12010-016-2227-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 08/26/2016] [Indexed: 10/21/2022]
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29
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Couturier M, Tangthirasunun N, Ning X, Brun S, Gautier V, Bennati-Granier C, Silar P, Berrin JG. Plant biomass degrading ability of the coprophilic ascomycete fungus Podospora anserina. Biotechnol Adv 2016; 34:976-983. [PMID: 27263000 DOI: 10.1016/j.biotechadv.2016.05.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 05/11/2016] [Accepted: 05/27/2016] [Indexed: 12/22/2022]
Abstract
The degradation of plant biomass is a major challenge towards the production of bio-based compounds and materials. As key lignocellulolytic enzyme producers, filamentous fungi represent a promising reservoir to tackle this challenge. Among them, the coprophilous ascomycete Podospora anserina has been used as a model organism to study various biological mechanisms because its genetics are well understood and controlled. In 2008, the sequencing of its genome revealed a great diversity of enzymes targeting plant carbohydrates and lignin. Since then, a large array of lignocellulose-acting enzymes has been characterized and genetic analyses have enabled the understanding of P. anserina metabolism and development on plant biomass. Overall, these research efforts shed light on P. anserina strategy to unlock recalcitrant lignocellulose deconstruction.
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Affiliation(s)
- Marie Couturier
- INRA, Aix Marseille Université, Polytech Marseille, UMR 1163, Biodiversité et Biotechnologie Fongiques, F-13288 Marseille, France
| | - Narumon Tangthirasunun
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Diderot, 35, rue Hélène Brion, F-75205 Paris, France
| | - Xie Ning
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Diderot, 35, rue Hélène Brion, F-75205 Paris, France
| | - Sylvain Brun
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Diderot, 35, rue Hélène Brion, F-75205 Paris, France
| | - Valérie Gautier
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Diderot, 35, rue Hélène Brion, F-75205 Paris, France
| | - Chloé Bennati-Granier
- INRA, Aix Marseille Université, Polytech Marseille, UMR 1163, Biodiversité et Biotechnologie Fongiques, F-13288 Marseille, France
| | - Philippe Silar
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Diderot, 35, rue Hélène Brion, F-75205 Paris, France.
| | - Jean-Guy Berrin
- INRA, Aix Marseille Université, Polytech Marseille, UMR 1163, Biodiversité et Biotechnologie Fongiques, F-13288 Marseille, France.
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30
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Insights into the mechanism of enzymatic hydrolysis of xylan. Appl Microbiol Biotechnol 2016; 100:5205-14. [PMID: 27112349 DOI: 10.1007/s00253-016-7555-z] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 04/11/2016] [Accepted: 04/14/2016] [Indexed: 01/06/2023]
Abstract
Hemicelluloses are a vast group of complex, non-cellulosic heteropolysaccharides that are classified according to the principal monosaccharides present in its structure. Xylan is the most abundant hemicellulose found in lignocellulosic biomass. In the current trend of a more effective utilization of lignocellulosic biomass and developments of environmentally friendly industrial processes, increasing research activities have been directed to a practical application of the xylan component of plants and plant residues as biopolymer resources. A variety of enzymes, including main- and side-chain acting enzymes, are responsible for xylan breakdown. Xylanase is a main-chain enzyme that randomly cleaves the β-1,4 linkages between the xylopyranosyl residues in xylan backbone. This enzyme presents varying folds, mechanisms of action, substrate specificities, hydrolytic activities, and physicochemical characteristics. This review pays particular attention to different aspects of the mechanisms of action of xylan-degrading enzymes and their contribution to improve the production of bioproducts from plant biomass. Furthermore, the influence of phenolic compounds on xylanase activity is also discussed.
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31
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Wilkens C, Andersen S, Petersen BO, Li A, Busse-Wicher M, Birch J, Cockburn D, Nakai H, Christensen HEM, Kragelund BB, Dupree P, McCleary B, Hindsgaul O, Hachem MA, Svensson B. An efficient arabinoxylan-debranching α-l-arabinofuranosidase of family GH62 from Aspergillus nidulans contains a secondary carbohydrate binding site. Appl Microbiol Biotechnol 2016; 100:6265-6277. [DOI: 10.1007/s00253-016-7417-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 02/07/2016] [Accepted: 02/22/2016] [Indexed: 10/22/2022]
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32
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Pérez R, Eyzaguirre J. Aspergillus fumigatus Produces Two Arabinofuranosidases From Glycosyl Hydrolase Family 62: Comparative Properties of the Recombinant Enzymes. Appl Biochem Biotechnol 2016; 179:143-54. [DOI: 10.1007/s12010-016-1984-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 01/07/2016] [Indexed: 10/22/2022]
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33
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Couturier M, Mathieu Y, Li A, Navarro D, Drula E, Haon M, Grisel S, Ludwig R, Berrin JG. Characterization of a new aryl-alcohol oxidase secreted by the phytopathogenic fungus Ustilago maydis. Appl Microbiol Biotechnol 2015; 100:697-706. [DOI: 10.1007/s00253-015-7021-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 08/12/2015] [Accepted: 09/06/2015] [Indexed: 10/22/2022]
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34
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Haon M, Grisel S, Navarro D, Gruet A, Berrin JG, Bignon C. Recombinant protein production facility for fungal biomass-degrading enzymes using the yeast Pichia pastoris. Front Microbiol 2015; 6:1002. [PMID: 26441929 PMCID: PMC4585289 DOI: 10.3389/fmicb.2015.01002] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 09/07/2015] [Indexed: 01/15/2023] Open
Abstract
Filamentous fungi are the predominant source of lignocellulolytic enzymes used in industry for the transformation of plant biomass into high-value molecules and biofuels. The rapidity with which new fungal genomic and post-genomic data are being produced is vastly outpacing functional studies. This underscores the critical need for developing platforms dedicated to the recombinant expression of enzymes lacking confident functional annotation, a prerequisite to their functional and structural study. In the last decade, the yeast Pichia pastoris has become increasingly popular as a host for the production of fungal biomass-degrading enzymes, and particularly carbohydrate-active enzymes (CAZymes). This study aimed at setting-up a platform to easily and quickly screen the extracellular expression of biomass-degrading enzymes in P. pastoris. We first used three fungal glycoside hydrolases (GHs) that we previously expressed using the protocol devised by Invitrogen to try different modifications of the original protocol. Considering the gain in time and convenience provided by the new protocol, we used it as basis to set-up the facility and produce a suite of fungal CAZymes (GHs, carbohydrate esterases and auxiliary activity enzyme families) out of which more than 70% were successfully expressed. The platform tasks range from gene cloning to automated protein purifications and activity tests, and is open to the CAZyme users' community.
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Affiliation(s)
- Mireille Haon
- INRA, UMR 1163 Biodiversité et Biotechnologie Fongiques Marseille, France ; Aix-Marseille Université, Polytech Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques Marseille, France
| | - Sacha Grisel
- INRA, UMR 1163 Biodiversité et Biotechnologie Fongiques Marseille, France ; Aix-Marseille Université, Polytech Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques Marseille, France
| | - David Navarro
- INRA, UMR 1163 Biodiversité et Biotechnologie Fongiques Marseille, France ; Aix-Marseille Université, Polytech Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques Marseille, France
| | - Antoine Gruet
- INRA, UMR 1163 Biodiversité et Biotechnologie Fongiques Marseille, France ; Aix-Marseille Université, Polytech Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques Marseille, France ; Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York NY, USA
| | - Jean-Guy Berrin
- INRA, UMR 1163 Biodiversité et Biotechnologie Fongiques Marseille, France ; Aix-Marseille Université, Polytech Marseille, UMR1163 Biodiversité et Biotechnologie Fongiques Marseille, France
| | - Christophe Bignon
- Architecture et Fonction des Macromolècules Biologiques, CNRS-Aix-Marseille University UMR 7257 Marseille, France ; INRA, USC 1408 AFMB Marseille, France
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35
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Hydrolysis of wheat flour arabinoxylan, acid-debranched wheat flour arabinoxylan and arabino-xylo-oligosaccharides by β-xylanase, α-l-arabinofuranosidase and β-xylosidase. Carbohydr Res 2015; 407:79-96. [DOI: 10.1016/j.carres.2015.01.017] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 01/21/2015] [Accepted: 01/23/2015] [Indexed: 11/21/2022]
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36
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Wilkens C, Cockburn D, Andersen S, Ole Petersen B, Ruzanski C, A. Field R, Hindsgaul O, Nakai H, McCleary B, M. Smith A, Abou Hachem M, Svensson B. Analysis of Surface Binding Sites (SBS) within GH62, GH13, and GH77. J Appl Glycosci (1999) 2015. [DOI: 10.5458/jag.jag.jag-2015_006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Casper Wilkens
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark
| | - Darrell Cockburn
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark
| | - Susan Andersen
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark
| | - Bent Ole Petersen
- Carbohydrate Chemistry Group, Carlsberg Laboratory, Gamle Carlsberg Vej 10
| | | | | | - Ole Hindsgaul
- Carbohydrate Chemistry Group, Carlsberg Laboratory, Gamle Carlsberg Vej 10
| | - Hiroyuki Nakai
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark
| | | | | | - Maher Abou Hachem
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark
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37
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Kaur AP, Nocek BP, Xu X, Lowden MJ, Leyva JF, Stogios PJ, Cui H, Di Leo R, Powlowski J, Tsang A, Savchenko A. Functional and structural diversity in GH62 α-L-arabinofuranosidases from the thermophilic fungus Scytalidium thermophilum. Microb Biotechnol 2014; 8:419-33. [PMID: 25267315 PMCID: PMC4408175 DOI: 10.1111/1751-7915.12168] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 08/16/2014] [Indexed: 01/22/2023] Open
Abstract
The genome of the thermophilic fungus Scytalidium thermophilum (strain CBS 625.91) harbours a wide range of genes involved in carbohydrate degradation, including three genes, abf62A, abf62B and abf62C, predicted to encode glycoside hydrolase family 62 (GH62) enzymes. Transcriptome analysis showed that only abf62A and abf62C are actively expressed during growth on diverse substrates including straws from barley, alfalfa, triticale and canola. The abf62A and abf62C genes were expressed in Escherichia coli and the resulting recombinant proteins were characterized. Calcium-free crystal structures of Abf62C in apo and xylotriose bound forms were determined to 1.23 and 1.48 Å resolution respectively. Site-directed mutagenesis confirmed Asp55, Asp171 and Glu230 as catalytic triad residues, and revealed the critical role of non-catalytic residues Asp194, Trp229 and Tyr338 in positioning the scissile α-L-arabinofuranoside bond at the catalytic site. Further, the +2R substrate-binding site residues Tyr168 and Asn339, as well as the +2NR residue Tyr226, are involved in accommodating long-chain xylan polymers. Overall, our structural and functional analysis highlights characteristic differences between Abf62A and Abf62C, which represent divergent subgroups in the GH62 family.
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Affiliation(s)
- Amrit Pal Kaur
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON, M5S 3E5, Canada
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Elucidation of the molecular basis for arabinoxylan-debranching activity of a thermostable family GH62 α-l-arabinofuranosidase from Streptomyces thermoviolaceus. Appl Environ Microbiol 2014; 80:5317-29. [PMID: 24951792 DOI: 10.1128/aem.00685-14] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xylan-debranching enzymes facilitate the complete hydrolysis of xylan and can be used to alter xylan chemistry. Here, the family GH62 α-l-arabinofuranosidase from Streptomyces thermoviolaceus (SthAbf62A) was shown to have a half-life of 60 min at 60°C and the ability to cleave α-1,3 l-arabinofuranose (l-Araf) from singly substituted xylopyranosyl (Xylp) backbone residues in wheat arabinoxylan; low levels of activity on arabinan as well as 4-nitrophenyl α-l-arabinofuranoside were also detected. After selective removal of α-1,3 l-Araf substituents from disubstituted Xylp residues present in wheat arabinoxylan, SthAbf62A could also cleave the remaining α-1,2 l-Araf substituents, confirming the ability of SthAbf62A to remove α-l-Araf residues that are (1→2) and (1→3) linked to monosubstituted β-d-Xylp sugars. Three-dimensional structures of SthAbf62A and its complex with xylotetraose and l-arabinose confirmed a five-bladed β-propeller fold and revealed a molecular Velcro in blade V between the β1 and β21 strands, a disulfide bond between Cys27 and Cys297, and a calcium ion coordinated in the central channel of the fold. The enzyme-arabinose complex structure further revealed a narrow and seemingly rigid l-arabinose binding pocket situated at the center of one side of the β propeller, which stabilized the arabinofuranosyl substituent through several hydrogen-bonding and hydrophobic interactions. The predicted catalytic amino acids were oriented toward this binding pocket, and the catalytic essentiality of Asp53 and Glu213 was confirmed by site-specific mutagenesis. Complex structures with xylotetraose revealed a shallow cleft for xylan backbone binding that is open at both ends and comprises multiple binding subsites above and flanking the l-arabinose binding pocket.
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Maehara T, Fujimoto Z, Ichinose H, Michikawa M, Harazono K, Kaneko S. Crystal structure and characterization of the glycoside hydrolase family 62 α-L-arabinofuranosidase from Streptomyces coelicolor. J Biol Chem 2014; 289:7962-72. [PMID: 24482228 DOI: 10.1074/jbc.m113.540542] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
α-L-arabinofuranosidase, which belongs to the glycoside hydrolase family 62 (GH62), hydrolyzes arabinoxylan but not arabinan or arabinogalactan. The crystal structures of several α-L-arabinofuranosidases have been determined, although the structures, catalytic mechanisms, and substrate specificities of GH62 enzymes remain unclear. To evaluate the substrate specificity of a GH62 enzyme, we determined the crystal structure of α-L-arabinofuranosidase, which comprises a carbohydrate-binding module family 13 domain at its N terminus and a catalytic domain at its C terminus, from Streptomyces coelicolor. The catalytic domain was a five-bladed β-propeller consisting of five radially oriented anti-parallel β-sheets. Sugar complex structures with l-arabinose, xylotriose, and xylohexaose revealed five subsites in the catalytic cleft and an l-arabinose-binding pocket at the bottom of the cleft. The entire structure of this GH62 family enzyme was very similar to that of glycoside hydrolase 43 family enzymes, and the catalytically important acidic residues found in family 43 enzymes were conserved in GH62. Mutagenesis studies revealed that Asp(202) and Glu(361) were catalytic residues, and Trp(270), Tyr(461), and Asn(462) were involved in the substrate-binding site for discriminating the substrate structures. In particular, hydrogen bonding between Asn(462) and xylose at the nonreducing end subsite +2 was important for the higher activity of substituted arabinofuranosyl residues than that for terminal arabinofuranoses.
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Affiliation(s)
- Tomoko Maehara
- From the Food Biotechnology Division, National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642
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