Details of a Researcher - Kaneko Satoshi

Published Papers - Kaneko Satoshi

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Characterization of an α-L-arabinofuranosidase GH51 from the brown-rot fungus Gloeophyllum trabeum

Tsukida Rikako, Yoshida Makoto, Kaneko Satoshi

Ｊｏｕｒｎａｌ　ｏｆ　Ａｐｐｌｉｅｄ　Ｇｌｙｃｏｓｃｉｅｎｃｅ ( 日本応用糖質科学会 ) advpub ( 0 ) 9 - 14 2022.12 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

Woody biomass is anticipated to be a resource for a decarbonized society, but the difficulty of isolating woody components is a significant challenge. Brown-rot fungi, a type of wood rotting fungi, decompose hemicellulose particularly efficiently. However, there are few reports on the hemicellulases from brown-rot fungi. An α-L-arabinofuranosidase belonging to glycoside hydrolase family 51 (GH51) from the brown-rot fungus Gloeophyllum trabeum (GtAbf51A) was cloned and characterized in the present study. Analyses of the phylogeny of GH51 enzymes in wood rotting fungi revealed the existence of two groups, intercellular and extracellular enzymes. After deglycosylation, the recombinant GtAbf51A produced by Pichia pastoris appeared on SDS-PAGE as approximately 71,777 daltons, which is the expected molecular weight based on the amino acid sequence of GtAbf51A. Maximum enzyme activity occurred between pH 2.2 and 4.0 and at 50°C, while it was stable between pH 2.2 and 10.0 and up to 40°C. Due to the presence of a signal peptide, GtAbf51A was thought to hydrolyze polysaccharide containing arabinose. However, the hydrolysis rate of arabinosyl linkages in polysaccharides was only 3%–4% for arabinoxylan and 17% for arabinan. GtAbf51A, in contrast, efficiently hydrolyzed arabinoxylooligosaccharides, particularly O-α-L-arabinofuranosyl-(1→3)-O-β-D-xylopyranosyl-(1→4)-β-Dxylopyranose, which is the principal product of GH10 β-xylanase. These data suggest that GtAbf51A cooperates with other xylan-degrading enzymes, such as β-xylanase, to degrade xylan in nature.

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Microorganisms capable of producing polysaccharides from D-xylose

Tsutsui Sosyu, Hatano Tomohiro, Funada Ryo, Kaneko Satoshi

Ｊｏｕｒｎａｌ　ｏｆ　Ａｐｐｌｉｅｄ　Ｇｌｙｃｏｓｃｉｅｎｃｅ ( 日本応用糖質科学会 ) advpub ( 0 ) 83 - 89 2022.10 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

In recent years, the importance of biomass utilization has increased, but it has not been effectively exploited. In particular, it is difficult to use hemicellulose, the second most abundant biopolymer of biomass. Therefore, in order to promote the utilization of hemicellulose, we screened for microorganisms capable of producing polysaccharides from xylose. The following four strains were selected from samples collected from various regions of Okinawa Prefecture: Kosakonia sp. (SO_001), Papiliotrema terrestris (SO_005), Pseudoarthrobacter sp. (SO_006), and Williamsia sp. (SO_009). Observation with a scanning electron microscope (SEM) confirmed that each bacterium produced polysaccharides with different shapes. In addition, the molecular weight and sugar composition of the polysaccharides produced by each bacterium were distinct. The selected microorganisms include closely related species known to promote plant growth and known to suppress postharvest pathogens. Since these microorganisms may be used not only in known fields but also in new fields, the results of this research are expected to greatly expand the uses of hemicellulose.

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Molecular and biochemical characteristics of inulosucrase InuBK from Alkalihalobacillus krulwichiae JCM 11691.

Yokoi KJ, Tsutsui S, Arakawa GY, Takaba M, Fujii K, Kaneko S

Bioscience, biotechnology, and biochemistry ( Bioscience, Biotechnology and Biochemistry ) 85 ( 8 ) 1830 - 1838 2021.07 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Substrate Specificities of GH8, GH39, and GH52 β-xylosidases from Bacillus halodurans C-125 Toward Substituted Xylooligosaccharides.

Teramoto K, Tsutsui S, Sato T, Fujimoto Z, Kaneko S

Applied biochemistry and biotechnology ( Applied Biochemistry and Biotechnology ) 193 ( 4 ) 1042 - 1055 2021.04 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Structure-based substrate specificity analysis of GH11 xylanase from Streptomyces olivaceoviridis E-86.

Fujimoto Z, Kishine N, Teramoto K, Tsutsui S, Kaneko S

Applied microbiology and biotechnology ( Applied Microbiology and Biotechnology ) 105 ( 5 ) 1943 - 1952 2021.03 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Unique active-site and subsite features in the arabinogalactan-degrading GH43 exo-β-1,3-galactanase from Phanerochaete chrysosporium.

Matsuyama K, Kishine N, Fujimoto Z, Sunagawa N, Kotake T, Tsumuraya Y, Samejima M, Igarashi K, Kaneko S

The Journal of biological chemistry ( Journal of Biological Chemistry ) 295 ( 52 ) 18539 - 18552 2020.12 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Domain architecture divergence leads to functional divergence in binding and catalytic domains of bacterial and fungal cellobiohydrolases.

Nakamura A, Ishiwata D, Visootsat A, Uchiyama T, Mizutani K, Kaneko S, Murata T, Igarashi K, Iino R

The Journal of biological chemistry ( Journal of Biological Chemistry ) 295 ( 43 ) 14606 - 14617 2020.10 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Convergent evolution of processivity in bacterial and fungal cellulases.

Uchiyama T, Uchihashi T, Nakamura A, Watanabe H, Kaneko S, Samejima M, Igarashi K

Proceedings of the National Academy of Sciences of the United States of America ( Proceedings of the National Academy of Sciences of the United States of America ) 117 ( 33 ) 19896 - 19903 2020.08 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Evaluation of Ammonia Pretreatment for Enzymatic Hydrolysis of Sugarcane Bagasse to Recover Xylooligosaccharides

Tsutsui Sosyu, Sakuragi Kiyoshi, Igarashi Kiyohiko, Samejima Masahiro, Kaneko Satoshi

Journal of Applied Glycoscience ( 日本応用糖質科学会 ) 67 ( 1 ) 17 - 22 2020.02

Type of publication: Research paper (scientific journal)

Sugarcane bagasse is a useful biomass resource. In the present study, we examined the efficacy of ammonia pretreatment for selective release of hemicellulose from bagasse. Pretreatment of bagasse with aqueous ammonia resulted in significant loss of xylan. In contrast, pretreatment of bagasse with anhydrous ammonia resulted in almost no xylan loss. Aqueous ammonia or anhydrous ammonia-pretreated bagasse was then subjected to enzymatic digestion with a xylanase from the glycoside hydrolase (GH) family 10 or a xylanase from the GH family 11. The hydrolysis rate of xylan in bagasse pretreated with aqueous ammonia was approximately 50 %. In contrast, in the anhydrous ammonia-treated bagasse, xylan hydrolysis was > 80 %. These results suggested that anhydrous ammonia pretreatment would be an effective method for preparation of sugarcane bagasse for enzymatic hydrolysis to recover xylooligosaccharides.

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Effect of C-6 Methylol Groups on Substrate Recognition of Glucose/Xylose Mixed Oligosaccharides by Cellobiose Dehydrogenase from the Basidiomycete Phanerochaete chrysosporium.

Igarashi K, Kaneko S, Kitaoka M, Samejima M

Journal of applied glycoscience ( 日本応用糖質科学会 ) 67 ( 2 ) 51 - 57 2020

Type of publication: Research paper (scientific journal)

Cellobiose dehydrogenase (CDH) is a flavocytochrome catalyzing oxidation of the reducing end of cellobiose and cellooligosaccharides, and has a key role in the degradation of cellulosic biomass by filamentous fungi. Here, we use a lineup of glucose/xylose-mixed β-1,4-linked disaccharides and trisaccharides, enzymatically synthesized by means of the reverse reaction of cellobiose phosphorylase and cellodextrin phosphorylase, to investigate the substrate recognition of CDH. We found that CDH utilizes β-D-xylopyranosyl-(1→4)-D-glucopyranose (Xyl-Glc) as an electron donor with similar Km and kcat values to cellobiose. β-D-Glucopyranosyl-(1→4)-D-xylopyranose (Glc-Xyl) shows a higher Km value, while xylobiose does not serve as a substrate. Trisaccharides show similar behavior; i.e., trisaccharides with cellobiose and Xyl-Glc units at the reducing end show similar kinetics, while the enzyme was less active towards those with Glc-Xyl, and inactive towards those with xylobiose. We also use docking simulation to evaluate substrate recognition of the disaccharides, and we discuss possible molecular mechanisms of substrate recognition by CDH.

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Functional Characterization of the GH10 and GH11 Xylanases from Streptomyces olivaceoviridis E-86 Provide Insights into the Advantage of GH11 Xylanase in Catalyzing Biomass Degradation:GH10 and GH11 Xylanases from Streptomyces olivaceoviridis E-86

Yagi Haruka, Takehara Ryo, Tamaki Aika, Teramoto Koji, Tsutsui Sosyu, Kaneko Satoshi

Journal of Applied Glycoscience ( 日本応用糖質科学会 ) 66 ( 1 ) 29 - 35 2019.02

Type of publication: Research paper (scientific journal)

We functionally characterized the GH10 xylanase (SoXyn10A) and the GH11 xylanase (SoXyn11B) derived from the actinomycete Streptomyces olivaceoviridis E-86. Each enzyme exhibited differences in the produced reducing power upon degradation of xylan substrates. SoXyn10A produced higher reducing power than SoXyn11B. Gel filtration of the hydrolysates generated by both enzymes revealed that the original substrate was completely decomposed. Enzyme mixtures of SoXyn10A and SoXyn11B produced the same level of reducing power as SoXyn10A alone. These observations were in good agreement with the composition of the hydrolysis products. The hydrolysis products derived from the incubation of soluble birchwood xylan with a mixture of SoXyn10A and SoXyn11B produced the same products as SoXyn10A alone with similar compositions. Furthermore, the addition of SoXyn10A following SoXyn11B-mediated digestion of xylan produced the same products as SoXyn10A alone with similar compositions. Thus, it was hypothesized that SoXyn10A could degrade xylans to a smaller size than SoXyn11B. In contrast to the soluble xylans as the substrate, the produced reducing power generated by both enzymes was not significantly different when pretreated milled bagasses were used as substrates. Quantification of the pentose content in the milled bagasse residues after the enzyme digestions revealed that SoXyn11B hydrolyzed xylans in pretreated milled bagasses much more efficiently than SoXyn10A. These data suggested that the GH10 xylanases can degrade soluble xylans smaller than the GH11 xylanases. However, the GH11 xylanases may be more efficient at catalyzing xylan degradation in natural environments (e.g. biomass) where xylans interact with celluloses and lignins.

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Structural characterization of hemicellulose released from corn cob in continuous flow type hydrothermal reactor.

Arai T, Biely P, Uhliariková I, Sato N, Makishima S, Mizuno M, Nozaki K, Kaneko S, Amano Y

Journal of bioscience and bioengineering ( Journal of Bioscience and Bioengineering ) 127 ( 2 ) 222 - 230 2019.02

Type of publication: Research paper (scientific journal)

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Degradative enzymes for type II arabinogalactan side chains in Bifidobacterium longum subsp. longum.

Fujita K, Sakamoto A, Kaneko S, Kotake T, Tsumuraya Y, Kitahara K

Applied microbiology and biotechnology ( Applied Microbiology and Biotechnology ) 103 ( 3 ) 1299 - 1310 2019.02

Type of publication: Research paper (scientific journal)

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Ruminiclostridium josui Abf62A-Axe6A: A tri-functional xylanolytic enzyme exhibiting α-l-arabinofuranosidase, endoxylanase, and acetylxylan esterase activities.

Wang Y, Sakka M, Yagi H, Kaneko S, Katsuzaki H, Kunitake E, Kimura T, Sakka K

Enzyme and microbial technology ( Enzyme and Microbial Technology ) 117 1 - 8 2018.10

Type of publication: Research paper (scientific journal)

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Purification, Cloning, Functional Expression, Structure, and Characterization of a Thermostable β-Mannanase from Talaromyces trachyspermus B168 and Its Efficiency in Production of Mannooligosaccharides from Coffee Wastes

Suzuki Kentaro, Michikawa Mari, Sato Haruna, Yuki Masahiro, Kamino Kei, Ogasawara Wataru, Fushinobu Shinya, Kaneko Satoshi

Journal of Applied Glycoscience ( 日本応用糖質科学会 ) 65 ( 2 ) 13 - 21 2018.05

Type of publication: Research paper (scientific journal)

Highly thermostable β-mannanase, belonging to glycoside hydrolase family 5 subfamily 7, was purified from the culture supernatant of Talaromyces trachyspermus B168 and the cDNA of its transcript was cloned. The recombinant enzyme showed maximal activity at pH 4.5 and 85 °C. It retained more than 90 % of its activity below 60 °C. Obtaining the crystal structure of the enzyme helped us to understand the mechanism of its thermostability. An antiparallel β-sheet, salt-bridges, hydrophobic packing, proline residues in the loops, and loop shortening are considered to be related to the thermostability of the enzyme. The enzyme hydrolyzed mannans such as locust bean gum, carob galactomannan, guar gum, konjac glucomannan, and ivory nut mannan. It hydrolyzed 50.7 % of the total mannans from coffee waste, producing mannooligosaccharides. The enzyme has the highest optimum temperature among the known fungal β-mannanases and has potential for use in industrial applications.

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Enhanced Azidolysis by the Formation of Stable Ser–His Catalytic Dyad in a Glycoside Hydrolase Family 10 Xylanase Mutant

Suzuki Ryuichiro, Fujimoto Zui, Kaneko Satoshi, Hasegawa Tsunemi, Kuno Atsushi

Journal of Applied Glycoscience ( 日本応用糖質科学会 ) 65 ( 1 ) 1 - 8 2018.02

Type of publication: Research paper (scientific journal)

Glycoside hydrolases require carboxyl groups as catalysts for their activity. A retaining xylanase from Streptomyces olivaceoviridis E-86 belonging to glycoside hydrolase family 10 possesses Glu128 and Glu236 that respectively function as acid/base and nucleophile. We previously developed a unique mutant of the retaining xylanase, N127S/E128H, whose deglycosylation is triggered by azide. A crystallographic study reported that the transient formation of a Ser–His catalytic dyad in the reaction cycle possibly reduced the azidolysis reaction. In the present study, we engineered a catalytic dyad with enhanced stability by site-directed mutagenesis and crystallographic study of N127S/E128H. Comparison of the Michaelis complexes of N127S/E128H with pNP-X2 and with xylopentaose showed that Ser127 could form an alternative hydrogen bond with Thr82, which disrupts the formation of the Ser–His catalytic dyad. The introduction of T82A mutation in N127S/E128H produces an enhanced first-order rate constant (6 times that of N127S/E128H). We confirmed the presence of a stable Ser–His hydrogen bond in the Michaelis complex of the triple mutant, which forms the productive tautomer of His128 that acts as an acid catalyst. Because the glycosyl azide is applicable in the bioconjugation of glycans by using click chemistry, the enzyme-assisted production of the glycosyl azide may contribute to the field of glycobiology.

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GH30 Glucuronoxylan-Specific Xylanase from Streptomyces turgidiscabies C56.

Maehara T, Yagi H, Sato T, Ohnishi-Kameyama M, Fujimoto Z, Kamino K, Kitamura Y, St John F, Yaoi K, Kaneko S

Applied and environmental microbiology ( Applied and Environmental Microbiology ) 84 ( 4 ) 2018.02

Type of publication: Research paper (scientific journal)

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Ten years of CAZypedia: a living encyclopedia of carbohydrate-active enzymes

Abbott, W; Alber, O; Bayer, E; Berrin, JG; Boraston, A; Brumer, H; Brzezinski, R; Clarke, A; Cobucci-Ponzano, B; Cockburn, D; Coutinho, P; Czjzek, M; Dassa, B; Davies, GJ; Eijsink, V; Eklöf, J; Felice, A; Ficko-Blean, E; Pincher, G; Fontaine, T; Fujimoto, Z; Fujita, K; Fushinobu, S; Gilbert, H; Gloster, T; Goddard-Borger, E; Greig, I; Hehemann, JH; Hemsworth, G; Henrissat, B; Hidaka, M; Hurtado-Guerrero, R; Igarashi, K; Ishida, T; Janecek, S; Jongkees, S; Juge, N; Kaneko, S; Katayama, T; Kitaoka, M; Konno, N; Kracher, D; Kulminskaya, A; van Bueren, AL; Larsen, S; Lee, J; Linder, M; LoLeggio, L; Ludwig, R; Luis, A; Maksimainen, M; Mark, B; McLean, R; Michel, G; Michel, G; Montanier, C; Moracci, M; Mori, H; Nakai, H; Nerinckx, W; Ohnuma, T; Pickersgill, R; Piens, K; Pons, T; Rebuffet, E; Reilly, P; Remaud-Simeon, M; Rempel, B; Robinson, K; Rose, D; Rouvinen, J; Saburi, W; Sakamoto, Y; Sandgren, M; Shaikh, F; Shoham, Y; St John, F; Stahlberg, J; Suits, M; Sulzenbacher, G; Sumida, T; Suzuki, R; Svensson, B; Taira, T; Taylor, E; Tonozuka, T; Urbanowicz, B; Vaaje-Kolstad, G; Van den Ende, W; Varrot, A; Versluys, M; Vincent, F; Vocadlo, D; Wakarchuk, W; Wennekes, T; Williams, R; Williams, S; Wilson, D; Withers, S; Yaoi, K; Yip, V; Zhang, R

GLYCOBIOLOGY 28 ( 1 ) 3 - 8 2018.01 [ Peer Review Accepted ]

Type of publication: Research paper (scientific journal)

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Properties of two fungal endo-β-1,3-galactanases and their synergistic action with an exo-β-1,3-galactanase in degrading arabinogalactan-proteins.

Yoshimi Y, Yaguchi K, Kaneko S, Tsumuraya Y, Kotake T

Carbohydrate research ( Carbohydrate Research ) 453-454 26 - 35 2017.12

Type of publication: Research paper (scientific journal)

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4-O-Methyl Modifications of Glucuronic Acids in Xylans Are Indispensable for Substrate Discrimination by GH67 α-Glucuronidase from Bacillus halodurans C-125

Yagi Haruka, Maehara Tomoko, Tanaka Tsuyoshi, Takehara Ryo, Teramoto Koji, Yaoi Katsuro, Kaneko Satoshi

Ｊｏｕｒｎａｌ　ｏｆ　Ａｐｐｌｉｅｄ　Ｇｌｙｃｏｓｃｉｅｎｃｅ ( 日本応用糖質科学会 ) 64 ( 4 ) 115 - 121 2017.11

Type of publication: Research paper (scientific journal)

A GH67 α-glucuronidase gene derived from Bacillus halodurans C-125 was expressed in E. coli to obtain a recombinant enzyme (BhGlcA67). Using the purified enzyme, the enzymatic properties and substrate specificities of the enzyme were investigated. BhGlcA67 showed maximum activity at pH 5.4 and 45 °C. When BhGlcA67 was incubated with birchwood, oat spelts, and cotton seed xylan, the enzyme did not release any glucuronic acid or 4-O-methyl-glucuronic acid from these substrates. BhGlcA67 acted only on 4-O-methyl-α-D-glucuronopyranosyl-(1→2)-β-D-xylopyranosyl-(1→4)-β-D-xylopyranosyl-(1→4)-β-D-xylopyranose (MeGlcA3Xyl3), which has a glucuronic acid side chain with a 4-O-methyl group located at its non-reducing end, but did not on β-D-xylopyranosyl-(1→4)-[4-O-methyl-α-D-glucuronopyranosyl-(l→2)]-β-D-xylopyranosyl-(1→4)-β-D-xylopyranosyl-(1→4)-β-D-xylop- yranose (MeGlcA3Xyl4) and α-D-glucuronopyranosyl-(l→2)-β-D-xylopyranosyl-(1→4)-β-D-xylopyranosyl-(1→4)-β-D-xylopyranose (GlcA3Xyl3). The environment for recognizing the 4-O-methyl group of glucuronic acid was observed in all the crystal structures of reported GH67 glucuronidases, and the amino acids for discriminating the 4-O-methyl group of glucuronic acid were widely conserved in the primary sequences of the GH67 family, suggesting that the 4-O-methyl group is critical for the activities of the GH67 family.

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