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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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Akkaya A, Ensari Y, Ozseker EE, Batur OO, Buyuran G, Evran S. Recombinant Production and Biochemical Characterization of Thermostable Arabinofuranosidase from Acidothermophilic Alicyclobacillus Acidocaldarius. Protein J 2023:10.1007/s10930-023-10117-5. [PMID: 37119380 DOI: 10.1007/s10930-023-10117-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2023] [Indexed: 05/01/2023]
Abstract
The complete enzymatic degradation of lignocellulosic biomass requires the cooperative action of cellulosic, hemicellulosic, and lignolytic enzymes such as cellulase, xylanase, laccase, galactosidase, and arabinofuranosidase. Arabinofuranosidases (E.C 3.2.1.55), which belong to the glycoside hydrolase family of enzymes, hydrolyze the 1,3- and 1,5-α-arabinosyl bonds in L-arabinose- containing molecules. L-arabinoses are present in hemicellulosic part of lignocellulosic biomass. Arabinofuranosidases also play an important role in the complete hydrolysis of arabinoxylans. Analysis of the genome project and CAZY database revealed two putative arabinofuranosidase genes in the A. acidocaldarius genome. The aim of the study was cloning, heterologous expression, purification and biochemical characterization of the arabinofuranosidase enzyme encoded in A. acidocaldarius genome. For this purpose, the AbfA gene of the arabinofuranosidase protein was cloned into the pQE-40 vector, heterologously expressed in E. coli BL21 GOLD (DE3) and successfully purified using His-Tag. Biochemical characterization of the purified enzyme revealed that A. acidocaldarius arabinofuranosidase exhibited activity over a wide pH and temperature range with optimum activity at 45 ºC and pH 6.5 in phosphate buffer towards 4-nitrophenyl-α-L-arabinofuranoside as the substrate. In addition, the enzyme is highly stable over wide range of temperature and maintaining 60% of its activity after 90 min of incubation at 80 ºC. Through the bioinformatics studies, the homology model of A. acidocaldarius arabinofuranosidase was generated and the substrate binding site and residues located in this site were identified. Further molecular docking analysis revealed that the substrate located in the catalytically active pose and, residues N174, E175, and E294 have direct interaction with 4-nitrophenyl-α-L-arabinofuranoside. Moreover, based on phylogenetic analysis, A. acidocaldarius arabinofuranosidase exists in the sub-group of intracellular arabinofuranosidases, and G. stearothermophilus and B.subtilis arabinofuranosidases are close relatives of A. acidocaldarius arabinofuranosidase. This is the first study to report the gene cloning, recombinant expression and biochemical and bioinformatic characterization of an auxiliary GH51 arabinofuranosidase from an acidothermophilic bacterium A. acidocaldarius.
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Affiliation(s)
- Alper Akkaya
- Faculty of Science, Biochemistry Department, Ege University, Bornova, Izmir, 35100, Turkey
| | - Yunus Ensari
- Faculty of Engineering and Architecture, Bioengineering Department, Kafkas University, Kars, 36000, Turkey.
| | - Emine Erdogan Ozseker
- Faculty of Science, Biochemistry Department, Ege University, Bornova, Izmir, 35100, Turkey
| | - Ozge Ozsen Batur
- Faculty of Science, Department of Chemistry, Eskişehir Osmangazi University, Eskişehir, 26480, Turkey
| | - Gozde Buyuran
- Vocational School of Health Services, Kırşehir Ahi Evran University, Kırşehir, 40100, Turkey
| | - Serap Evran
- Faculty of Science, Biochemistry Department, Ege University, Bornova, Izmir, 35100, Turkey
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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] [Key Words] [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
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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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Morais MAB, Coines J, Domingues MN, Pirolla RAS, Tonoli CCC, Santos CR, Correa JBL, Gozzo FC, Rovira C, Murakami MT. Two distinct catalytic pathways for GH43 xylanolytic enzymes unveiled by X-ray and QM/MM simulations. Nat Commun 2021; 12:367. [PMID: 33446650 PMCID: PMC7809346 DOI: 10.1038/s41467-020-20620-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023] Open
Abstract
Xylanolytic enzymes from glycoside hydrolase family 43 (GH43) are involved in the breakdown of hemicellulose, the second most abundant carbohydrate in plants. Here, we kinetically and mechanistically describe the non-reducing-end xylose-releasing exo-oligoxylanase activity and report the crystal structure of a native GH43 Michaelis complex with its substrate prior to hydrolysis. Two distinct calcium-stabilized conformations of the active site xylosyl unit are found, suggesting two alternative catalytic routes. These results are confirmed by QM/MM simulations that unveil the complete hydrolysis mechanism and identify two possible reaction pathways, involving different transition state conformations for the cleavage of xylooligosaccharides. Such catalytic conformational promiscuity in glycosidases is related to the open architecture of the active site and thus might be extended to other exo-acting enzymes. These findings expand the current general model of catalytic mechanism of glycosidases, a main reaction in nature, and impact on our understanding about their interaction with substrates and inhibitors.
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Affiliation(s)
- Mariana A B Morais
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
- Departament de Química Inorgànica i Orgànica & Institut de Química Teórica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, 08028, Spain
| | - Joan Coines
- Departament de Química Inorgànica i Orgànica & Institut de Química Teórica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, 08028, Spain
| | - Mariane N Domingues
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Renan A S Pirolla
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Celisa C C Tonoli
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Camila R Santos
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Jessica B L Correa
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Fabio C Gozzo
- Dalton Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, Campinas, 13083-970, Brazil
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & Institut de Química Teórica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, 08028, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, 08010, Spain.
| | - Mario T Murakami
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil.
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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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Kujawska M, La Rosa SL, Roger LC, Pope PB, Hoyles L, McCartney AL, Hall LJ. Succession of Bifidobacterium longum Strains in Response to a Changing Early Life Nutritional Environment Reveals Dietary Substrate Adaptations. iScience 2020; 23:101368. [PMID: 32721872 PMCID: PMC7390879 DOI: 10.1016/j.isci.2020.101368] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/16/2020] [Accepted: 07/13/2020] [Indexed: 12/11/2022] Open
Abstract
Diet-microbe interactions play a crucial role in modulation of the early life microbiota and infant health. Bifidobacterium dominates the breast-fed infant gut and may persist in individuals during transition from a milk-based to a more diversified diet. Here, we investigated adaptation of Bifidobacterium longum to the changing nutritional environment. Genomic characterization of 75 strains isolated from nine either exclusively breast- or formula-fed (pre-weaning) infants in their first 18 months revealed subspecies- and strain-specific intra-individual genomic diversity with respect to carbohydrate metabolism, which corresponded to different dietary stages. Complementary phenotypic studies indicated strain-specific differences in utilization of human milk oligosaccharides and plant carbohydrates, whereas proteomic profiling identified gene clusters involved in metabolism of selected carbohydrates. Our results indicate a strong link between infant diet and B. longum diversity and provide additional insights into possible competitive advantage mechanisms of this Bifidobacterium species and its persistence in a single host.
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Affiliation(s)
- Magdalena Kujawska
- Gut Microbes & Health, Quadram Institute Biosciences, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Sabina Leanti La Rosa
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1433 Aas, Norway
| | - Laure C Roger
- Department of Food & Nutritional Sciences, University of Reading, Reading RG6 6LA, UK
| | - Phillip B Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1433 Aas, Norway; Faculty of Biosciences, Norwegian University of Life Sciences, 1433 Aas, Norway
| | - Lesley Hoyles
- Department of Biosciences, Nottingham Trent University, Nottingham NG11 8NS, UK
| | - Anne L McCartney
- Department of Food & Nutritional Sciences, University of Reading, Reading RG6 6LA, UK
| | - Lindsay J Hall
- Gut Microbes & Health, Quadram Institute Biosciences, Norwich Research Park, Norwich NR4 7UQ, UK; Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; Chair of Intestinal Microbiome, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.
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Thakur A, Sharma K, Jamaldheen SB, Goyal A. Molecular Characterization, Regioselective and Synergistic Action of First Recombinant Type III α-L-arabinofuranosidase of Family 43 Glycoside Hydrolase (PsGH43_12) from Pseudopedobacter saltans. Mol Biotechnol 2020; 62:443-455. [DOI: 10.1007/s12033-020-00263-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2020] [Indexed: 01/26/2023]
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Sharma K, Fontes CMGA, Najmudin S, Goyal A. Small angle X-ray scattering based structure, modeling and molecular dynamics analyses of family 43 glycoside hydrolase α-L-arabinofuranosidase from Clostridium thermocellum. J Biomol Struct Dyn 2019; 39:209-218. [PMID: 31856699 DOI: 10.1080/07391102.2019.1707119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Enzymes that participate in the hydrolysis of complex carbohydrates display a modular architecture, although the significance of enzyme modularity to flexibility and catalytic efficacy is not fully understood. α-L-arabinofuranosidase from Clostridium thermocellum (CtAraf43) catalyzes the release of α-1,2-, α-1,3-, or α-1,5- linked L-arabinose from arabinose decorated polysaccharides. CtAraf43 comprises an N-terminal catalytic domain (CtAbf43A) connected with two family 6 carbohydrate-binding modules (CBMs), termed as CtCBM6A and CtCBM6B, through flexible linker peptides. Here, we modeled the structure of CtAraf43 revealing that the module, CtAbf43A displays a 5-fold β-propeller fold and the CBMs the typical jellyroll type β-sandwich folds. Ramachandran plot showed 98.5% residues in the favored region and 1.5% residues in the disallowed region. Molecular dynamics simulation analysis of CtAraf43 revealed significant flexibility that is more expressive in the C-terminal CtCBM6B module in terms of structure and orientation. Small angle X-ray scattering analysis of CtAraf43 revealed its elongated structure. CtAraf43 at 1.2 mg/mL demonstrated the monomeric nature and a multi-modular shaped molecular envelope in solution with a Dmax of 12 nm. However, at 4.7 mg/mL, CtAraf43 displayed a dimeric structure and elongated molecular envelope. Kratky plot analysis revealed the folded state of CtAraf43 with limited flexibility at both concentrations. The data revealed higher flexibility at the C-terminal of CtAraf43 suggesting a coordinated action of the N-terminal catalytic module CtAbf43A and the internal CtCBM6A.AbbreviationCBMsCarbohydrate Binding ModulesCtAraf43α-L-arabinofuranosidaseGHsGlycoside HydrolasesMDMolecular DynamicsRMSDRoot Mean Square DeviationRMSFRoot Mean Square FluctuationSAXSSmall angle X-ray scatteringCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kedar Sharma
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Carlos M G A Fontes
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
| | - Shabir Najmudin
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
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Sharma K, Thakur A, Kumar R, Goyal A. Structure and biochemical characterization of glucose tolerant β-1,4 glucosidase (HtBgl) of family 1 glycoside hydrolase from Hungateiclostridium thermocellum. Carbohydr Res 2019; 483:107750. [PMID: 31357130 DOI: 10.1016/j.carres.2019.107750] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 06/14/2019] [Accepted: 07/16/2019] [Indexed: 12/15/2022]
Abstract
β-1,4-glucosidase (HtBgl) of family 1 glycoside hydrolase from Hungateiclostridium thermocellum was cloned in pET28a(+) vector, expressed, biochemically and structurally characterized. HtBgl displayed 67 U/mg activity against 4-nitrophenyl-β-d-glucopyranoside, followed by 180 U/mg against cellobiose and 42 U/mg activity against 4-nitrophenyl-β-d-galactopyranoside. HtBgl displayed an optimum temperature of 65 °C and an optimum pH of 6.0. HtBgl was stable in the pH range, 4.0-8.0 and displayed the thermostability up to 60 °C for 1 h. HtBgl displayed the glucose tolerance up to 750 mM and retained ~70% activity after 20 h. HtBgl crystal structure submitted (PDB id 5OGZ) by others exhibited a classical Triosephosphate Isomerase, (β/α)8-barrel fold. Protein melting analysis of HtBgl exhibited a single peak at 78 °C and the addition of 5 mM Mg2+ shifted the peak to 82 °C. Molecular dynamics studies showed that the amino acid residues from 351 to 375 exhibit the flexibility due to the presence of the catalytic acid residue. The structure comparison of HtBgl with homologous proteins and its docking analysis with probable ligands revealed that the residues, E166 and E355 are involved in the catalysis. The SAXS analysis of HtBgl showed that the protein is monomeric and present in a fully folded state. The radius of gyration (Rg) found was 2.15-2.26 nm. The bell-shaped curve obtained by Kratky plot analysis displayed the globular shape and fully folded state with flexibility in the N-terminal region. The HtBgl crystal structure superposed well with the SAXS derived dummy atom model.
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Affiliation(s)
- Kedar Sharma
- DBT PAN-IIT Centre of Bioenergy, Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Abhijeet Thakur
- DBT PAN-IIT Centre of Bioenergy, Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Rajeev Kumar
- DBT PAN-IIT Centre of Bioenergy, Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Arun Goyal
- DBT PAN-IIT Centre of Bioenergy, Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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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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12
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Sharma K, Fontes CMGA, Najmudin S, Goyal A. Molecular organization and protein stability of the Clostridium thermocellum glucuronoxylan endo-β-1,4-xylanase of family 30 glycoside hydrolase in solution. J Struct Biol 2019; 206:335-344. [PMID: 30959107 DOI: 10.1016/j.jsb.2019.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/02/2019] [Accepted: 04/04/2019] [Indexed: 11/19/2022]
Abstract
Glucuronoxylan-β-1,4-xylanohydrolase from Clostridium thermocellum (CtXynGH30) hydrolyzes β-1,4-xylosidic linkages in 4-O-Methyl-D-glucuronoxylan. CtXynGH30 comprises an N-terminal catalytic domain, CtXyn30A, joined by a typical linker sequence to a family 6 carbohydrate-binding module, termed CtCBM6. ITC, mass spectrometric and enzyme activity analyses of CtXyn30A:CtCBM6 (1:1 M ratio), CtXyn30A and CtXynGH30 showed that the linker peptide plays a key role in connecting and orienting CtXyn30A and CtCBM6 modules resulting in the enhanced activity of CtXynGH30. To visualize the disposition of the two protein domains of CtXynGH30, SAXS analysis revealed that CtXynGH30 is monomeric and has a boot-shaped molecular envelope in solution with a Dmax of 18 nm and Rg of 3.6 nm. Kratky plot displayed the protein in a fully folded and flexible state. The ab initio derived dummy atom model of CtXynGH30 superposed well with the modelled structure.
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Affiliation(s)
- Kedar Sharma
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Carlos M G A Fontes
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Av. da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Shabir Najmudin
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Av. da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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Fortune B, Mhlongo S, van Zyl LJ, Huddy R, Smart M, Trindade M. Characterisation of three novel α-L-arabinofuranosidases from a compost metagenome. BMC Biotechnol 2019; 19:22. [PMID: 30999885 PMCID: PMC6472066 DOI: 10.1186/s12896-019-0510-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 03/13/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The importance of the accessory enzymes such as α-L-arabinofuranosidases (AFases) in synergistic interactions within cellulolytic mixtures has introduced a paradigm shift in the search for hydrolytic enzymes. The aim of this study was to characterize novel AFase genes encoding enzymes with differing temperature optima and thermostabilities for use in hydrolytic cocktails. RESULTS Three fosmids, pFos-H4, E3 and D3 were selected from the cloned metagenome of high temperature compost, expressed in Escherichia coli and subsequently purified to homogeneity from cell lysate. All the AFases were clustered within the GH51 AFase family and shared a homo-hexameric structure. Both AFase-E3 and H4 showed optimal activity at 60 °C while AFase-D3 had unique properties as it showed optimal activity at 25 °C as well as the ability to maintain substantial activity at temperatures as high as 90 °C. However, AFase-E3 was the most thermostable amongst the three AFases showing full activity even at 70 °C. The maximum activity was observed at a pH profile between pH 4.0-6.0 for all three AFases with optimal activity for AFase H4, D3 and E3 at pH 5.0, 4.5 and 4.0, respectively. All the AFases showed KM range between 0.31 mM and 0.43 mM, Kcat range between 131 s- 1 and 219 s- 1 and the specific activity for AFase-H4, AFases-E3 and was 143, 228 and 175 U/mg, respectively. AFases-E3 and D3 displayed activities against pNP-β-L-arabinopyranoside and pNP-β-L-mannopyranoside respectively, and both hydrolysed pNP-β-D-glucopyranoside. CONCLUSION All three AFases displayed different biochemical characteristics despite all showing conserved overall structural similarity with typical domains of AFases belonging to GH51 family. The hydrolysis of cellobiose by a GH51 family AFase is demonstrated for the first time in this study.
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Affiliation(s)
- Brent Fortune
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa
| | - Sizwe Mhlongo
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa
| | - Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa
| | - Robert Huddy
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa.,Centre for Bioprocess Engineering Research, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Mariette Smart
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa.,Centre for Bioprocess Engineering Research, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa.
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14
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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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15
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α-l-Arabinofuranosidase: A Potential Enzyme for the Food Industry. ENERGY, ENVIRONMENT, AND SUSTAINABILITY 2019. [DOI: 10.1007/978-981-13-3263-0_12] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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16
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Jamaldheen SB, Sharma K, Rani A, Moholkar VS, Goyal A. Comparative analysis of pretreatment methods on sorghum (Sorghum durra) stalk agrowaste for holocellulose content. Prep Biochem Biotechnol 2018; 48:457-464. [DOI: 10.1080/10826068.2018.1466148] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Sumitha Banu Jamaldheen
- Centre for Energy, Indian Institute of Technology Guwahati, Guwahati, India
- DBT PAN-IIT Center for Bioenergy, Indian Institute of Technology Guwahati, Guwahati, India
| | - Kedar Sharma
- DBT PAN-IIT Center for Bioenergy, Indian Institute of Technology Guwahati, Guwahati, India
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Aruna Rani
- DBT PAN-IIT Center for Bioenergy, Indian Institute of Technology Guwahati, Guwahati, India
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Vijayanand S. Moholkar
- Centre for Energy, Indian Institute of Technology Guwahati, Guwahati, India
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Arun Goyal
- Centre for Energy, Indian Institute of Technology Guwahati, Guwahati, India
- DBT PAN-IIT Center for Bioenergy, Indian Institute of Technology Guwahati, Guwahati, India
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
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17
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Low-resolution SAXS and comparative modeling based structure analysis of endo-β-1,4-xylanase a family 10 glycoside hydrolase from Pseudopedobacter saltans comb. nov. Int J Biol Macromol 2018; 112:1104-1114. [DOI: 10.1016/j.ijbiomac.2018.02.037] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 02/05/2018] [Accepted: 02/07/2018] [Indexed: 11/20/2022]
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18
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A thermophilic α-l-Arabinofuranosidase from Geobacillus vulcani GS90: heterologous expression, biochemical characterization, and its synergistic action in fruit juice enrichment. Eur Food Res Technol 2018. [DOI: 10.1007/s00217-018-3075-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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19
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de Camargo BR, Claassens NJ, Quirino BF, Noronha EF, Kengen SW. Heterologous expression and characterization of a putative glycoside hydrolase family 43 arabinofuranosidase from Clostridium thermocellum B8. Enzyme Microb Technol 2018; 109:74-83. [DOI: 10.1016/j.enzmictec.2017.09.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 09/28/2017] [Accepted: 09/30/2017] [Indexed: 11/30/2022]
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20
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Maruthamuthu M, Jiménez DJ, van Elsas JD. Characterization of a furan aldehyde-tolerant β-xylosidase/α-arabinosidase obtained through a synthetic metagenomics approach. J Appl Microbiol 2017; 123:145-158. [PMID: 28489302 DOI: 10.1111/jam.13484] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 04/26/2017] [Accepted: 05/03/2017] [Indexed: 12/16/2022]
Abstract
AIMS The aim of the study was to characterize 10 hemicellulolytic enzymes obtained from a wheat straw-degrading microbial consortium. METHODS AND RESULTS Based on previous metagenomics analyses, 10 glycosyl hydrolases were selected, codon-optimized, synthetized, cloned and expressed in Escherichia coli. Nine of the overexpressed recombinant proteins accumulated in cellular inclusion bodies, whereas one, a 37·5-kDa protein encoded by gene xylM1989, was found in the soluble fractions. The resulting protein, denoted XylM1989, showed β-xylosidase and α-arabinosidase activities. It fell in the GH43 family and resembled a Sphingobacterium sp. protein. The XylM1989 showed optimum activity at 20°C and pH 8·0. Interestingly, it kept approximately 80% of its β-xylosidase activity in the presence of 0·5% (w/v) furfural and 0·1% (w/v) 5-hydroxymethylfurfural. Additionally, the presence of Ca2+ , Mg2+ and Mn2+ ions increased the enzymatic activity and conferred complete tolerance to 500 mmol l-1 of xylose. Protein XylM1989 is also able to release sugars from complex polysaccharides. CONCLUSION We report the characterization of a novel bifunctional hemicellulolytic enzyme obtained through a targeted synthetic metagenomics approach. SIGNIFICANCE AND IMPACT OF THE STUDY The properties of XylM1989 turn this protein into a promising enzyme that could be useful for the efficient saccharification of plant biomass.
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Affiliation(s)
- M Maruthamuthu
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - D J Jiménez
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - J D van Elsas
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
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21
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Goyal A, Ahmed S, Sharma K, Gupta V, Bule P, Alves VD, Fontes CMGA, Najmudin S. Molecular determinants of substrate specificity revealed by the structure of Clostridium thermocellum arabinofuranosidase 43A from glycosyl hydrolase family 43 subfamily 16. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:1281-1289. [PMID: 27917828 DOI: 10.1107/s205979831601737x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/28/2016] [Indexed: 11/11/2022]
Abstract
The recent division of the large glycoside hydrolase family 43 (GH43) into subfamilies offers a renewed opportunity to develop structure-function studies aimed at clarifying the molecular determinants of substrate specificity in carbohydrate-degrading enzymes. α-L-Arabinofuranosidases (EC 3.2.1.55) remove arabinose side chains from heteropolysaccharides such as xylan and arabinan. However, there is some evidence suggesting that arabinofuranosidases are substrate-specific, being unable to display a debranching activity on different polysaccharides. Here, the structure of Clostridium thermocellum arabinofuranosidase 43A (CtAbf43A), which has been shown to act in the removal of arabinose side chains from arabinoxylan but not from pectic arabinan, is reported. CtAbf43A belongs to GH43 subfamily 16, the members of which have a restricted capacity to attack xylans. The crystal structure of CtAbf43A comprises a five-bladed β-propeller fold typical of GH43 enzymes. CtAbf43A displays a highly compact architecture compatible with its high thermostability. Analysis of CtAbf43A along with the other member of GH43 subfamily 16 with known structure, the Bacillus subtilis arabinofuranosidase BsAXH-m2,3, suggests that the specificity of subfamily 16 for arabinoxylan is conferred by a long surface substrate-binding cleft that is complementary to the xylan backbone. The lack of a curved-shaped carbohydrate-interacting platform precludes GH43 subfamily 16 enzymes from interacting with the nonlinear arabinan scaffold and therefore from deconstructing this polysaccharide.
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Affiliation(s)
- Arun Goyal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India
| | - Shadab Ahmed
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411 007, India
| | - Kedar Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India
| | - Vikas Gupta
- Qiagen Aarhus, Silkeborgvej 2, 8000 Aarhus C, Denmark
| | - Pedro Bule
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1360-477 Lisbon, Portugal
| | - Victor D Alves
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1360-477 Lisbon, Portugal
| | - Carlos M G A Fontes
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1360-477 Lisbon, Portugal
| | - Shabir Najmudin
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1360-477 Lisbon, Portugal
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22
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Freire F, Verma A, Bule P, Alves VD, Fontes CMGA, Goyal A, Najmudin S. Conservation in the mechanism of glucuronoxylan hydrolysis revealed by the structure of glucuronoxylan xylanohydrolase (CtXyn30A) from Clostridium thermocellum. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:1162-1173. [PMID: 27841749 DOI: 10.1107/s2059798316014376] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 09/09/2016] [Indexed: 11/10/2022]
Abstract
Glucuronoxylan endo-β-1,4-xylanases cleave the xylan chain specifically at sites containing 4-O-methylglucuronic acid substitutions. These enzymes have recently received considerable attention owing to their importance in the cooperative hydrolysis of heteropolysaccharides. However, little is known about the hydrolysis of glucuronoxylans in extreme environments. Here, the structure of a thermostable family 30 glucuronoxylan endo-β-1,4-xylanase (CtXyn30A) from Clostridium thermocellum is reported. CtXyn30A is part of the cellulosome, a highly elaborate multi-enzyme complex secreted by the bacterium to efficiently deconstruct plant cell-wall carbohydrates. CtXyn30A preferably hydrolyses glucuronoxylans and displays maximum activity at pH 6.0 and 70°C. The structure of CtXyn30A displays a (β/α)8 TIM-barrel core with a side-associated β-sheet domain. Structural analysis of the CtXyn30A mutant E225A, solved in the presence of xylotetraose, revealed xylotetraose-cleavage oligosaccharides partially occupying subsites -3 to +2. The sugar ring at the +1 subsite is held in place by hydrophobic stacking interactions between Tyr139 and Tyr200 and hydrogen bonds to the OH group of Tyr227. Although family 30 glycoside hydrolases are retaining enzymes, the xylopyranosyl ring at the -1 subsite of CtXyn30A-E225A appears in the α-anomeric configuration. A set of residues were found to be strictly conserved in glucuronoxylan endo-β-1,4-xylanases and constitute the molecular determinants of the restricted specificity displayed by these enzymes. CtXyn30A is the first thermostable glucuronoxylan endo-β-1,4-xylanase described to date. This work reveals that substrate recognition by both thermophilic and mesophilic glucuronoxylan endo-β-1,4-xylanases is modulated by a conserved set of residues.
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Affiliation(s)
- Filipe Freire
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Anil Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India
| | - Pedro Bule
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Victor D Alves
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Carlos M G A Fontes
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Arun Goyal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India
| | - Shabir Najmudin
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
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Novel Trifunctional Xylanolytic Enzyme Axy43A from Paenibacillus curdlanolyticus Strain B-6 Exhibiting Endo-Xylanase, β-d-Xylosidase, and Arabinoxylan Arabinofuranohydrolase Activities. Appl Environ Microbiol 2016; 82:6942-6951. [PMID: 27663030 DOI: 10.1128/aem.02256-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/13/2016] [Indexed: 11/20/2022] Open
Abstract
The axy43A gene encoding the intracellular trifunctional xylanolytic enzyme from Paenibacillus curdlanolyticus B-6 was cloned and expressed in Escherichia coli Recombinant PcAxy43A consisting of a glycoside hydrolase family 43 and a family 6 carbohydrate-binding module exhibited endo-xylanase, β-xylosidase, and arabinoxylan arabinofuranohydrolase activities. PcAxy43A hydrolyzed xylohexaose and birch wood xylan to release a series of xylooligosaccharides, indicating that PcAxy43A contained endo-xylanase activity. PcAxy43A exhibited β-xylosidase activity toward a chromogenic substrate, p-nitrophenyl-β-d-xylopyranoside, and xylobiose, while it preferred to hydrolyze long-chain xylooligosaccharides rather than xylobiose. In addition, surprisingly, PcAxy43A showed arabinoxylan arabinofuranohydrolase activity; that is, it released arabinose from both singly and doubly arabinosylated xylose, α-l-Araf-(1→2)-d-Xylp or α-l-Araf-(1→3)-d-Xylp and α-l-Araf-(1→2)-[α-l-Araf-(1→3)]-β-d-Xylp Moreover, the combination of PcAxy43A and P. curdlanolyticus B-6 endo-xylanase Xyn10C greatly improved the efficiency of xylose and arabinose production from the highly substituted rye arabinoxylan, suggesting that these two enzymes function synergistically to depolymerize arabinoxylan. Therefore, PcAxy43A has the potential for the saccharification of arabinoxylan into simple sugars for many applications. IMPORTANCE In this study, the glycoside hydrolase 43 (GH43) intracellular multifunctional endo-xylanase, β-xylosidase, and arabinoxylan arabinofuranohydrolase (AXH) from P. curdlanolyticus B-6 were characterized. Interestingly, PcAxy43A AXH showed a new property that acted on both the C(O)-2 and C(O)-3 positions of xylose residues doubly substituted with arabinosyl, which usually obstruct the action of xylanolytic enzymes. Furthermore, the studies here show interesting properties for the processing of xylans from cereal grains, particularly rye arabinoxylan, and show a novel relationship between PcAxy43A and endo-xylanase Xyn10C from strain B-6, providing novel metabolic potential for processing arabinoxylans into xylose and arabinose.
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A novel member of family 30 glycoside hydrolase subfamily 8 glucuronoxylan endo-β-1,4-xylanase (CtXynGH30) from Clostridium thermocellum orchestrates catalysis on arabinose decorated xylans. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.04.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Coyle T, Brumer H, Stubbs KA. An improved preparation of some aryl α-l-arabinofuranosides for use as chromogenic substrates for α-l-arabinofuranosidases. CAN J CHEM 2015. [DOI: 10.1139/cjc-2015-0227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A short, robust, and expedient synthesis of various aryl α-l-arabinofuranosides using a trichloroacetimidate precursor is described. The procedure is compatible with a range of phenols with varying pKa values and may be amenable for preparing a wide range of other glycosides.
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Affiliation(s)
- Travis Coyle
- School of Chemistry and Biochemistry, the University of Western Australia, Crawley, WA 6009, Australia
| | - Harry Brumer
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Keith A. Stubbs
- School of Chemistry and Biochemistry, the University of Western Australia, Crawley, WA 6009, Australia
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Gupta A, Das SP, Ghosh A, Choudhary R, Das D, Goyal A. Bioethanol production from hemicellulose rich Populus nigra involving recombinant hemicellulases from Clostridium thermocellum. BIORESOURCE TECHNOLOGY 2014; 165:205-13. [PMID: 24767793 DOI: 10.1016/j.biortech.2014.03.132] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 03/22/2014] [Accepted: 03/24/2014] [Indexed: 05/11/2023]
Abstract
Bioethanol was produced from poplar leafy biomass rich in hemicelluloses content involving recombinant Clostridium thermocellum hemicellulases and pentose sugar utilizing Candida shehatae. FT-IR analysis revealed effective AFEX pretreatment of poplar leaves. Repetitive batch strategy yielded ∼1.5-fold rise in cell biomass and specific activity of both, acetylxylanesterase (Axe) and GH43 hemicellulase. TLC and HPAEC exhibited xylose and arabinose release from hydrolyzed biomass. SSF trial with 1% (wv(-1)) pretreated poplar and mixed enzymes showed ∼1.5-fold higher ethanol titre as compared with SHF. The shake flask SSF with 5% (wv(-1)) pretreated poplar furnished 4.56 and 5.43gL(-1) ethanol with Axe and mixed enzymes, respectively. Whereas, bioreactor scale-up exhibited ∼1.25-fold increase in ethanol titres (5.68, 6.75gL(-1)) as compared with shake flask with an yield of 0.295 (gg(-1)) and 0.351 (gg(-1)), respectively with Axe and mixed enzymes.
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Affiliation(s)
- Ashutosh Gupta
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Saprativ P Das
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Arabinda Ghosh
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Rajan Choudhary
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur 713209, West Bengal, India
| | - Debasish Das
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Arun Goyal
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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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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Goyal A, Ahmed S, Fontes CMGA, Najmudin S. Crystallization and preliminary X-ray crystallographic analysis of a novel α-L-arabinofuranosidase (CtGH43) from Clostridium thermocellum ATCC 27405. Acta Crystallogr F Struct Biol Commun 2014; 70:616-8. [PMID: 24817722 PMCID: PMC4014331 DOI: 10.1107/s2053230x14006402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 03/22/2014] [Indexed: 11/10/2022] Open
Abstract
The truncated carbohydrate-active enzyme belonging to family 43 glycoside hydrolase from Clostridium thermocellum (CtGH43) is an α-L-arabinofuranosidase that in combination with endoxylanase leads to complete breakdown of L-arabinosyl-substituted xylans. The recombinant enzyme CtGH43 from C. thermocellum was overexpressed in Escherichia coli and purified by immobilized metal-ion affinity chromatography. The recombinant CtGH43 has a molecular mass of 35.86 kDa. Preliminary structural characterization was carried out on CtGH43 crystallized from different conditions, which gave either cube-shaped or brick-shaped crystals. These diffracted to a resolution of 1.65 Å for the cubic form and 1.1 Å for the monoclinic form. Molecular replacement was used to solve the CtGH43 structure.
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Affiliation(s)
- Arun Goyal
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, 781 039, India
- CIISA–Faculdade de Medicina Veterinaria, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
| | - Shadab Ahmed
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, 781 039, India
| | - Carlos M. G. A. Fontes
- CIISA–Faculdade de Medicina Veterinaria, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
| | - Shabir Najmudin
- CIISA–Faculdade de Medicina Veterinaria, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
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