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Maeda Y, Hirakawa T, Suzuki S, Suhaimi N, Shamsol Anuar NS, Yoneda K, Shintani M, Suzuki K, Sunagawa N, Kawachi M, Suzuki I, Hara H. Chromosome-scale genome assembly of an acidophilic microalga Tetratostichococcus sp. P1 isolated from a tropical peatland in Malaysia. Microbiol Resour Announc 2024; 13:e0081623. [PMID: 38179908 PMCID: PMC10868215 DOI: 10.1128/mra.00816-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/17/2023] [Indexed: 01/06/2024] Open
Abstract
Tetratostichococcus sp. P1 shows an acidophilic phenotype which could allow mass-scale monoculture of this green microalga without severe contamination by environmental microorganisms. In this study, we report a chromosome-scale genome assembly for Tetratostichococcus sp. P1.
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Affiliation(s)
- Yoshiaki Maeda
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Toshiki Hirakawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Shigekatsu Suzuki
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Noraiza Suhaimi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Nurul Syahirah Shamsol Anuar
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kohei Yoneda
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Masaki Shintani
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Kenshi Suzuki
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masanobu Kawachi
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Iwane Suzuki
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Hirofumi Hara
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
- Department of Chemical and Environmental Engineering, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Kuala Lumpur, Malaysia
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Katsuhara S, Sunagawa N, Igarashi K, Takeuchi Y, Takahashi K, Yamamoto T, Li F, Tajima K, Isono T, Satoh T. Effect of degree of substitution on the microphase separation and mechanical properties of cellooligosaccharide acetate-based elastomers. Carbohydr Polym 2023; 316:120976. [PMID: 37321706 DOI: 10.1016/j.carbpol.2023.120976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/27/2023] [Accepted: 04/30/2023] [Indexed: 06/17/2023]
Abstract
Thermoplastic elastomers (TPEs) have long been used in a wide range of industries. However, most existing TPEs are petroleum-derived polymers. To realize environmentally benign alternatives to conventional TPEs, cellulose acetate is a promising TPE hard segment because of its sufficient mechanical properties, availability from renewable sources, and biodegradability in natural environments. Because the degree of substitution (DS) of cellulose acetate governs a range of physical properties, it is a useful parameter for designing novel cellulose acetate-based TPEs. In this study, we synthesized cellulose acetate-based ABA-type triblock copolymers (AcCelx-b-PDL-b-AcCelx) containing a celloologosaccharide acetate hard A segment (AcCelx, where x is the DS; x = 3.0, 2.6, and 2.3) and a poly(δ-decanolactone) (PDL) soft B segment. Small-angle X-ray scattering showed that decreasing the DS of AcCelx-b-PDL-b-AcCelx resulted in the formation of a more ordered microphase-separated structure. Owing to the microphase separation of the hard cellulosic and soft PDL segments, all the AcCelx-b-PDL-b-AcCelx samples exhibited elastomer-like properties. Moreover, the decrease in DS improved toughness and suppressed stress relaxation. Furthermore, preliminary biodegradation tests in an aqueous environment revealed that the decrease in DS endowed AcCelx-b-PDL-b-AcCelx with greater biodegradability potential. This work demonstrates the usefulness of cellulose acetate-based TPEs as next-generation sustainable materials.
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Affiliation(s)
- Satoshi Katsuhara
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan; VTT Technical Research Centre of Finland Ltd., VTT FI-02044, Finland
| | - Yutaka Takeuchi
- Noto Center for Fisheries Science and Technology, Faculty of Biological Science and Technology, Kanazawa University, Noto-cho, Ishikawa 927-0552, Japan
| | - Kenji Takahashi
- Faculty of Biological Science and Technology, Institute of Science and Engineering, Kanazawa University, Kanazawa 920-1192, Japan
| | - Takuya Yamamoto
- Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Feng Li
- Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Kenji Tajima
- Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan.
| | - Takuya Isono
- Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan.
| | - Toshifumi Satoh
- Faculty of Engineering, Hokkaido University, Sapporo 060-8628, Japan.
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Kojima K, Sunagawa N, Yoshimi Y, Tryfona T, Samejima M, Dupree P, Igarashi K. Acetylated xylan degradation by glycoside hydrolase family 10 and 11 xylanases from the white-rot fungus <i>Phanerochaete chrysosporium</i>. J Appl Glycosci (1999) 2022; 69:35-43. [PMID: 35891899 PMCID: PMC9276525 DOI: 10.5458/jag.jag.jag-2021_0017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 02/28/2022] [Indexed: 11/22/2022] Open
Abstract
Endo-type xylanases are key enzymes in microbial xylanolytic systems, and xylanases belonging to glycoside hydrolase (GH) families 10 or 11 are the major enzymes degrading xylan in nature. These enzymes have typically been characterized using xylan prepared by alkaline extraction, which removes acetyl sidechains from the substrate, and thus the effect of acetyl groups on xylan degradation remains unclear. Here, we compare the ability of GH10 and 11 xylanases, PcXyn10A and PcXyn11B, from the white-rot basidiomycete Phanerochaete chrysosporium to degrade acetylated and deacetylated xylan from various plants. Product quantification revealed that PcXyn10A effectively degraded both acetylated xylan extracted from Arabidopsis thaliana and the deacetylated xylan obtained by alkaline treatment, generating xylooligosaccharides. In contrast, PcXyn11B showed limited activity towards acetyl xylan, but showed significantly increased activity after deacetylation of the xylan. Polysaccharide analysis using carbohydrate gel electrophoresis showed that PcXyn11B generated a broad range of products from native acetylated xylans extracted from birch wood and rice straw, including large residual xylooligosaccharides, while non-acetylated xylan from Japanese cedar was readily degraded into xylooligosaccharides. These results suggest that the degradability of native xylan by GH11 xylanases is highly dependent on the extent of acetyl group substitution. Analysis of 31 fungal genomes in the Carbohydrate-Active enZymes database indicated that the presence of GH11 xylanases is correlated to that of carbohydrate esterase (CE) family 1 acetyl xylan esterases (AXEs), while this is not the case for GH10 xylanases. These findings may imply co-evolution of GH11 xylanases and CE1 AXEs.
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Affiliation(s)
- Keisuke Kojima
- Department of Biomaterial Sciences, The University of Tokyo
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, The University of Tokyo
| | | | | | | | - Paul Dupree
- Department of Biochemistry, University of Cambridge
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Kojima K, Sunagawa N, Mikkelsen NE, Hansson H, Karkehabadi S, Samejima M, Sandgren M, Igarashi K. Comparison of Glycoside Hydrolase family 3 β-xylosidases from basidiomycetes and ascomycetes reveals evolutionarily distinct xylan degradation systems. J Biol Chem 2022; 298:101670. [PMID: 35120929 PMCID: PMC8913315 DOI: 10.1016/j.jbc.2022.101670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 11/28/2022] Open
Abstract
Xylan is the most common hemicellulose in plant cell walls, though the structure of xylan polymers differs between plant species. Here, to gain a better understanding of fungal xylan degradation systems, which can enhance enzymatic saccharification of plant cell walls in industrial processes, we conducted a comparative study of two glycoside hydrolase family 3 (GH3) β-xylosidases (Bxls), one from the basidiomycete Phanerochaete chrysosporium (PcBxl3), and the other from the ascomycete Trichoderma reesei (TrXyl3A). A comparison of the crystal structures of the two enzymes, both with saccharide bound at the catalytic center, provided insight into the basis of substrate binding at each subsite. PcBxl3 has a substrate-binding pocket at subsite -1, while TrXyl3A has an extra loop that contains additional binding subsites. Furthermore, kinetic experiments revealed that PcBxl3 degraded xylooligosaccharides faster than TrXyl3A, while the KM values of TrXyl3A were lower than those of PcBxl3. The relationship between substrate specificity and degree of polymerization of substrates suggested that PcBxl3 preferentially degrades xylobiose (X2), while TrXyl3A degrades longer xylooligosaccharides. Moreover, docking simulation supported the existence of extended positive subsites of TrXyl3A in the extra loop located at the N-terminus of the protein. Finally, phylogenetic analysis suggests that wood-decaying basidiomycetes use Bxls such as PcBxl3 that act efficiently on xylan structures from woody plants, whereas molds use instead Bxls that efficiently degrade xylan from grass. Our results provide added insights into fungal efficient xylan degradation systems.
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Affiliation(s)
- Keisuke Kojima
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Nils Egil Mikkelsen
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - Henrik Hansson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - Saeid Karkehabadi
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - Masahiro Samejima
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; Faculty of Engineering, Shinshu University, 4-17-1, Wakasato, Nagano 380-8533, Japan
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; VTT Technical Research Centre of Finland, PO Box 1000, Tietotie 2, Espoo FI-02044 VTT, Finland.
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5
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Kuga T, Sunagawa N, Igarashi K. Enzymatic synthesis of cellulose in space: gravity is a crucial factor for building cellulose II gel structure. Cellulose (Lond) 2022; 29:2999-3015. [PMID: 35125685 PMCID: PMC8800430 DOI: 10.1007/s10570-021-04399-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
ABSTRACT We previously reported in vitro synthesis of highly ordered crystalline cellulose II by reverse reaction of cellodextrin phosphorylase from the cellulolytic bacterium Clostridium (Hungateiclostridium) thermocellum (CtCDP), but the formation mechanism of the cellulose crystals and highly ordered structure has long been unclear. Considering the specific density of cellulose versus water, the formation of crystalline and highly ordered structure in an aqueous solution should be affected by gravity. Thus, we synthesized cellulose with CtCDP stable variant at the International Space Station, where sedimentation and convection due to gravity are negligible. Optical microscopic observation suggested that cellulose in space has a gel-like appearance without apparent aggregation, in contrast to cellulose synthesized on the ground. Small-angle X-ray scattering (SAXS) and wide-angle X-ray scattering (WAXS) indicated that cellulose synthesized in space has a more uniform particle distribution in the ~ 100 nm scale region than cellulose synthesized on the ground. Scanning electron microscopy (SEM) showed that both celluloses have a micrometer scale network structure, whereas a fine fiber network was constructed only under microgravity. These results indicate that gravity plays a role in cellulose II crystal sedimentation and the building of network structure, and synthesis in space could play a role in designing unique materials. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10570-021-04399-0.
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Affiliation(s)
- Tomohiro Kuga
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
- VTT Technical Research Centre of Finland, Tietotie 2 VTT, P. O. Box 1000, 02044 Espoo, Finland
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Uto T, Ikeda Y, Sunagawa N, Tajima K, Yao M, Yui T. Molecular Dynamics Simulation of Cellulose Synthase Subunit D Octamer with Cellulose Chains from Acetic Acid Bacteria: Insight into Dynamic Behaviors and Thermodynamics on Substrate Recognition. J Chem Theory Comput 2021; 17:488-496. [PMID: 33382615 DOI: 10.1021/acs.jctc.0c01027] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The present study reports the building of a computerized model and molecular dynamics (MD) simulation of cellulose synthase subunit D octamer (CesD) from Komagataeibacter hansenii. CesD was complexed with four cellulose chains having DP = 12 (G12) by model building, which revealed unexpected S-shaped pathways with bending regions. Combined conventional and accelerated MD simulations of CesD complex models were carried out, while the pyranose ring conformations of the glucose residues were restrained to avoid undesirable deviations of the ring conformation from the 4C1 form. The N-terminal regions and parts of the secondary structures of CesD established appreciable contacts with the G12 chains. Hybrid quantum mechanical (QM) and molecular mechanical (MM) simulations of the CesD complex model were performed. Glucose residues located at the pathway bends exhibited reversible changes to the ring conformation into either skewed or boat forms, which might be related to the function of CesD in regulating microfibril production.
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Affiliation(s)
- Takuya Uto
- Organization for Promotion of Tenure Track, University of Miyazaki, Nishi 1-1 Gakuen-Kibanadai, Miyazaki 889-2192, Japan
| | - Yuki Ikeda
- Faculty of Engineering, University of Miyazaki, Nishi 1-1 Gakuen-Kibanadai, Miyazaki 889-2192, Japan
| | - Naoki Sunagawa
- Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kenji Tajima
- Faculty of Engineering, Hokkaido University, N13W8, Kita-ku, Sapporo 060-8628, Japan
| | - Min Yao
- Faculty of Advanced Life Science, Hokkaido University, N10W8, Kita-ku, Sapporo 060-0810, Japan
| | - Toshifumi Yui
- Faculty of Engineering, University of Miyazaki, Nishi 1-1 Gakuen-Kibanadai, Miyazaki 889-2192, Japan
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Matsuyama K, Kishine N, Fujimoto Z, Sunagawa N, Kotake T, Tsumuraya Y, Samejima M, Igarashi K, Kaneko S. Unique active-site and subsite features in the arabinogalactan-degrading GH43 exo-β-1,3-galactanase from Phanerochaete chrysosporium. J Biol Chem 2020; 295:18539-18552. [PMID: 33093171 PMCID: PMC7939473 DOI: 10.1074/jbc.ra120.016149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/20/2020] [Indexed: 12/27/2022] Open
Abstract
Arabinogalactan proteins (AGPs) are plant proteoglycans with functions in growth and development. However, these functions are largely unexplored, mainly because of the complexity of the sugar moieties. These carbohydrate sequences are generally analyzed with the aid of glycoside hydrolases. The exo-β-1,3-galactanase is a glycoside hydrolase from the basidiomycete Phanerochaete chrysosporium (Pc1,3Gal43A), which specifically cleaves AGPs. However, its structure is not known in relation to its mechanism bypassing side chains. In this study, we solved the apo and liganded structures of Pc1,3Gal43A, which reveal a glycoside hydrolase family 43 subfamily 24 (GH43_sub24) catalytic domain together with a carbohydrate-binding module family 35 (CBM35) binding domain. GH43_sub24 is known to lack the catalytic base Asp conserved among other GH43 subfamilies. Our structure in combination with kinetic analyses reveals that the tautomerized imidic acid group of Gln263 serves as the catalytic base residue instead. Pc1,3Gal43A has three subsites that continue from the bottom of the catalytic pocket to the solvent. Subsite -1 contains a space that can accommodate the C-6 methylol of Gal, enabling the enzyme to bypass the β-1,6-linked galactan side chains of AGPs. Furthermore, the galactan-binding domain in CBM35 has a different ligand interaction mechanism from other sugar-binding CBM35s, including those that bind galactomannan. Specifically, we noted a Gly → Trp substitution, which affects pyranose stacking, and an Asp → Asn substitution in the binding pocket, which recognizes β-linked rather than α-linked Gal residues. These findings should facilitate further structural analysis of AGPs and may also be helpful in engineering designer enzymes for efficient biomass utilization.
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Affiliation(s)
- Kaori Matsuyama
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Naomi Kishine
- Advanced Analysis Center, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Zui Fujimoto
- Advanced Analysis Center, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Toshihisa Kotake
- Department of Biochemistry and Molecular Biology, Faculty of Science, Saitama University, Saitama, Japan
| | - Yoichi Tsumuraya
- Department of Biochemistry and Molecular Biology, Faculty of Science, Saitama University, Saitama, Japan
| | - Masahiro Samejima
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan; Faculty of Engineering, Shinshu University, Nagano, Japan
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan; VTT Technical Research Centre of Finland, Espoo, Finland.
| | - Satoshi Kaneko
- Department of Subtropical Bioscience and Biotechnology, Faculty of Agriculture, University of the Ryukyus, Nishihara, Okinawa, Japan
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Matsuyama K, Sunagawa N, Igarashi K. Mutation of cysteine residues increases heterologous expression of peach expansin in the methylotrophic yeast Pichia pastoris. Plant Biotechnol (Tokyo) 2020; 37:397-403. [PMID: 33850426 PMCID: PMC8034678 DOI: 10.5511/plantbiotechnology.20.0713a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 07/13/2020] [Indexed: 05/25/2023]
Abstract
The study of Carbohydrate-Active enZymes (CAZymes) associated with plant cell wall metabolism is important for elucidating the developmental mechanisms of plants and also for the utilization of plants as a biomass resource. The use of recombinant proteins is common in this context, but heterologous expression of plant proteins is particularly difficult, in part because the presence of many cysteine residues promotes denaturation, aggregation and/or protein misfolding. In this study, we evaluated two phenotypes of methylotrophic yeast Pichia pastoris as expression hosts for expansin from peach (Prunus persica (L.) Batsch, PpEXP1), which is one of the most challenging targets for heterologous expression. cDNAs encoding wild-type expansin (PpEXP1_WT) and a mutant in which all cysteine residues were replaced with serine (PpEXP1_CS) were each inserted into expression vectors, and the protein expression levels were compared. The total amount of secreted protein in PpEXP1_WT culture was approximately twice that of PpEXP1_CS. However, the amounts of recombinant expansin were 0.58 and 4.3 mg l-1, corresponding to 0.18% and 2.37% of total expressed protein, respectively. This 13-fold increase in production of the mutant in P. pastoris indicates that the replacement of cysteine residues stabilizes recombinant PpEXP1.
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Affiliation(s)
- Kaori Matsuyama
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- VTT Technical Research Centre of Finland, PO Box 1000, Tietotie 2, Espoo FI-02044 VTT, Finland
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Kohno M, Arakawa T, Sunagawa N, Mori T, Igarashi K, Nishimoto T, Fushinobu S. Molecular analysis of cyclic α-maltosyl-(1→6)-maltose binding protein in the bacterial metabolic pathway. PLoS One 2020; 15:e0241912. [PMID: 33211750 PMCID: PMC7676653 DOI: 10.1371/journal.pone.0241912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/22/2020] [Indexed: 11/18/2022] Open
Abstract
Cyclic α-maltosyl-(1→6)-maltose (CMM) is a cyclic glucotetrasaccharide with alternating α-1,4 and α-1,6 linkages. Here, we report functional and structural analyses on CMM-binding protein (CMMBP), which is a substrate-binding protein (SBP) of an ABC importer system of the bacteria Arthrobacter globiformis. Isothermal titration calorimetry analysis revealed that CMMBP specifically bound to CMM with a Kd value of 9.6 nM. The crystal structure of CMMBP was determined at a resolution of 1.47 Å, and a panose molecule was bound in a cleft between two domains. To delineate its structural features, the crystal structure of CMMBP was compared with other SBPs specific for carbohydrates, such as cyclic α-nigerosyl-(1→6)-nigerose and cyclodextrins. These results indicate that A. globiformis has a unique metabolic pathway specialized for CMM.
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Affiliation(s)
- Masaki Kohno
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- R&D Division, HAYASHIBARA CO., LTD., Okayama, Japan
| | - Takatoshi Arakawa
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, The University of Tokyo, Tokyo, Japan
| | - Tetsuya Mori
- R&D Division, HAYASHIBARA CO., LTD., Okayama, Japan
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, The University of Tokyo, Tokyo, Japan
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | | | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
- * E-mail:
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10
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Pylkkänen R, Mohammadi P, Arola S, de Ruijter JC, Sunagawa N, Igarashi K, Penttilä M. In Vitro Synthesis and Self-Assembly of Cellulose II Nanofibrils Catalyzed by the Reverse Reaction of Clostridium thermocellum Cellodextrin Phosphorylase. Biomacromolecules 2020; 21:4355-4364. [PMID: 32960595 DOI: 10.1021/acs.biomac.0c01162] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In nature, various organisms produce cellulose as microfibrils, which are processed into their nano- and microfibrillar and/or crystalline components by humans in order to obtain desired material properties. Interestingly, the natural synthesis machinery can be circumvented by enzymatically synthesizing cellulose from precursor molecules in vitro. This approach is appealing for producing tailor-made cellulosic particles and materials because it enables optimization of the reaction conditions for cellulose synthesis in order to generate particles with a desired morphology in their pure form. Here, we present enzymatic cellulose synthesis catalyzed by the reverse reaction of Clostridium thermocellum cellodextrin phosphorylase in vitro. We were able to produce cellulose II nanofibril networks in all conditions tested, using varying concentrations of the glycosyl acceptors d-glucose or d-cellobiose (0.5, 5, and 50 mM). We show that shorter cellulose chains assemble into flat ribbon-like fibrils with greater diameter, while longer chains assemble into cylindrical fibrils with smaller diameter.
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Affiliation(s)
- Robert Pylkkänen
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16300, FI-00076 Espoo, Finland.,VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Finland
| | - Pezhman Mohammadi
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Finland
| | - Suvi Arola
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Finland
| | - Jorg C de Ruijter
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Finland
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, 113-8657 Tokyo, Japan
| | - Kiyohiko Igarashi
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Finland.,Department of Biomaterial Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, 113-8657 Tokyo, Japan
| | - Merja Penttilä
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16300, FI-00076 Espoo, Finland.,VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT, Finland
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11
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Yamaguchi S, Sunagawa N, Tachioka M, Igarashi K, Samejima M. Thermostable Mutants of Glycoside Hydrolase Family 6 Cellobiohydrolase from the Basidiomycete Phanerochaete chrysosporium. J Appl Glycosci (1999) 2020; 67:79-86. [PMID: 34354533 PMCID: PMC8132074 DOI: 10.5458/jag.jag.jag-2020_0004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 06/09/2020] [Indexed: 11/24/2022] Open
Abstract
Thermal inactivation of saccharifying enzymes is a crucial issue for the efficient utilization of cellulosic biomass as a renewable resource. Cellobiohydrolases (CBHs) are a kind of cellulase. In general, CBHs belonging to glycoside hydrolase (GH) family 6 (Cel6) act synergistically with CBHs of GH family 7 (Cel7) and other carbohydrate-active enzymes during the degradation of cellulosic biomass. However, while the catalytic rate of enzymes generally becomes faster at higher temperatures, Cel6 CBHs are inactivated at lower temperatures than Cel7 CBHs, and this represents a limiting factor for industrial utilization. In this study, we produced a series of mutants of the glycoside hydrolase family 6 cellobiohydrolase Pc Cel6A from the fungus Phanerochaete chrysosporium , and compared their thermal stability. Eight mutants from a random mutagenesis library and one rationally designed mutant were selected as candidate thermostable mutants and produced by heterologous expression in the yeast Pichia pastoris . Comparison of the hydrolytic activities at 50 and 60 °C indicated that the thermal stability of Pc Cel6A is influenced by the number and position of cysteine residues that are not involved in disulfide bonds.
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Affiliation(s)
- Sora Yamaguchi
- 1 Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Naoki Sunagawa
- 1 Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Mikako Tachioka
- 1 Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo.,2 Deep-Sea Nanoscience Research Group, Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology
| | - Kiyohiko Igarashi
- 1 Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo.,3 VTT Technical Research Centre of Finland
| | - Masahiro Samejima
- 1 Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo.,4 Faculty of Engineering, Shinshu University
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12
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Abe K, Sunagawa N, Terada T, Takahashi Y, Arakawa T, Igarashi K, Samejima M, Nakai H, Taguchi H, Nakajima M, Fushinobu S. Structural and thermodynamic insights into β-1,2-glucooligosaccharide capture by a solute-binding protein in Listeria innocua. J Biol Chem 2018; 293:8812-8828. [PMID: 29678880 DOI: 10.1074/jbc.ra117.001536] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 04/18/2018] [Indexed: 12/26/2022] Open
Abstract
β-1,2-Glucans are bacterial carbohydrates that exist in cyclic or linear forms and play an important role in infections and symbioses involving Gram-negative bacteria. Although several β-1,2-glucan-associated enzymes have been characterized, little is known about how β-1,2-glucan and its shorter oligosaccharides (Sop n s) are captured and imported into the bacterial cell. Here, we report the biochemical and structural characteristics of the Sop n -binding protein (SO-BP, Lin1841) associated with the ATP-binding cassette (ABC) transporter from the Gram-positive bacterium Listeria innocua Calorimetric analysis revealed that SO-BP specifically binds to Sop n s with a degree of polymerization of 3 or more, with Kd values in the micromolar range. The crystal structures of SO-BP in an unliganded open form and in closed complexes with tri-, tetra-, and pentaoligosaccharides (Sop3-5) were determined to a maximum resolution of 1.6 Å. The binding site displayed shape complementarity to Sop n , which adopted a zigzag conformation. We noted that water-mediated hydrogen bonds and stacking interactions play a pivotal role in the recognition of Sop3-5 by SO-BP, consistent with its binding thermodynamics. Computational free-energy calculations and a mutational analysis confirmed that interactions with the third glucose moiety of Sop n s are significantly responsible for ligand binding. A reduction in unfavorable changes in binding entropy that were in proportion to the lengths of the Sop n s was explained by conformational entropy changes. Phylogenetic and sequence analyses indicated that SO-BP ABC transporter homologs, glycoside hydrolases, and other related proteins are co-localized in the genomes of several bacteria. This study may improve our understanding of bacterial β-1,2-glucan metabolism and promote the discovery of unidentified β-1,2-glucan-associated proteins.
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Affiliation(s)
- Koichi Abe
- From the Department of Biotechnology.,Agricultural Bioinformatics Research Unit, and
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | | | - Yuta Takahashi
- the Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan
| | | | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,the VTT Technical Research Centre of Finland, Espoo FI-02044 VTT, Finland, and
| | - Masahiro Samejima
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hiroyuki Nakai
- the Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan
| | - Hayao Taguchi
- the Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Masahiro Nakajima
- the Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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13
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Harada H, Onoda A, Uchihashi T, Watanabe H, Sunagawa N, Samejima M, Igarashi K, Hayashi T. Interdomain flip-flop motion visualized in flavocytochrome cellobiose dehydrogenase using high-speed atomic force microscopy during catalysis. Chem Sci 2017; 8:6561-6565. [PMID: 28989682 PMCID: PMC5627353 DOI: 10.1039/c7sc01672g] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/15/2017] [Indexed: 12/02/2022] Open
Abstract
To visualize the dynamic domain motion of class-I CDH from Phanerochaete chrysosporium (PcCDH) during catalysis using high-speed atomic force microscopy, the apo-form of PcCDH was anchored to a heme-immobilized flat gold surface that can fix the orientation of the CYT domain.
Cellobiose dehydrogenase (CDH) is a dual domain flavocytochrome, which consists of a dehydrogenase (DH) domain containing a flavin adenine dinucleotide and a cytochrome (CYT) domain containing b-type heme. To directly visualize the dynamic domain motion of class-I CDH from Phanerochaete chrysosporium (PcCDH) during catalysis using high-speed atomic force microscopy, the apo-form of PcCDH was anchored to a heme-immobilized flat gold surface that can specifically fix the orientation of the CYT domain. The two domains of CDH are found to be immobile in the absence of cellobiose, whereas the addition of cellobiose triggers an interdomain flip-flop motion involving domain–domain association and dissociation. Our results indicate that dynamic motion of a dual domain enzyme during catalysis induces efficient electron transfer to an external electron acceptor.
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Affiliation(s)
- Hirofumi Harada
- Department of Applied Chemistry , Graduate School of Engineering , Osaka University , 2-1 Yamadaoka , Suita , Osaka 565-0871 , Japan . ;
| | - Akira Onoda
- Department of Applied Chemistry , Graduate School of Engineering , Osaka University , 2-1 Yamadaoka , Suita , Osaka 565-0871 , Japan . ;
| | - Takayuki Uchihashi
- Department of Physics , Nagoya University , Furo-cho, Chikusa-ku , Nagoya , 464-8602 , Japan .
| | - Hiroki Watanabe
- Faculty of Natural Science and Technology , Kanazawa University , Kakuma , Kanazawa , 920-1192 , Japan
| | - Naoki Sunagawa
- Department of Biomaterials Sciences , Graduate School of Agricultural and Life Sciences , The University of Tokyo , Bunkyo-ku , 113-8657 , Japan .
| | - Masahiro Samejima
- Department of Biomaterials Sciences , Graduate School of Agricultural and Life Sciences , The University of Tokyo , Bunkyo-ku , 113-8657 , Japan .
| | - Kiyohiko Igarashi
- Department of Biomaterials Sciences , Graduate School of Agricultural and Life Sciences , The University of Tokyo , Bunkyo-ku , 113-8657 , Japan . .,VTT Technical Research Centre of Finland , P.O. Box 1000, Tietotie 2 , Espoo FI-02044 VTT , Finland
| | - Takashi Hayashi
- Department of Applied Chemistry , Graduate School of Engineering , Osaka University , 2-1 Yamadaoka , Suita , Osaka 565-0871 , Japan . ;
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14
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Shinohara N, Sunagawa N, Tamura S, Yokoyama R, Ueda M, Igarashi K, Nishitani K. The plant cell-wall enzyme AtXTH3 catalyses covalent cross-linking between cellulose and cello-oligosaccharide. Sci Rep 2017; 7:46099. [PMID: 28443615 PMCID: PMC5405413 DOI: 10.1038/srep46099] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/02/2017] [Indexed: 11/09/2022] Open
Abstract
Cellulose is an economically important material, but routes of its industrial processing have not been fully explored. The plant cell wall - the major source of cellulose - harbours enzymes of the xyloglucan endotransglucosylase/hydrolase (XTH) family. This class of enzymes is unique in that it is capable of elongating polysaccharide chains without the requirement for activated nucleotide sugars (e.g., UDP-glucose) and in seamlessly splitting and reconnecting chains of xyloglucan, a naturally occurring soluble analogue of cellulose. Here, we show that a recombinant version of AtXTH3, a thus far uncharacterized member of the Arabidopsis XTH family, catalysed the transglycosylation between cellulose and cello-oligosaccharide, between cellulose and xyloglucan-oligosaccharide, and between xyloglucan and xyloglucan-oligosaccharide, with the highest reaction rate observed for the latter reaction. In addition, this enzyme formed cellulose-like insoluble material from a soluble cello-oligosaccharide in the absence of additional substrates. This newly found activity (designated "cellulose endotransglucosylase," or CET) can potentially be involved in the formation of covalent linkages between cellulose microfibrils in the plant cell wall. It can also comprise a new route of industrial cellulose functionalization.
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Affiliation(s)
- Naoki Shinohara
- Plant Cell Wall Biology Laboratory, Graduate School of Life Sciences, Tohoku University, Aoba-Ku, Sendai, 980-8578, Japan
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, 113-8657, Japan
| | - Satoru Tamura
- Laboratory of Organic Chemistry, Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-Ku, Sendai 980-8578, Japan
| | - Ryusuke Yokoyama
- Plant Cell Wall Biology Laboratory, Graduate School of Life Sciences, Tohoku University, Aoba-Ku, Sendai, 980-8578, Japan
| | - Minoru Ueda
- Laboratory of Organic Chemistry, Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-Ku, Sendai 980-8578, Japan
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, 113-8657, Japan.,VTT Technical Research Centre of Finland, P.O. Box 1000, Tietotie 2, Espoo FI-02044, Finland
| | - Kazuhiko Nishitani
- Plant Cell Wall Biology Laboratory, Graduate School of Life Sciences, Tohoku University, Aoba-Ku, Sendai, 980-8578, Japan
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15
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Tachioka M, Sugimoto N, Nakamura A, Sunagawa N, Ishida T, Uchiyama T, Igarashi K, Samejima M. Development of simple random mutagenesis protocol for the protein expression system in Pichia pastoris. Biotechnol Biofuels 2016; 9:199. [PMID: 27660653 PMCID: PMC5028916 DOI: 10.1186/s13068-016-0613-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 09/07/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Random mutagenesis is a powerful technique to obtain mutant proteins with different properties from the wild-type molecule. Error-prone PCR is often employed for random mutagenesis in bacterial protein expression systems, but has rarely been used in the methylotrophic yeast Pichia pastoris system, despite its significant advantages, mainly because large (μg-level) amounts of plasmids are required for transformation. RESULTS We developed a quick and easy technique for random mutagenesis in P. pastoris by sequential Phi29 DNA polymerase-based amplification methods, error-prone rolling circle amplification (RCA) and multiple displacement amplification (MDA). The methodology was validated by applying it for random mutation of the gene encoding cellulase from the basidiomycete Phanerochaete chrysosporium (PcCel6A), a key enzyme in degradation of cellulosic biomass. In the error-prone RCA step, the concentrations of manganese ion (Mn(2+)) and cellulase gene-containing plasmid were varied, and the products obtained under each condition were subjected to the second MDA step in the absence of Mn(2+). The maximum error rate was 2.6 mutations/kb, as evaluated from the results of large-scale sequencing. Several μg of MDA products was transformed by electroporation into Pichia cells, and the activities of extracellularly expressed PcCel6A mutants towards crystalline and amorphous celluloses were compared with those of wild-type enzyme to identify key amino acid residues affecting degradation of crystalline cellulose. CONCLUSIONS We present a rapid and convenient random mutagenesis method that does not require laborious steps such as ligation, cloning, and synthesis of specific primers. This method was successfully applied to the protein expression system in P. pastoris.
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Affiliation(s)
- Mikako Tachioka
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Naohisa Sugimoto
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
- Biomaterial in Tokyo Co., Ltd., Fukuoka Lab, Ōnojō, Fukuoka 816-0905 Japan
| | - Akihiko Nakamura
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
- Institute for Molecular Science, National Institute of Natural Sciences, Okazaki, 444-8787 Japan
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Takuya Ishida
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Taku Uchiyama
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Masahiro Samejima
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan
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16
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Sunagawa N, Fujiwara T, Yoda T, Kawano S, Satoh Y, Yao M, Tajima K, Dairi T. Cellulose complementing factor (Ccp) is a new member of the cellulose synthase complex (terminal complex) in Acetobacter xylinum. J Biosci Bioeng 2013; 115:607-12. [DOI: 10.1016/j.jbiosc.2012.12.021] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 12/26/2012] [Accepted: 12/27/2012] [Indexed: 11/26/2022]
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17
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Hu SQ, Gao YG, Tajima K, Sunagawa N, Zhou Y, Kawano S, Fujiwara T, Yoda T, Shimura D, Satoh Y, Munekata M, Tanaka I, Yao M. Structure of bacterial cellulose synthase subunit D octamer with four inner passageways. Proc Natl Acad Sci U S A 2010; 107:17957-61. [PMID: 20921370 PMCID: PMC2964256 DOI: 10.1073/pnas.1000601107] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The cellulose synthesizing terminal complex consisting of subunits A, B, C, and D in Acetobacter xylinum spans the outer and inner cell membranes to synthesize and extrude glucan chains, which are assembled into subelementary fibrils and further into a ribbon. We determined the structures of subunit D (AxCeSD/AxBcsD) with both N- and C-terminal His(6) tags, and in complex with cellopentaose. The structure of AxCeSD shows an exquisite cylinder shape (height: ∼65 Å, outer diameter: ∼90 Å, and inner diameter: ∼25 Å) with a right-hand twisted dimer interface on the cylinder wall, formed by octamer as a functional unit. All N termini of the octamer are positioned inside the AxCeSD cylinder and create four passageways. The location of cellopentaoses in the complex structure suggests that four glucan chains are extruded individually through their own passageway along the dimer interface in a twisted manner. The complex structure also shows that the N-terminal loop, especially residue Lys6, seems to be important for cellulose production, as confirmed by in vivo assay using mutant cells with axcesD gene disruption and N-terminus truncation. Taking all results together, a model of the bacterial terminal complex is discussed.
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Affiliation(s)
- Song-Qing Hu
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan; and
| | - Yong-Gui Gao
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan; and
| | - Kenji Tajima
- Division of Biotechnology and Macromolecular Chemistry, Graduate School of Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Naoki Sunagawa
- Division of Biotechnology and Macromolecular Chemistry, Graduate School of Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Yong Zhou
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan; and
| | - Shin Kawano
- Division of Biotechnology and Macromolecular Chemistry, Graduate School of Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Takaaki Fujiwara
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan; and
| | - Takanori Yoda
- Division of Biotechnology and Macromolecular Chemistry, Graduate School of Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Daisuke Shimura
- Division of Biotechnology and Macromolecular Chemistry, Graduate School of Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Yasuharu Satoh
- Division of Biotechnology and Macromolecular Chemistry, Graduate School of Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Masanobu Munekata
- Division of Biotechnology and Macromolecular Chemistry, Graduate School of Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Isao Tanaka
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan; and
| | - Min Yao
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan; and
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18
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Yao M, Hu SQ, Tajima K, Gao YQ, Sunagawa N, Zhou Y, Shimura D, Munekata M, Tanaka I. A novel octamer structure of bacterial cellulose synthesis component AxCesD. Acta Crystallogr A 2008. [DOI: 10.1107/s0108767308089204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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19
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Narita M, Akai H, Kita T, Nagumo Y, Narita M, Sunagawa N, Hara C, Hasebe K, Nagase H, Suzuki T. Involvement of mitogen-stimulated p70-S6 kinase in the development of sensitization to the methamphetamine-induced rewarding effect in rats. Neuroscience 2005; 132:553-60. [PMID: 15837117 DOI: 10.1016/j.neuroscience.2004.12.050] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2004] [Indexed: 10/25/2022]
Abstract
The neural plasticity associated with behavioral sensitization following repeated administration of a psychostimulant methamphetamine (METH) is thought to require synthesis of new proteins. The aim of the present study was to investigate the role of p70-S6 kinase (p70-S6K) phosphorylation, which contributes to the selective translation of a unique family of mRNA, in mediating both the METH-induced rewarding effect and its sensitization. An intra-nucleus accumbens (N.Acc.) pre-injection with 0.025 pmol/rat of a selective p70-S6K inhibitor rapamycin failed to affect the METH-induced conditioned place preference. However, this treatment clearly abolished the development of sensitization of the METH-induced conditioned place preference. Consistent with the behavioral assay, the level of the immunoreactivity of phosporylated-p70-S6K was not changed in the cytosolic fraction of the N.Acc. obtained from rats that had revealed the METH-induced rewarding effect. In contrast, the immunoreactivities in the cytosolic preparation for Western blotting and immunohistochemical density of phosphorylated-p70-S6K were significantly increased in the N.Acc. obtained from METH-sensitized rats as compared with those with chronic saline treatment. However, the immunoreactivities of phosphorylated-extracellular signal-regulated kinase and phosphorylated-ribosomal S6 protein were not significantly altered in the N.Acc. under the same condition. The present data provide evidence for the change in the translation rate, which can be regulated by S6K phosphorylation, in the N.Acc. during the development of sensitization to METH-induced rewarding effects in rats.
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Affiliation(s)
- M Narita
- Department of Toxicology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, Shinagawa-ku, Tokyo 142-8501, Japan.
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20
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Narita M, Akai H, Nagumo Y, Sunagawa N, Hasebe K, Nagase H, Kita T, Hara C, Suzuki T. Implications of protein kinase C in the nucleus accumbens in the development of sensitization to methamphetamine in rats. Neuroscience 2004; 127:941-8. [PMID: 15312906 DOI: 10.1016/j.neuroscience.2004.06.017] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2004] [Indexed: 11/21/2022]
Abstract
Repeated treatment with methamphetamine leads to an enhancement in the methamphetamine-induced dopamine release and its related behaviors. This phenomenon is called sensitization or reverse tolerance. Protein kinase C (PKC) controls numerous signaling cascades by virtue of its ability to phosphorylate target proteins that include other kinases. The purpose of study was then to investigate the implication of PKC in the development of sensitization to the rewarding effect and to the extracellular dopamine release induced by methamphetamine in rats. The conditioned place preference paradigm and in vivo microdialysis assay were performed in the present study. An intra-nucleus accumbens injection of a selective PKC inhibitor chelerythrine chloride abolished the enhancement of the methamphetamine-induced place preference following repeated treatment with methamphetamine. Furthermore, intra-nucleus accumbens injection of chelerythrine chloride blocked the development of sensitization to dopamine release and to the decrease in the major dopamine metabolites, 3'4-dihydroxyphenylacetic acid and homovanillic acid, in the nucleus accumbens induced by repeated methamphetamine treatment. Under these conditions, the immunoreactivity of the cytosolic phosphorylated conventional- or classic-type PKC in the limbic forebrain region including the nucleus accumbens was slightly, but significantly increased in methamphetamine-sensitized rats. The present data provide evidence for the implication of PKC in the nucleus accumbens in the development of sensitization to the methamphetamine-induced rewarding effect, dopamine release and inhibition of dopamine metabolism/re-uptake in rats.
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Affiliation(s)
- M Narita
- Department of Toxicology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan.
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21
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Okimoto N, Sunagawa N, Asaoka N, Ohba H, Yoneyama H, Kobashi Y, Soejima R. [Influence of steroid inhalation therapy on microorganism of respiratory infections in patients with bronchial asthma]. Kansenshogaku Zasshi 1999; 73:1165-6. [PMID: 10624099 DOI: 10.11150/kansenshogakuzasshi1970.73.1165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- N Okimoto
- Department of Medicine, Kawasaki Medical School Kawasaki Hospital
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22
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Kurihara H, Sunagawa N, Kobayashi T, Kimura K, Takasu N, Shike T. Monoclonal antibody P-31 recognizes a novel intermediate filament-associated protein (p250) in rat podocytes. Am J Physiol 1998; 274:F986-97. [PMID: 9612338 DOI: 10.1152/ajprenal.1998.274.5.f986] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The visceral glomerular epithelial cells (GECs) or podocytes of the renal glomerulus constitute a highly specialized epithelium. To study the nature of podocytes, we established mouse monoclonal antibodies against GEC. Clone P-31 reacted exclusively with the cytoplasm of GEC by immunofluorescence. Immunoblot analysis with P-31 showed that a single band of 250 kDa was detectable in a glomerular lysate. The 250-kDa polypeptide (p250) was recovered from Triton X-100-insoluble fractions of isolated glomeruli, suggesting that this molecule is associated with the cytoskeleton. Immunogold staining with P-31 demonstrated that the gold particles were located at the intersections of vimentin-type intermediate filaments of podocytes. In developing kidney, this protein first appeared in immature GECs during the S-shaped body stage. In puromycin aminonucleoside nephrosis, p250 was dramatically increased in glomeruli where enhanced desmin expression was observed in GECs. These results indicate that p250 is a novel intermediate filament-associated protein and plays a role in the organization of the intermediate filament network in both normal and diseased conditions.
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Affiliation(s)
- H Kurihara
- Shionogi Research Laboratories, Osaka, Japan
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Shinosaki T, Takagawa I, Sunagawa N, Yonetani Y, Kurihara H. Dual effects of lisinopril on puromycin aminonucleoside nephrosis in unilaterally nephrectomized rats. Jpn J Pharmacol 1997; 73:337-345. [PMID: 9165371 DOI: 10.1254/jjp.73.337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The therapeutic effects of angiotensin converting enzyme inhibitor, lisinopril, on puromycin aminonucleoside (PAN)-induced nephrosis were investigated using unilaterally nephrectomized rats. Lisinopril showed potent dual effects on PAN nephrosis. Lisinopril treatment (50 mg/l in drinking water) from day 5 or day 9 reduced urinary protein excretion and suppressed the development of glomerular sclerosis at 8 weeks after PAN injection (150 mg/kg, i.p.), indicating a therapeutic effect on the nephrosis. Recovery of decreased anionic charge sites on the glomerular basement membrane was involved, at least in part, in the therapeutic action of lisinopril against proteinuria. On the other hand, oliguria and progressive azotemia derived from continuous deterioration of the renal function was induced if the treatment of lisinopril was started on the same day as PAN injection. The renal dysfunction induced by simultaneous administration of lisinopril with PAN could be abolished by combination dosing with sarcosine, an angiotensin II (AII)-receptor agonist. These results indicate that lisinopril treatment attenuates proteinuria by ameliorating the anionic charge barrier on the glomerular basement membrane and that it also protects against the development of chronic renal disease with segmental glomerular sclerosis, although AII depletion during the acute nephrotic stage exacerbates the renal damage in PAN nephrosis of unilaterally nephrectomized rats.
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Affiliation(s)
- T Shinosaki
- Shionogi Discovery Research Laboratories II, Shionogi & Co., Ltd., Osaka, Japan
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Abstract
The morphological properties of poly(beta-hydroxybutyric acid) (PHB) or poly(L-lactic acid) microspheres loading flomoxef sodium (FMOX) were investigated with regard to FMOX release. The release profiles of FMOX from the microspheres could be divided into two types, a sustained release type and a burst one. Two representative PHB microspheres, the release profiles of which were quite different from those of FMOX, were compared in detail from a morphological point of view. The shapes of their surfaces and sections were observed by using scanning electron microscopy (SEM), and FMOX distribution was analyzed by using electron probe microanalysis. The crystallinity of polymers was further measured by powder X-ray diffratometry. There was little difference in the FMOX distribution and their microscopic properties such as sphere size, specific surface area, shape of surface and section. In contrast, water penetration into the inside of the microspheres was found to be clearly different by use of cryogenic SEM. A significant difference was also observed in the crystallinity of polymers forming the microspheres. The release of FMOX from the microspheres was affected by the crystallinity of polymers forming the microspheres, and burst phenomena occurred in case the polymer was highly crystallized. It was speculated that the crystallization of polymer induced micro voids in the microspheres which functioned as channels for water penetration.
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Affiliation(s)
- K Takeshima
- Shionogi Research Laboratories, Shionogi & Co., Ltd., Osaka, Japan
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Takeo S, Yamada H, Tanonaka K, Hayashi M, Sunagawa N. Possible involvement of membrane-stabilizing action in beneficial effect of beta adrenoceptor blocking agents on hypoxic and posthypoxic myocardium. J Pharmacol Exp Ther 1990; 254:847-56. [PMID: 1975623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The present study was designed to elucidate a possible involvement of membrane-stabilizing action of beta blocking agents in posthypoxic recovery of cardiac contractile function and myocardial metabolism. Propranolol and acebutolol, which possess a membrane-stabilizing action, and atenolol and metoprolol, which lack this action, were used in the isolated, perfused rabbit heart. The membrane-stabilizing effects of these agents were assessed on the basis of the effects on the maximal driving frequency of the left atria. Reoxygenation of hearts for 45 min following 20-min hypoxia resulted in little recovery of cardiac contractile force, sustained rise in resting tension, insufficient recovery of myocardial high-energy phosphates, accumulation of the tissue calcium and sodium and marked release of creatine kinase and ATP metabolites from the hearts. Treatment of hypoxic hearts with either 100 microM propranolol, 200 microM acebutolol, 200 microM atenolol or 100 microM metoprolol was commenced when the contractile force declined to 30% of the initial level and terminated at 20-min hypoxia. Treatment with either propranolol or acebutolol produced a significant posthypoxic recovery of cardiac contractile force, resting tension and myocardial high-energy phosphates, and a profound suppression of the tissue calcium and sodium accumulation and the loss of ATP metabolites from perfused hearts. In contrast, neither atenolol nor metoprolol affected these changes induced by the hypoxic insult and the following reoxygenation. The results suggest that membrane-stabilizing action of beta blocking agents plays an important role in the protection against posthypoxic cardiac contractile dysfunction and metabolic disturbances.
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Affiliation(s)
- S Takeo
- Department of Pharmacology, Tokyo College of Pharmacy, Japan
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Matsuura S, Sunagawa N, Katagiri K, Endo H, Tada M. Antitumor activity of phenazine di-N-oxides. II. Sci Rep Res Inst Tohoku Univ Med 1969; 16:15-7. [PMID: 5375993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Harada Y, Sunagawa N, Katagiri K. Segregation of the nucleolar materials produced by quinoxaline antibiotics in JTC-13 cells. Comparison of effects among 4-nitro-quinoline 1-oxide, actinomycin-B, and quinoxaline antibiotics. Gan 1968; 59:513-22. [PMID: 4181158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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