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Zhu E, Hiramatsu K, Inoue T, Mori K, Tashiro K, Fujita K, Karashima T, Takashita H, Okutsu K, Yoshizaki Y, Takamine K, Tamaki H, Futagami T. Deficiency of β-xylosidase activity in Aspergillus luchuensis mut. kawachii IFO 4308. Biosci Biotechnol Biochem 2024; 88:816-823. [PMID: 38621718 DOI: 10.1093/bbb/zbae046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/09/2024] [Indexed: 04/17/2024]
Abstract
In this study, we investigated a deleterious mutation in the β-xylosidase gene, xylA (AkxylA), in Aspergillus luchuensis mut. kawachii IFO 4308 by constructing an AkxylA disruptant and complementation strains of AkxylA and xylA derived from A. luchuensis RIB2604 (AlxylA), which does not harbor the mutation in xylA. Only the AlxylA complementation strain exhibited significantly higher growth and substantial β-xylosidase activity in medium containing xylan, accompanied by an increase in XylA expression. This resulted in lower xylobiose and higher xylose concentrations in the mash of barley shochu. These findings suggest that the mutation in xylA affects xylose levels during the fermentation process. Because the mutation in xylA was identified not only in the genome of strain IFO 4308 but also the genomes of other industrial strains of A. luchuensis and A. luchuensis mut. kawachii, these findings enhance our understanding of the genetic factors that affect the fermentation characteristics.
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Affiliation(s)
- Enkang Zhu
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Korimoto, Kagoshima, Japan
- School of Food Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Kentaro Hiramatsu
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Taiga Inoue
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Kazuki Mori
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Motooka, Nishi-ku, Fukuoka, Japan
| | - Kosuke Tashiro
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Motooka, Nishi-ku, Fukuoka, Japan
| | - Kiyotaka Fujita
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Korimoto, Kagoshima, Japan
| | | | | | - Kayu Okutsu
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Korimoto, Kagoshima, Japan
- United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Yumiko Yoshizaki
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Korimoto, Kagoshima, Japan
- United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima, Japan
- Education and Research Center for Fermentation Studies, Faculty of Agriculture, Korimoto, Kagoshima University, Kagoshima, Japan
| | - Kazunori Takamine
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Korimoto, Kagoshima, Japan
- United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima, Japan
- Education and Research Center for Fermentation Studies, Faculty of Agriculture, Korimoto, Kagoshima University, Kagoshima, Japan
| | - Hisanori Tamaki
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Korimoto, Kagoshima, Japan
- United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima, Japan
- Education and Research Center for Fermentation Studies, Faculty of Agriculture, Korimoto, Kagoshima University, Kagoshima, Japan
| | - Taiki Futagami
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, Korimoto, Kagoshima, Japan
- United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima, Japan
- Education and Research Center for Fermentation Studies, Faculty of Agriculture, Korimoto, Kagoshima University, Kagoshima, Japan
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Fujita K, Tsunomachi H, Lixia P, Maruyama S, Miyake M, Dakeshita A, Kitahara K, Tanaka K, Ito Y, Ishiwata A, Fushinobu S. Bifidobacterial GH146 β-L-arabinofuranosidase for the removal of β1,3-L-arabinofuranosides on plant glycans. Appl Microbiol Biotechnol 2024; 108:199. [PMID: 38324037 PMCID: PMC10850190 DOI: 10.1007/s00253-024-13014-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/29/2023] [Accepted: 01/14/2024] [Indexed: 02/08/2024]
Abstract
L-Arabinofuranosides with β-linkages are present in several plant molecules, such as arabinogalactan proteins (AGPs), extensin, arabinan, and rhamnogalacturonan-II. We previously characterized a β-L-arabinofuranosidase from Bifidobacterium longum subsp. longum JCM 1217, Bll1HypBA1, which was found to belong to the glycoside hydrolase (GH) family 127. This strain encodes two GH127 genes and two GH146 genes. In the present study, we characterized a GH146 β-L-arabinofuranosidase, Bll3HypBA1 (BLLJ_1848), which was found to constitute a gene cluster with AGP-degrading enzymes. This recombinant enzyme degraded AGPs and arabinan, which contain Araf-β1,3-Araf structures. In addition, the recombinant enzyme hydrolyzed oligosaccharides containing Araf-β1,3-Araf structures but not those containing Araf-β1,2-Araf and Araf-β1,5-Araf structures. The crystal structures of Bll3HypBA1 were determined at resolutions up to 1.7 Å. The monomeric structure of Bll3HypBA1 comprised a catalytic (α/α)6 barrel and two β-sandwich domains. A hairpin structure with two β-strands was observed in Bll3HypBA1, to extend from a β-sandwich domain and partially cover the active site. The active site contains a Zn2+ ion coordinated by Cys3-Glu and exhibits structural conservation of the GH127 cysteine glycosidase Bll1HypBA1. This is the first study to report on a β1,3-specific β-L-arabinofuranosidase. KEY POINTS: • β1,3-l-Arabinofuranose residues are present in arabinogalactan proteins and arabinans as a terminal sugar. • β-l-Arabinofuranosidases are widely present in intestinal bacteria. • Bll3HypBA1 is the first enzyme characterized as a β1,3-linkage-specific β-l-arabinofuranosidase.
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Affiliation(s)
- Kiyotaka Fujita
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan.
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan.
| | - Hanako Tsunomachi
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
| | - Pan Lixia
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan
- National Key Laboratory of Non-food Biomass Energy Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, 530007, China
| | - Shun Maruyama
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan
| | - Masayuki Miyake
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan
| | - Aimi Dakeshita
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
| | - Kanefumi Kitahara
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
| | - Katsunori Tanaka
- RIKEN, Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-Ku, Tokyo, 152-8552, Japan
| | - Yukishige Ito
- RIKEN, Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Graduate School of Science, Osaka University, 1-1 Machikaneyama-Cho, Toyonaka, Osaka, 560-0043, Japan
| | - Akihiro Ishiwata
- RIKEN, Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan.
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Hu Y, Hong H, Zhou J, Cui Y, Zhang B, Zhao J. Recent advances in enzymatic properties, preparation methods, and functions of glycoside hydrolase from Bifidobacterium: a review. World J Microbiol Biotechnol 2023; 39:344. [PMID: 37843698 DOI: 10.1007/s11274-023-03770-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/15/2023] [Indexed: 10/17/2023]
Abstract
Bifidobacterium is a major probiotic of intestinal gut flora and exerts many physiological activities, and it is widely applied in the fields of food and medicine. As an important part of Bifidobacterium, glycoside hydrolase plays a role in its physiological activity. With the continuous development and improvement of genetic engineering technology, research on this type of enzyme will play a crucial role in promoting the further development of Bifidobacterium in the field of probiotics. In this review, the preparation methods, enzymatic properties, and functions of glycoside hydrolase extracted from Bifidobacterium are described and summarized. The common method for preparing glycoside hydrolase derived from Bifidobacterium is heterologous expression in Escherichia coli BL21. The optimal pH range for these glycoside hydrolase enzymes is between 4.5 and 7.5; the optimal temperature is between 30 and 50 °C, which is close to the optimal growth condition of Bifidobacterium. Based on substrate specificity, these glycoside hydrolase could hydrolyze synthetic substrates and natural oligosaccharides, including a series of pNP artificial substrates, disaccharide, and trisaccharides, while they have little ability to hydrolyze polysaccharide substrates. This review will be expected to provide a basis for the development of Bifidobacterium as a probiotic element.
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Affiliation(s)
- Yanbo Hu
- School of Food Sciences and Engineering, Chang Chun University, Changchun, 130024, People's Republic of China
| | - Huili Hong
- School of Food Sciences and Engineering, Chang Chun University, Changchun, 130024, People's Republic of China
| | - Jianing Zhou
- School of Food Sciences and Engineering, Chang Chun University, Changchun, 130024, People's Republic of China
| | - Yangyang Cui
- School of Food Sciences and Engineering, Chang Chun University, Changchun, 130024, People's Republic of China
| | - Baochun Zhang
- School of Food Sciences and Engineering, Chang Chun University, Changchun, 130024, People's Republic of China
| | - Jun Zhao
- School of Food Sciences and Engineering, Chang Chun University, Changchun, 130024, People's Republic of China.
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Zhu Z, He M, Huang CH, Ko TP, Zeng YF, Huang YN, Jia S, Lu F, Liu JR, Guo RT. Crystallization and preliminary X-ray diffraction analysis of a novel β-L-arabinofuranosidase (HypBA1) from Bifidobacterium longum. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:636-8. [PMID: 24817727 DOI: 10.1107/s2053230x14001812] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Accepted: 01/25/2014] [Indexed: 11/10/2022]
Abstract
The β-L-arabinofuranosidase (HypBA1) from Bifidobacterium longum JCM 1217 hydrolyzes the β-1,2-linked arabinofuranose disaccharide to release L-arabinoses. HypBA1 was classified into glycoside hydrolase family 127 (GH127) by the CAZy website (http://www.cazy.org/). The enzyme was expressed in Escherichia coli and the purified recombinant protein was crystallized. Crystals belonging to the primitive hexagonal space group P3x21, with unit-cell parameters a = b = 75.9, c = 254.0Å, were obtained by the sitting-drop vapour-diffusion method and diffracted to 2.78Å resolution. A BLASTP search (http://blast.ncbi.nlm.nih.gov/) of the Protein Data Bank did not reveal any similar crystal structures. Structural determination by using SeMet MAD and MIR methods is in progress.
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Affiliation(s)
- Zhen Zhu
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Miao He
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Chun Hsiang Huang
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, People's Republic of China
| | - Tzu Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Yi Fang Zeng
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Yu Ning Huang
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Shiru Jia
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Fuping Lu
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Je Ruei Liu
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Rey Ting Guo
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, People's Republic of China
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Bonnin E, Garnier C, Ralet MC. Pectin-modifying enzymes and pectin-derived materials: applications and impacts. Appl Microbiol Biotechnol 2013; 98:519-32. [DOI: 10.1007/s00253-013-5388-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 11/05/2013] [Accepted: 11/05/2013] [Indexed: 11/30/2022]
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Kaeothip S, Ishiwata A, Ito T, Fushinobu S, Fujita K, Ito Y. Preparation of p-nitrophenyl β-l-arabinofuranoside as a substrate of β-l-arabinofuranosidase. Carbohydr Res 2013; 382:95-100. [PMID: 24239541 DOI: 10.1016/j.carres.2013.10.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 09/30/2013] [Accepted: 10/07/2013] [Indexed: 01/09/2023]
Abstract
Synthesis of p-nitrophenyl β-l-arabinofuranoside 1 as the substrate for novel β-l-arabinofuranosidase has been achieved by using both our inter- and intra-molecular glycosylation methodologies. Although the intermolecular glycosylation with l-Araf donors 3 and 4 resulted in a mixture of both α- and β-isomers, NAP ether-mediated IAD with 3 and 6 afforded the desired β-l-arabinofuranoside stereospecifically which was confirmed by NMR analysis on the (3)JH1-H2 coupling constant and (13)C chemical shift of C1. As expected, 1 has been revealed to be an efficient substrate in the biological study of a novel β-arabinofuranosidase such as HypBA1 with higher apparent affinity compared with other reported substrates.
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Affiliation(s)
- Sophon Kaeothip
- ERATO Glycotrilogy Project, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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Benoit I, Coutinho PM, Schols HA, Gerlach JP, Henrissat B, de Vries RP. Degradation of different pectins by fungi: correlations and contrasts between the pectinolytic enzyme sets identified in genomes and the growth on pectins of different origin. BMC Genomics 2012; 13:321. [PMID: 22812459 PMCID: PMC3460790 DOI: 10.1186/1471-2164-13-321] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 07/07/2012] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Pectins are diverse and very complex biomolecules and their structure depends on the plant species and tissue. It was previously shown that derivatives of pectic polymers and oligosaccharides from pectins have positive effects on human health. To obtain specific pectic oligosaccharides, highly defined enzymatic mixes are required. Filamentous fungi are specialized in plant cell wall degradation and some produce a broad range of pectinases. They may therefore shed light on the enzyme mixes needed for partial hydrolysis. RESULTS The growth profiles of 12 fungi on four pectins and four structural elements of pectins show that the presence/absence of pectinolytic genes in the fungal genome clearly correlates with their ability to degrade pectins. However, this correlation is less clear when we zoom in to the pectic structural elements. CONCLUSIONS This study highlights the complexity of the mechanisms involved in fungal degradation of complex carbon sources such as pectins. Mining genomes and comparative genomics are promising first steps towards the production of specific pectinolytic fractions.
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Affiliation(s)
- Isabelle Benoit
- Microbiology & Kluyver Centre for Genomics of Industrial Fermentations, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Pedro M Coutinho
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, CNRS UMR 7257, Case 932, 163 Av de Luminy, Marseille cedex 9, 13288, France
| | - Henk A Schols
- Laboratory of Food Chemistry, Wageningen University, Bomenweg 2, Wageningen, 6703HD, The Netherlands
| | - Jan P Gerlach
- Microbiology & Kluyver Centre for Genomics of Industrial Fermentations, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, CNRS UMR 7257, Case 932, 163 Av de Luminy, Marseille cedex 9, 13288, France
| | - Ronald P de Vries
- Microbiology & Kluyver Centre for Genomics of Industrial Fermentations, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
- Fungal Physiology, CBS-KNAW, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
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