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11. Insight into the mechanism of thermostabilization of GH10 xylanase from Bacillus sp. strain TAR-1 by the mutation of S92 to E

Author

Suzuki, Manami, primary, Takita, Teisuke, additional, Kuwata, Kohei, additional, Nakatani, Kota, additional, Li, Tongyang, additional, Katano, Yuta, additional, Kojima, Kenji, additional, Mizutani, Kimihiko, additional, Mikami, Bunzo, additional, Yatsunami, Rie, additional, Nakamura, Satoshi, additional, and Yasukawa, Kiyoshi, additional

Published
2021
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19. Insight into the mechanism of thermostabilization of GH10 xylanase from Bacillussp. strain TAR-1 by the mutation of S92 to E

Author

Suzuki, Manami, Takita, Teisuke, Kuwata, Kohei, Nakatani, Kota, Li, Tongyang, Katano, Yuta, Kojima, Kenji, Mizutani, Kimihiko, Mikami, Bunzo, Yatsunami, Rie, Nakamura, Satoshi, and Yasukawa, Kiyoshi

Abstract

The mechanism of thermostabilization of GH10 xylanase, XynR, from Bacillussp. strain TAR-1 by the mutation of S92 to E was investigated. Thermodynamic analysis revealed that thermostabilization was driven by the decrease in entropy change of activation for thermal inactivation. Crystallographic analysis suggested that this mutation suppressed the fluctuation of the amino acid residues at position 92-95.

Published
2021
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22. Isolation of four xylanases capable of hydrolyzing corn fiber xylan from Paenibacillussp. H2C

Author

Hagiwara, Yusuke, Mihara, Yasuhiro, Sakagami, Koichi, Sagara, Ryuta, Bat-Erdene, Undramaa, Yatsunami, Rie, and Nakamura, Satoshi

Abstract

ABSTRACTCorn fibre xylan (CX) shows high resistance to enzymatic hydrolysis due to its densely decorated side chains. To find enzymes capable of hydrolyzing CX, we isolated a bacterial strain (named H2C) from soil, by enrichment culture using non-starch polysaccharides of corn as the sole carbon source. Analysis based on the 16S rRNA sequence placed strain H2C within genus Paenibacillus. Enzymes were purified from supernatant of culture broth of strain H2C based on solubilizing activities toward CX. Four enzymes, Xyn5A, Xyn10B, Xyn11A, and Xyn30A, were successfully identified, which belong to glycoside hydrolase (GH) families, 5, 10, 11, and 30, respectively. Phylogenetic analysis classified Xyn5A in subfamily 35 of GH family 5, a subfamily of unknown function. Their activities toward beechwood xylan and/or wheat arabinoxylan indicated that these enzymes are β-1,4-xylanases. They showed high solubilizing activities toward a feed material, corn dried distiller’s grains with solubles, compared to five previously characterized xylanases.Abbreviations: CX: corn fibre xylan; DDGS: corn dried distiller’s grains with solubles

Published
2020
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25. 生体分子と自己修復

Author

Yatsunami, Rie and Nakamura, Satoshi

Abstract

生物における情報の源であるDNAは, 複製ミスあるいは紫外線照射といった損傷の危機に常に曝されている。その損傷の修復なしに, 生命機能を維持することはできない。そのため, DNA修復系はあらゆる生物に備わっており, 重要な細胞機能として位置づけられている。本稿では, 初めにDNAの構造について述べ, ついで生物がいかにして損傷したDNAを修復しているかについて概説する。また, DNA複製と老化・発ガンとの関連にも言及する。

Published
2000

29. Identification of carotenoids from the extremely halophilic archaeon Haloarcula japonica

Author

Yatsunami, Rie, primary, Ando, Ai, additional, Yang, Ying, additional, Takaichi, Shinichi, additional, Kohno, Masahiro, additional, Matsumura, Yuriko, additional, Ikeda, Hiroshi, additional, Fukui, Toshiaki, additional, Nakasone, Kaoru, additional, Fujita, Nobuyuki, additional, Sekine, Mitsuo, additional, Takashina, Tomonori, additional, and Nakamura, Satoshi, additional

Published
2014
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30. Increase in the thermostability of Bacillussp. strain TAR-1 xylanase using a site saturation mutagenesis library

Author

Nakatani, Kota, Katano, Yuta, Kojima, Kenji, Takita, Teisuke, Yatsunami, Rie, Nakamura, Satoshi, and Yasukawa, Kiyoshi

Abstract

ABSTRACTSite saturation mutagenesis library is a recently developed technique, in which any one out of all amino acid residues in a target region is substituted into other 19 amino acid residues. In this study, we used this technique to increase the thermostability of a GH10 xylanase, XynR, from Bacillussp. strain TAR-1. We hypothesized that the substrate binding region of XynR is flexible, and that the thermostability of XynR will increase if the flexibility of the substrate binding region is decreased without impairing the substrate binding ability. Site saturation mutagenesis libraries of amino acid residues Tyr43–Lys115 and Ala300–Asn325 of XynR were constructed. By screening 480 clones, S92E was selected as the most thermostable one, exhibiting the residual activity of 80% after heat treatment at 80°C for 15 min in the hydrolysis of Remazol Brilliant Blue-xylan. Our results suggest that this strategy is effective for stabilization of GH10 xylanase.Abbreviations: DNS: 3,5-dinitrosalicylic acid; RBB-xylan: Remazol Brilliant Blue-xylan

Published
2018
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46. Mutational Analysis of a CBM Family 5 Chitin-Binding Domain of an Alkaline Chitinase from Bacillus sp. J813.

Author

Uni, Fumiya, Lee, Sunmi, Yatsunami, Rie, Fukui, Toshiaki, and Nakamura, Satoshi

Subjects
CHITIN, GLYCOSIDES, BIOMOLECULES, BACILLUS (Bacteria), HYDROLASES, GENETIC mutation, CARBOHYDRATES
Abstract

The article discusses the mutational analysis of a carbohydrate binding molecule (CBM) family 5 chitin binding domain (ChBD) from alkaliphilic species J813 of the bacterium bacillus. It states that the binding of ChBD to insoluble chitin enhances the degradation of chitin by the catalytic domain (CatD) of the bacillus glycoside hydrolase family. The investigation of roles of aromatic residues exposed on the surface of the ChBD was mediated by single and double mutations of the residues.

Published
2012
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47. Additional Carbohydrate-Binding Modules Enhance the Insoluble Substrate-Hydrolytic Activity of β-1,3-Glucanase from Alkaliphilic Nocardiopsis sp. F96.

Author

Koizumi, Naoya, Masuda, Sumiko, Maeda, Kiyoe, Isoda, Yuya, Yatsunami, Rie, Fukui, Toshiaki, and Nakamura, Satoshi

Subjects
GLUCANS, HYDROLASES, SACCHARIDES, OLIGONUCLEOTIDES, ENZYMES
Abstract

The article presents a study which aims to enhance the enzymatic properties of β-1,3-Glucanase (BgIF) from Nocardiopsis sp. F96. The study uses oligonucleotide primers, and various polysaccharides including laminarin, lichenan, and curlan. Accordingly, standard protocols were used to perform the DNA manipulations, and the chimeric enzymes that contain BglF and carbohydrate-binding module (CBM) were characterized. The results show similar hydrolytic activity of chimeric enzymes.

Published
2009
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48. Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8.

Author

Ihsanawati, Kumasaka, Takashi, Kaneko, Tomonori, Morokuma, Chihiro, Yatsunami, Rie, Sato, Takao, Nakamura, Satoshi, and Tanaka, Nobuo

Abstract

The crystal structure of xylanase 10B from Thermotoga maritima MSB8 (TmxB), a hyperthermostable xylanase, has been solved in its native form and in complex with xylobiose or xylotriose at 1.8 Å resolution. In order to gain insight into the substrate subsite and the molecular features for thermal stability, we compared TmxB with family 10 xylanase structures from nine microorganisms. As expected, TmxB folds into a (β/α)8-barrel structure, which is common among the glycoside hydrolase family 10. The enzyme active site and the environment surrounding the xylooligosaccharide of TmxB are highly similar to those of family 10 xylanases. However, only two xylose moieties were found in its binding pocket from the TmxB-xylotriose complex structure. This finding suggests that TmxB could be a potential biocatalyst for the large-scale production of xylobiose. The result of structural analyses also indicated that TmxB possesses some additional features that account for its thermostability. In particular, clusters of aromatic residues together with a lack of exposed hydrophobic residues are characteristic of the TmxB structure. TmxB has also a significant number of ion pairs on the protein surface that are not found in other thermophilic family 10 xylanases. Proteins 2005. © 2005 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

Published
2005
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49. Mutational Analysis of a CBM Family 5 Chitin-Binding Domain of an Alkaline Chitinase from Bacillussp. J813

Author

UNI, Fumiya, LEE, Sunmi, YATSUNAMI, Rie, FUKUI, Toshiaki, and NAKAMURA, Satoshi

Abstract

Chitinase J from alkaliphilic Bacillussp. J813 comprises a glycoside hydrolase (GH) family 18 catalytic domain (CatD), a fibronectin type III like domain, and a carbohydrate-binding module (CBM) family 5 chitin-binding domain (ChBD). It has been suggested that the ChBD binds to insoluble chitin and enhances its degradation by the CatD. To investigate the roles of two aromatic residues (Trp541 and Trp542), which are exposed on the surface of the ChBD, mutational analysis was performed. Single and double mutations of the two aromatic residues decreased binding and hydrolyzing abilities toward insoluble chitin. This result suggests that the ChBD binds to chitin by hydrophobic interactions viatwo surface-exposed aromatic residues. However, the double mutant, which has no such aromatic residue, bound to chitin at pH 5.2, probably by electrostatic interactions. Moreover, the ChBD bound to insoluble chitosan by electrostatic interactions.

Published
2012
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50. Additional Carbohydrate-Binding Modules Enhance the Insoluble Substrate-Hydrolytic Activity of β-1,3-Glucanase from Alkaliphilic Nocardiopsissp. F96

Author

KOIZUMI, Naoya, MASUDA, Sumiko, MAEDA, Kiyoe, ISODA, Yuya, YATSUNAMI, Rie, FUKUI, Toshiaki, and NAKAMURA, Satoshi

Abstract

β-1,3-Glucanase (BglF) from Nocardiopsissp. F96 is composed of only a catalytic domain. To improve the enzymatic properties of BglF, we attempted to construct chimeric enzymes consisting of BglF and some carbohydrate-binding modules, such as the C-terminal additional domain (CAD) and the N-terminal additional domain (NAD) of β-1,3-glucanase H from Bacillus circulansIAM1165 and the chitin-binding domain (ChBD) of chitinase from alkaliphilic Bacillussp. J813. CAD-fused BglF (BglF-CAD), NAD-fused BglF (NAD-BglF), both NAD- and CAD-fused BglF (NAD-BglF-CAD) and ChBD-fused BglF (BglF-ChBD) were constructed and characterized. The addition of CAD caused increases in binding abilities and hydrolytic activities toward insoluble β-1,3-glucans. As well as BglF-CAD, the binding ability and hydrolytic activity of BglF-ChBD toward pachyman were also increased. The hydrolytic activity of BglF-CAD at pH 9–10 was higher than that of BglF. The relative activities of BglF-CAD and BglF-ChBD at around 50–70 °C were higher than that of BglF.

Published
2009
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