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Biochemical characterization of a thermophilic exo-arabinanase from the filamentous fungus Rasamsonia emersonii. J Biosci Bioeng 2022; 133:316-322. [PMID: 35031213 DOI: 10.1016/j.jbiosc.2021.12.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 11/23/2022]
Abstract
Arabinan in plant cell wall constitutes a major source of arabinose and arabino-oligosaccharides in nature. Exo-α-l-1,5-arabinanases release arabinose or arabino-oligosaccharides from arabinan in an exo-acting manner and therefore contribute to arabinan degradation. In this study, an exo-α-l-1,5-arabinanase belonging to GH93 family was identified from the thermophilic filamentous fungus Rasamsonia emersonii. The corresponding encoding gene (Reabn93) was cloned from the R. emersonii genome and heterologously expressed in Pichia pastoris. The purified recombinant ReAbn93 exhibited the maximum activity at 70 °C and retained 70% of its activity after incubation at 70 °C for 3 h ReAbn93 had an acidic pH optimum (pH 4.0) but remained stable over a broad pH range (pH 3-9). The specific activity of ReAbn93 toward linear arabinan under optimal conditions was 466.08 U mg-1. Similar to the few other reported GH93 members, ReAbn93 degrades linear arabinan or arabino-oligosaccharides in an exo-acting manner with arabinobiose as the only hydrolytic product. Of note, ReAbn93 possessed remarkably better thermostability and higher specific activity compared to the only reported thermophilic counterpart in GH93, and therefore holds potential in relevant biotechnological applications.
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Kondo T, Kichijo M, Maruta A, Nakaya M, Takenaka S, Arakawa T, Fushinobu S, Sakamoto T. Structural and functional analysis of gum arabic l-rhamnose-α-1,4-d-glucuronate lyase establishes a novel polysaccharide lyase family. J Biol Chem 2021; 297:101001. [PMID: 34303708 PMCID: PMC8377490 DOI: 10.1016/j.jbc.2021.101001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 11/24/2022] Open
Abstract
Gum arabic (GA) is widely used as an emulsion stabilizer and coating in several industrial applications, such as foods and pharmaceuticals. GA contains a complex carbohydrate moiety, and the nonreducing ends of the side chains are often capped with l-rhamnose; thus, enzymes that can remove these caps are promising tools for the structural analysis of the carbohydrates comprising GA. In this study, GA-specific l-rhamnose-α-1,4-d-glucuronate lyase from the fungus Fusarium oxysporum 12S (FoRham1) was cloned and characterized. FoRham1 showed the highest amino acid sequence similarity with enzymes belonging to the glycoside hydrolase family 145; however, the catalytic residue on the posterior pocket of the β-propeller fold protein was not conserved. The catalytic residues of FoRham1 were instead conserved with ulvan lyases belonging to polysaccharide lyase family 24. Kinetic analysis showed that FoRham1 has the highest catalytic efficiency for the substrate α-l-rhamnose-(1→4)-d-glucuronic acid. The crystal structures of ligand-free and α-l-rhamnose-(1→4)-d-glucuronic acid –bound FoRham1 were determined, and the active site was identified on the anterior side of the β-propeller. The three-dimensional structure of the active site and mutagenesis analysis revealed the detailed catalytic mechanism of FoRham1. Our findings offer a new enzymatic tool for the further analysis of the GA carbohydrate structure and for elucidating its physiological functions in plants. Based on these results, we renamed glycoside hydrolase family 145 as a new polysaccharide lyase family 42, in which FoRham1 is included.
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Affiliation(s)
- Tatsuya Kondo
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Miyu Kichijo
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Akiho Maruta
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Makoto Nakaya
- Center for Research and Development of Bioresources, Organization for Research Promotion, Osaka Prefecture University, Osaka, Japan
- Department of Nutrition, Otemae College of Nutrition and Confectionery, Osaka, Japan
| | - Shigeo Takenaka
- Graduate School of Comprehensive Rehabilitation, Osaka Prefecture University, Osaka, Japan
| | - Takatoshi Arakawa
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Tatsuji Sakamoto
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
- For correspondence: Tatsuji Sakamoto
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Velasco J, Oliva B, Gonçalves AL, Lima AS, Ferreira G, França BA, Mulinari EJ, Gonçalves TA, Squina FM, Kadowaki MAS, Maiorano A, Polikarpov I, Oliveira LCD, Segato F. Functional characterization of a novel thermophilic exo-arabinanase from Thermothielavioides terrestris. Appl Microbiol Biotechnol 2020; 104:8309-8326. [PMID: 32813063 DOI: 10.1007/s00253-020-10806-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 07/06/2020] [Accepted: 08/02/2020] [Indexed: 10/23/2022]
Abstract
Arabinanases from glycoside hydrolase family GH93 are enzymes with exo-activity that hydrolyze the α-1,5 bonds between arabinose residues present on arabinan. Currently, several initiatives aiming to use byproducts rich in arabinan such as pectin and sugar beet pulp as raw material to produce various compounds of interest are being developed. However, it is necessary to use robust enzymes that have an optimal performance under pH and temperature conditions used in the industrial processes. In this work, the first GH93 from the thermophilic fungus Thermothielavioides terrestris (Abn93T) was heterologously expressed in Aspergillus nidulans, purified and biochemically characterized. The enzyme is a thermophilic glycoprotein (optimum activity at 70 °C) with prolonged stability in acid pHs (4.0 to 6.5). The presence of glycosylation affected slightly the hydrolytic capacity of the enzyme, which was further increased by 34% in the presence of 1 mM CoCl2. Small-angle X-ray scattering results show that Abn93T is a globular-like-shaped protein with a slight bulge at one end. The hydrolytic mechanism of the enzyme was elucidated using capillary zone electrophoresis and molecular docking calculations. Abn93T has an ability to produce (in synergism with arabinofuranosidases) arabinose and arabinobiose from sugar beet arabinan, which can be explored as fermentable sugars and prebiotics. KEY POINTS: • Thermophilic exo-arabinanase from family GH93 • Molecular basis of arabinan depolymerization.
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Affiliation(s)
- Josman Velasco
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Bianca Oliva
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Aline Larissa Gonçalves
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Awana Silva Lima
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Gislene Ferreira
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Bruno Alves França
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Evandro José Mulinari
- Departamento de Física e Ciências Aplicadas, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Thiago Augusto Gonçalves
- Departamento de Bioquímica, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil.,Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, SP, Brazil
| | - Fábio Márcio Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, SP, Brazil
| | - Marco Antonio Seiki Kadowaki
- Departamento de Física e Ciências Aplicadas, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Alfredo Maiorano
- Instituto de Pesquisas Tecnológicas do Estado de São Paulo, Diretoria de Operações e Negócios, Núcleo de Bionanomanufatura, São Paulo, SP, Brazil
| | - Igor Polikarpov
- Departamento de Física e Ciências Aplicadas, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Leandro Cristante de Oliveira
- Department of Physics - Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto, SP, Brazil
| | - Fernando Segato
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil.
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Iwata K, Terazima M, Masuhara H. Novel physical chemistry approaches in biophysical researches with advanced application of lasers: Detection and manipulation. Biochim Biophys Acta Gen Subj 2017; 1862:335-357. [PMID: 29108958 DOI: 10.1016/j.bbagen.2017.11.003] [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: 08/01/2017] [Revised: 10/30/2017] [Accepted: 11/01/2017] [Indexed: 10/18/2022]
Abstract
Novel methodologies utilizing pulsed or intense CW irradiation obtained from lasers have a major impact on biological sciences. In this article, recent development in biophysical researches fully utilizing the laser irradiation is described for three topics, time-resolved fluorescence spectroscopy, time-resolved thermodynamics, and manipulation of the biological assemblies by intense laser irradiation. First, experimental techniques for time-resolved fluorescence spectroscopy are concisely explained in Section 2. As an example of the recent application of time-resolved fluorescence spectroscopy to biological systems, evaluation of the viscosity of lipid bilayer membranes is described. The results of the spectroscopic experiments strongly suggest the presence of heterogeneous membrane structure with two different viscosity values in liposomes formed by a single phospholipid. Section 3 covers the time-resolved thermodynamics. Thermodynamical properties are important to characterize biomolecules. However, measurement of these quantities for short-lived intermediate species has been impossible by traditional thermodynamical techniques. Recently, development of a spectroscopic method based on the transient grating method enables us to measure these quantities and also to elucidate reaction kinetics which cannot be detected by other spectroscopic methods. The principle of the measurements and applications to some protein reactions are reviewed. Manipulation and fabrication of supramolecues, amino acids, proteins, and living cells by intense laser irradiation are described in Section 4. Unconventional assembly, crystallization and growth, amyloid fibril formation, and living cell manipulation are achieved by CW laser trapping and femtosecond laser-induced cavitation bubbling. Their spatio-temporal controllability is opening a new avenue in the relevant molecular and bioscience research fields. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Koichi Iwata
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan.
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Hiroshi Masuhara
- Department of Applied Chemistry, National Chiao Tung University, 1001 Ta Hsueh Rd., Hsinchu 30010, Taiwan.
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Coyle T, Debowski AW, Varrot A, Stubbs KA. Exploiting sp 2 -Hybridisation in the Development of Potent 1,5-α-l-Arabinanase Inhibitors. Chembiochem 2017; 18:974-978. [PMID: 28266777 DOI: 10.1002/cbic.201700073] [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: 02/14/2017] [Indexed: 11/07/2022]
Abstract
The synthesis of potent inhibitors of GH93 arabinanases as well as a synthesis of a chromogenic substrate to measure GH93 arabinanase activity are described. An insight into the reasons behind the potency of the inhibitors was gained through X-ray crystallographic analysis of the arabinanase Arb93A from Fusarium graminearum. These compounds lay a foundation for future inhibitor development as well as for the use of the chromogenic substrate in biochemical studies of GH93 arabinanases.
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Affiliation(s)
- Travis Coyle
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
- Present address: School of Chemistry, University College Dublin, Stillorgan Road, Belfield, Dublin, 4, Ireland
| | - Aleksandra W Debowski
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
- School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Annabelle Varrot
- CERMAV, Université Grenoble Alpes, CNRS, 38000, Grenoble, France
| | - Keith A Stubbs
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
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Lang C, Yang R, Yang Y, Gao B, Zhao L, Wei W, Wang H, Matsukawa S, Xie J, Wei D. An Acid-Adapted Endo-α-1,5-L-arabinanase for Pectin Releasing. Appl Biochem Biotechnol 2016; 180:900-916. [PMID: 27246002 DOI: 10.1007/s12010-016-2141-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 05/13/2016] [Indexed: 10/21/2022]
Abstract
An arabinanase gene was cloned by overlap-PCR from Penicillium sp. Y702 and expressed in Pichia pastoris. The recombinant enzyme was named AbnC702 with 20 U/mg of endo-arabinanase activity toward linear α-1,5-L-arabinan. The optimal pH and temperature of AbnC702 were 5.0 and 50 °C, respectively. The recombinant AbnC702 was highly stable at pH 5.0-7.0 and 50 °C. It could retain about 72.3 % of maximum specific activity at pH 5.0 after incubation for 2.5 h, which indicated AbnC702 was an acid-adapted enzyme. The K m and V max values were 24.8 ± 4.7 mg/ml and 88.5 ± 5.6 U/mg, respectively. A three-dimensional structure of AbnC702 was made by homology modeling, and the counting of acidic/basic amino residues within the region of 10 Å around the active site, as well the hydrogen bonds within the area of 5 Å around the active site, might theoretically interpret the acid adaptability of AbnC702. Analysis of hydrolysis products by thin layer chromatography (TLC) combined with high-performance liquid chromatography (HPLC) verified that the recombinant AbnC702 was an endo-1,5-α-L-arabinanase, which yielded arabinobiose and arabinotriose as major products. AbnC702 was applied in pectin extraction from apple pomace with synergistic action of α-L-arabinofuranosidase.
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Affiliation(s)
- Chong Lang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.,Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Rujian Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.,Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Ying Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.,Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Bei Gao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.,Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Li Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.,Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Wei Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.,Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Hualei Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.,Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Shingo Matsukawa
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, 108-8477, Japan
| | - Jingli Xie
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China. .,Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China. .,Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, People's Republic of China.
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.,Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.,Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, People's Republic of China
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Mardones W, Callegari E, Eyzaguirre J. Heterologous expression of a Penicillium purpurogenum exo-arabinanase in Pichia pastoris and its biochemical characterization. Fungal Biol 2015; 119:1267-1278. [DOI: 10.1016/j.funbio.2015.09.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 09/28/2015] [Accepted: 09/29/2015] [Indexed: 11/27/2022]
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Abstract
SUMMARY Biomass is constructed of dense recalcitrant polymeric materials: proteins, lignin, and holocellulose, a fraction constituting fibrous cellulose wrapped in hemicellulose-pectin. Bacteria and fungi are abundant in soil and forest floors, actively recycling biomass mainly by extracting sugars from holocellulose degradation. Here we review the genome-wide contents of seven Aspergillus species and unravel hundreds of gene models encoding holocellulose-degrading enzymes. Numerous apparent gene duplications followed functional evolution, grouping similar genes into smaller coherent functional families according to specialized structural features, domain organization, biochemical activity, and genus genome distribution. Aspergilli contain about 37 cellulase gene models, clustered in two mechanistic categories: 27 hydrolyze and 10 oxidize glycosidic bonds. Within the oxidative enzymes, we found two cellobiose dehydrogenases that produce oxygen radicals utilized by eight lytic polysaccharide monooxygenases that oxidize glycosidic linkages, breaking crystalline cellulose chains and making them accessible to hydrolytic enzymes. Among the hydrolases, six cellobiohydrolases with a tunnel-like structural fold embrace single crystalline cellulose chains and cooperate at nonreducing or reducing end termini, splitting off cellobiose. Five endoglucanases group into four structural families and interact randomly and internally with cellulose through an open cleft catalytic domain, and finally, seven extracellular β-glucosidases cleave cellobiose and related oligomers into glucose. Aspergilli contain, on average, 30 hemicellulase and 7 accessory gene models, distributed among 9 distinct functional categories: the backbone-attacking enzymes xylanase, mannosidase, arabinase, and xyloglucanase, the short-side-chain-removing enzymes xylan α-1,2-glucuronidase, arabinofuranosidase, and xylosidase, and the accessory enzymes acetyl xylan and feruloyl esterases.
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Yoshikawa HY, Murai R, Adachi H, Sugiyama S, Maruyama M, Takahashi Y, Takano K, Matsumura H, Inoue T, Murakami S, Masuhara H, Mori Y. Laser ablation for protein crystal nucleation and seeding. Chem Soc Rev 2014; 43:2147-58. [DOI: 10.1039/c3cs60226e] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Chlubnova I, Legentil L, Dureau R, Pennec A, Almendros M, Daniellou R, Nugier-Chauvin C, Ferrières V. Specific and non-specific enzymes for furanosyl-containing conjugates: biosynthesis, metabolism, and chemo-enzymatic synthesis. Carbohydr Res 2012; 356:44-61. [PMID: 22554502 DOI: 10.1016/j.carres.2012.04.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 04/02/2012] [Accepted: 04/03/2012] [Indexed: 11/27/2022]
Abstract
There is no doubt now that the synthesis of compounds of varying complexity such as saccharides and derivatives thereof continuously grows with enzymatic methods. This review focuses on recent basic knowledge on enzymes specifically involved in the biosynthesis and degradation of furanosyl-containing polysaccharides and conjugates. Moreover, and when possible, biocatalyzed approaches, alternative to standard synthesis, will be detailed in order to strengthen the high potential of these biocatalysts to go further with the preparation of rare furanosides. Interesting results will be also proposed with chemo-enzymatic processes based on nonfuranosyl-specific enzymes.
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Affiliation(s)
- Ilona Chlubnova
- Ecole Nationale Supérieure de Chimie de Rennes, CNRS, UMR 6226, Avenue du Général Leclerc, CS 50837, 35708 Rennes Cedex 7, France
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Goddard-Borger ED, Carapito R, Jeltsch JM, Phalip V, Stick RV, Varrot A. α-l-Arabinofuranosylated pyrrolidines as arabinanase inhibitors. Chem Commun (Camb) 2011; 47:9684-6. [DOI: 10.1039/c1cc13675e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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