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NODA Shuhei
Graduate School of Science, Technology and Innovation / Department of Science, Technology and Innovation
Associate Professor

Researcher basic information

■ Research Keyword
  • Metabolic Engineering
  • Synthetic Biology
  • Enzyme Engineering
  • Protein Engineering
  • 微生物ポリマー
■ Research Areas
  • Manufacturing technology (mechanical, electrical/electronic, chemical engineering) / Applied biofunctional and bioprocess engineering

Research activity information

■ Award
  • Mar. 2022 理化学研究所, 桜舞賞
    野田修平

  • Mar. 2021 The Society of Chemical Engineers, 研究奨励賞, 有用化合物合成のための微生物バイオプロセス構築に関する研究
    Shuhei Noda

  • Nov. 2019 酵素工学研究会, 酵素工学奨励賞, 微生物を用いた有用バルクケミカル合成プラットホーム開発に関する研究
    野田 修平

  • Dec. 2017 iBioS-2017, Best Poster Award
    Shuhei Noda

  • Oct. 2015 YABEC 2015: 21st Young Asian Biochemical Engineers’ Community, Best Poster Award
    Shuhei Noda

  • Oct. 2011 YABEC2011: 17st Young Asian Biochemical Engineers’ Community, Best Poster Award
    Shuhei Noda

■ Paper
  • Parallel metabolic pathway engineering for aerobic 1,2‐propanediol production in Escherichia coli
    Daisuke Nonaka, Yuuki Hirata, Mayumi Kishida, Ayana Mori, Ryosuke Fujiwara, Akihiko Kondo, Yutaro Mori, Shuhei Noda, Tsutomu Tanaka
    Aug. 2024, Biotechnology Journal, 19(8) (8), 2400210 - 2400210
    [Refereed]

  • Shuhei Noda, Yutaro Mori, Yuki Ogawa, Ryosuke Fujiwara, Mayumi Dainin, Tomokazu Shirai, Akihiko Kondo
    Elsevier BV, Jun. 2024, Bioresource Technology, 130927 - 130927
    [Refereed]
    Scientific journal

  • Styrene Production in Genetically Engineered Escherichia coli in a Two-Phase Culture
    Shuhei Noda, Ryosuke Fujiwara, Yutaro Mori, Mayumi Dainin, Tomokazu Shirai, Akihiko Kondo
    Jan. 2024, BioTech, 13(1) (1)
    [Refereed]

  • p-Nitrobenzoate production from glucose by utilizing p-aminobenzoate N-oxygenase: AurF
    Ayana Mori, Yuuki Hirata, Mayumi Kishida, Yutaro Mori, Akihiko Kondo, Shuhei Noda, Tsutomu Tanaka
    Dec. 2023, Enzyme and Microbial Technology, 171, 110321
    [Refereed]

  • Population Dynamics in the Biogenesis of Single-/Multi-Layered Membrane Vesicles Revealed by Encapsulated GFP-Monitoring Analysis
    Sangho Koh, Shuhei Noda, Seiichi Taguchi
    Sep. 2023, Applied Microbiology, 3(3) (3), 1027 - 1036
    [Refereed]

  • Kosuke Sakae, Daisuke Nonaka, Mayumi Kishida, Yuuki Hirata, Ryosuke Fujiwara, Akihiko Kondo, Shuhei Noda, Tsutomu Tanaka
    Elsevier BV, Mar. 2023, Enzyme and Microbial Technology, 164, 110193 - 110193
    [Refereed]
    Scientific journal

  • Nunthaphan Vikromvarasiri, Shuhei Noda, Tomokazu Shirai, Akihiko Kondo
    Abstract Background Flux Balance Analysis (FBA) is a well-known bioinformatics tool for metabolic engineering design. Previously, we have successfully used single-level FBA to design metabolic fluxes in Bacillus subtilis to enhance (R,R)-2,3-butanediol (2,3-BD) production from glycerol. OptKnock is another powerful technique for devising gene deletion strategies to maximize microbial growth coupling with improved biochemical production. It has never been used in B. subtilis. In this study, we aimed to compare the use of single-level FBA and OptKnock for designing enhanced 2,3-BD production from glycerol in B. subtilis. Results Single-level FBA and OptKnock were used to design metabolic engineering approaches for B. subtilis to enhance 2,3-BD production from glycerol. Single-level FBA indicated that deletion of ackA, pta, lctE, and mmgA would improve the production of 2,3-BD from glycerol, while OptKnock simulation suggested the deletion of ackA, pta, mmgA, and zwf. Consequently, strains LM01 (single-level FBA-based) and MZ02 (OptKnock-based) were constructed, and their capacity to produce 2,3-BD from glycerol was investigated. The deletion of multiple genes did not negatively affect strain growth and glycerol utilization. The highest 2,3-BD production was detected in strain LM01. Strain MZ02 produced 2,3-BD at a similar level as the wild type, indicating that the OptKnock prediction was erroneous. Two-step FBA was performed to examine the reason for the erroneous OptKnock prediction. Interestingly, we newly found that zwf gene deletion in strain MZ02 improved lactate production, which has never been reported to date. The predictions of single-level FBA for strain MZ02 were in line with experimental findings. Conclusions We showed that single-level FBA is an effective approach for metabolic design and manipulation to enhance 2,3-BD production from glycerol in B. subtilis. Further, while this approach predicted the phenotypes of generated strains with high precision, OptKnock prediction was not accurate. We suggest that OptKnock modelling predictions be evaluated by using single-level FBA to ensure the accuracy of metabolic pathway design. Furthermore, the zwf gene knockout resulted in the change of metabolic fluxes to enhance the lactate productivity.
    Springer Science and Business Media LLC, Jan. 2023, Journal of Biological Engineering, 17(1) (1), 3 - 13
    [Refereed]
    Scientific journal

  • Misa Doke, Mayumi Kishida, Yuuki Hirata, Mariko Nakano, Mayo Horita, Daisuke Nonaka, Yutaro Mori, Ryosuke Fujiwara, Akihiko Kondo, Shuhei Noda, Tsutomu Tanaka
    Sciscan Publishing Limited, 2023, Synthetic Biology and Engineering, 1(1) (1), 1 - 9
    [Refereed]
    Scientific journal

  • Ryosuke Fujiwara, Mariko Nakano, Yuuki Hirata, Chisako Otomo, Daisuke Nonaka, Sakiya Kawada, Hikaru Nakazawa, Mitsuo Umetsu, Tomokazu Shirai, Shuhei Noda, Tsutomu Tanaka, Akihiko Kondo
    Escherichia coli, the most studied prokaryote, is an excellent host for producing valuable chemicals from renewable resources as it is easy to manipulate genetically. Since the periplasmic environment can be easily controlled externally, elucidating how the localization of specific proteins or small molecules in the periplasm affects metabolism may lead to bioproduction development using E. coli. We investigated metabolic changes and its mechanisms occurring when specific proteins are localized to the E. coli periplasm. We found that the periplasmic localization of β-glucosidase promoted the shikimate pathway involved in the synthesis of aromatic chemicals. The periplasmic localization of other proteins with an affinity for glucose-6-phosphate (G6P), such as inactivated mutants of Pgi, Zwf, and PhoA, similarly accelerated the shikimate pathway. Our results indicate that G6P is transported from the cytoplasm to the periplasm by the glucose transporter protein EIICBGlc, and then captured by β-glucosidase.
    Corresponding, Jul. 2022, Metabolic Engineering, 72, 68 - 81, English, International magazine
    [Refereed]
    Scientific journal

  • Shuhei Noda, Yutaro Mori, Ryosuke Fujiwara, Tomokazu Shirai, Tsutomu Tanaka, Akihiko Kondo
    Microbial metabolic pathway engineering is a potent strategy used worldwide to produce aromatic compounds. We drastically rewired the primary metabolic pathway of Escherichia coli to produce aromatics and their derivatives. The metabolic pathway of E. coli was compartmentalized into the production and energy modules. We focused on the pyruvate-forming reaction in the biosynthesis pathway of some compounds as the reaction connecting those modules. E. coli strains were engineered to show no growth unless pyruvate was synthesized along with the compounds of interest production. Production of salicylate and maleate was demonstrated to confirm our strategy's versatility. In maleate production, the production, yield against the theoretical yield, and production rate reached 12.0 g L-1, 67%, and up to fourfold compared to that in previous reports, respectively; these are the highest values of maleate production in microbes to our knowledge. The results reveal that our strategy strongly promotes the production of aromatics and their derivatives.
    May 2021, Metabolic Engineering, 67, 1 - 10, English, International magazine
    [Refereed]
    Scientific journal

  • Yutaro Mori, Shuhei Noda, Tomokazu Shirai, Akihiko Kondo
    The C4 unsaturated compound 1,3-butadiene is an important monomer in synthetic rubber and engineering plastic production. However, microorganisms cannot directly produce 1,3-butadiene when glucose is used as a renewable carbon source via biological processes. In this study, we construct an artificial metabolic pathway for 1,3-butadiene production from glucose in Escherichia coli by combining the cis,cis-muconic acid (ccMA)-producing pathway together with tailored ferulic acid decarboxylase mutations. The rational design of the substrate-binding site of the enzyme by computational simulations improves ccMA decarboxylation and thus 1,3-butadiene production. We find that changing dissolved oxygen (DO) levels and controlling the pH are important factors for 1,3-butadiene production. Using DO-stat fed-batch fermentation, we produce 2.13 ± 0.17 g L-1 1,3-butadiene. The results indicate that we can produce unnatural/nonbiological compounds from glucose as a renewable carbon source via a rational enzyme design strategy.
    Apr. 2021, Nature Communications, 12(1) (1), 2195 - 2206, English, International magazine
    [Refereed]
    Scientific journal

  • Daichi Satowa, Ryosuke Fujiwara, Shogo Uchio, Mariko Nakano, Chisako Otomo, Yuuki Hirata, Takuya Matsumoto, Shuhei Noda, Tsutomu Tanaka, Akihiko Kondo
    Microbial production of mevalonate from renewable feedstock is a promising and sustainable approach for the production of value-added chemicals. We describe the metabolic engineering of Escherichia coli to enhance mevalonate production from glucose and cellobiose. First, the mevalonate-producing pathway was introduced into E. coli and the expression of the gene atoB, which encodes the gene for acetoacetyl-CoA synthetase, was increased. Then, the deletion of the pgi gene, which encodes phosphoglucose isomerase, increased the NADPH/NADP+ ratio in the cells but did not improve mevalonate production. Alternatively, to reduce flux toward the tricarboxylic acid cycle, gltA, which encodes citrate synthetase, was disrupted. The resultant strain, MGΔgltA-MV, increased levels of intracellular acetyl-CoA up to sevenfold higher than the wild-type strain. This strain produced 8.0 g/L of mevalonate from 20 g/L of glucose. We also engineered the sugar supply by displaying β-glucosidase (BGL) on the cell surface. When cellobiose was used as carbon source, the strain lacking gnd displaying BGL efficiently consumed cellobiose and produced mevalonate at 5.7 g/L. The yield of mevalonate was 0.25 g/g glucose (1 g of cellobiose corresponds to 1.1 g of glucose). These results demonstrate the feasibility of producing mevalonate from cellobiose or cellooligosaccharides using an engineered E. coli strain.
    Jul. 2020, Biotechnology and Bioengineering, 117(7) (7), 2153 - 2164, English, International magazine
    [Refereed]
    Scientific journal

  • Metabolic engineering of Escherichia coli for shikimate pathway derivative production from glucose–xylose co-substrate
    Ryosuke Fujiwara, Shuhei Noda, Tsutomu Tanaka, Akihiko Kondo
    Corresponding, Jan. 2020, Nature Communications, 11, 279 - 290
    [Refereed]

  • Noda Shuhei, Mori Yutaro, Oyama Sachiko, Kondo Akihiko, Araki Michihiro, Shirai Tomokazu
    Lead, Springer Science and Business Media LLC, Jul. 2019, Microbial Cell Factories, 18(1) (1)
    [Refereed]
    Scientific journal

  • Fujiwara Ryosuke, Noda Shuhei, Tanaka Tsutomu, Kondo Akihiko
    Corresponding, Nov. 2018, ACS Synthetic Biology, 7(11) (11), 2698 - 2705
    [Refereed]

  • Shuhei Noda, Tomokazu Shirai, Yutaro Mori, Sachiko Oyama, Akihiko Kondo
    Maleate is one of the most important dicarboxylic acids and is used to produce various polymer compounds and pharmaceuticals. Herein, microbial production of maleate is successfully achieved, to our knowledge for the first time, using genetically modified Escherichia coli. A synthetic pathway of maleate is constructed in E. coli by combining the polyketide biosynthesis pathway and benzene ring cleavage pathway. The metabolic engineering approach used to fine-tune the synthetic pathway drastically improves maleate production and demonstrates that one of the rate limiting steps exists in the conversion of chorismate to gentisate. In a batch culture of the optimised transformant, grown in a 1-L jar fermentor, the amount of produced maleate reaches 7.1 g L-1, and the yield is 0.221 mol mol(-1). Our results suggest that the construction of synthetic pathways by combining a secondary metabolite pathway and the benzene ring cleavage pathway is a powerful tool for producing various valuable chemicals.
    Lead, NATURE PUBLISHING GROUP, Oct. 2017, Nature Communications, 8(1) (1), 1153 - 1165, English
    [Refereed]
    Scientific journal

  • Shuhei Noda, Akihiko Kondo
    Along with the development of metabolic engineering and synthetic biology tools, various microbes are being used to produce aromatic chemicals. In microbes, aromatics are mainly produced via a common important precursor, chorismate, in the shikimate pathway. Natural or non-natural aromatics have been produced by engineering metabolic pathways involving chorismate. In the past decade, novel approaches have appeared to produce various aromatics or to increase their productivity, whereas previously, the targets were mainly aromatic amino acids and the strategy was deregulating feedback inhibition. In this review, we summarize recent studies of microbial production of aromatics based on metabolic engineering approaches. In addition, future perspectives and challenges in this research area are discussed.
    Lead, ELSEVIER SCIENCE LONDON, Aug. 2017, Trends in Biotechnology, 35(8) (8), 785 - 796, English
    [Refereed]

  • Ryosuke Fujiwara, Shuhei Noda, Tsutomu Tanaka, Akihiko Kondo
    To produce styrene from a biomass-derived carbon source, Streptomyces lividans was adopted as a host strain. The gene encoding ferulic acid decarboxylase from Saccharomyces cerevisiae (FDC1) was introduced into S. lividans, and the resulting S. lividans transformant successfully expressed FDC1 and converted trans-cinnamic acid (CA) to styrene. A key factor in styrene production using microbes is the recovery of volatile styrene. In the present study, we selected polystyrene resin beads XRD-4 as the absorbent agent to recover styrene produced using S. lividans transformants, which enabled recovery of styrene from the culture broth. For styrene production from biomass-derived carbon sources, S. lividans/FDC1 was cultured together with S. lividans/p-encP, which we previously reported as a CA-producing S. lividans strain. This coculture system combined with the recovery of styrene using XAD-4 allowed the production of styrene from glucose, cellobiose, or xylo-oligosaccharide, respectively. (C) 2016, The Society for Biotechnology, Japan. All rights reserved.
    SOC BIOSCIENCE BIOENGINEERING JAPAN, Dec. 2016, Journal of Bioscience and Bioengineering, 122(6) (6), 730 - 735, English
    [Refereed]
    Scientific journal

  • Lili Jia, Geisa A. L. G. Budinova, Yusaku Takasugi, Shuhei Noda, Tsutomu Tanaka, Hirofumi Ichinose, Masahiro Goto, Noriho Kamiya
    Effective degradation of hemicellulose is of utmost importance in a wide variety of applications in bioindustry. Five endoxylanases from different glycoside hydrolase families and microorganisms were tested with an arabinofuranosidase, Araf51A, for the hydrolysis of insoluble wheat arabinoxylan, which is a structural component of hemicellulose. The optimized combination was XynZ/Xyn11A/Araf51A with a loading ratio of 2:2:1, and the value of degree of synergy increased with the increase of Araf51A proportion in the enzyme mixture. Afterwards, selected enzymes were immobilized on commercial magnetic nanoparticles through covalent bonding. Both free and immobilized enzymes showed a similar conversion to reducing sugars after hydrolysis for 48 h. After 10 cycles, approximately 20% of the initial enzymatic activity of both the individual or mixture of immobilized enzymes was retained. A 5.5-fold increase in the production of sugars was obtained with a mixture of enzymes immobilized after 10 cycles in total compared with free enzymes. Importantly, a sustainable synergism between immobilized arabinofuranosidase and immobilized endoxylanases in the hydrolysis of arabinoxylan was demonstrated. (C) 2016 Elsevier B.V. All rights reserved.
    ELSEVIER SCIENCE BV, Oct. 2016, Biochemical Engineering Journal, 114, 271 - 278, English
    [Refereed]
    Scientific journal

  • Ryosuke Fujiwara, Shuhei Noda, Yoshifumi Kawai, Tsutomu Tanaka, Akihiko Kondo
    To find a novel host for the production of 4-vinylphenol (4VPh) by screening Streptomyces species. The conversion of p-coumaric acid (pHCA) to 4VPh in Streptomyces mobaraense was evaluated using a medium containing pHCA. S. mobaraense readily assimilated pHCA after 24 h of cultivation to produce 4VPh. A phenolic acid decarboxylase, derived from S. mobaraense (SmPAD), was purified following heterologous expression in Escherichia coli. SmPAD was evaluated under various conditions, and the enzyme's k(cat)/K-m value was 0.54 mM (-1) s(-1). Using intergenetic conjugation, a gene from Rhodobacter sphaeroides encoding a tyrosine ammonia lyase, which catalyzes the conversion of l-tyrosine to p-coumaric acid, was introduced into S. mobaraense. The resulting S. mobaraense transformant produced 273 mg 4VPh l(-1) from 10 g glucose l(-1). A novel strain suitable for the production of 4VPh and potentially other aromatic compounds was isolated.
    SPRINGER, Sep. 2016, Biotechnology Letters, 38(9) (9), 1543 - 1549, English
    [Refereed]
    Scientific journal

  • Shuhei Noda, Tomokazu Shirai, Sachiko Oyama, Akihiko Kondo
    A synthetic metabolic pathway suitable for the production of chorismate derivatives was designed in Escherichia coil. An L-phenylalanine-overproducing E. coil strain was engineered to enhance the availability of phosphoenolpyruvate (PEP), which is a key precursor in the biosynthesis of aromatic compounds in microbes. Two major reactions converting PEP to pyruvate were inactivated. Using this modified E.coli as a base strain, we tested our system by carrying out the production of salicylate, a highdemand aromatic chemical. The titer of salicylate reached 11.5 g/L in batch culture after 48 h cultivation in a 2-liter jar fermentor, and the yield from glucose as the sole carbon source exceeded 40% (mol/mol). In this test case, we found that pyruvate was synthesized primarily via salicylate formation and the reaction converting oxaloacetate to pyruvate. In order to demonstrate the generality of our designed strain, we employed this platform for the production of each of 7 different chorismate derivatives. Each of these industrially important chemicals was successfully produced to levels of 1-3 g/L in test tube-scale culture. (C) 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.
    Lead, ACADEMIC PRESS INC ELSEVIER SCIENCE, Jan. 2016, Metabolic Engineering, 33, 119 - 129, English
    [Refereed]
    Scientific journal

  • Lili Jia, Geisa A. L. Goncalves, Yusaku Takasugi, Yutaro Mori, Shuhei Noda, Tsutomu Tanaka, Hirofumi Ichinose, Noriho Kamiya
    The effect of pretreatment with peracetic acid (PAA) or an ionic liquid (1-ethyl-3-methylimidazolium acetate, [Emim][OAc]) on the synergism between endoglucanase and endoxylanase in the hydrolysis of bagasse was investigated. An endoglucanase, Cel6A, with a carbohydrate-binding module (CBM) and two endoxylanases, XynZ-C without a CBM and Xyn11A with an intrinsic xylan/cellulose binding module (XBM), were selected. The hemicellulose content, especially arabinan, and the cellulose crystallinity of bagasse were found to affect the cellulase-xylanase synergism. More specifically, higher synergism (above 3.4) was observed for glucan conversion, at low levels of arabinan (0.9%), during the hydrolysis of PAA pretreated bagasse. In contrast, [Emim][OAc] pretreated bagasse, showed lower cellulose crystallinity and achieved higher synergism (over 1.9) for xylan conversion. Ultimately, the combination of Cel6A and Xyn11A resulted in higher synergism for glucan conversion than the combination of Cel6A with XynZ-C, indicating the importance of the molecular architecture of enzymes for metabolic synergism. (C) 2015 Elsevier Ltd. All rights reserved.
    ELSEVIER SCI LTD, Jun. 2015, Bioresource Technology, 185, 158 - 164, English
    [Refereed]
    Scientific journal

  • Shuhei Noda, Tomokazu Shirai, Keiichi Mochida, Fumio Matsuda, Sachiko Oyama, Mami Okamoto, Akihiko Kondo
    To demonstrate that herbaceous biomass is a versatile gene resource, we focused on the model plant Brachypodium distachyon, and screened the B. distachyon for homologs of tyrosine decarboxylase (TDC), which is involved in the modification of aromatic compounds. A total of 5 candidate genes were identified in cDNA libraries of B. distachyon and were introduced into Saccharomyces cerevisiae to evaluate TDC expression and tyramine production. It is suggested that two TDCs encoded in the transcripts Bradi2g51120.1 and Bradi2g51170.1 have L-tyrosine decarboxylation activity. Bradi2g51170.1 was introduced into the L-tyrosine over-producing strain of S. cerevisiae that was constructed by the introduction of mutant genes that promote deregulated feedback inhibition. The amount of tyramine produced by the resulting transformant was 6.6-fold higher (approximately 200 mg/L) than the control strain, indicating that B. distachyon TDC effectively converts L-tyrosine to tyramine. Our results suggest that B. distachyon possesses enzymes that are capable of modifying aromatic residues, and that S. cerevisiae is a suitable host for the production of L-tyrosine derivatives.
    Lead, PUBLIC LIBRARY SCIENCE, May 2015, PLOS ONE, 10(5) (5), e0125488, English
    [Refereed]
    Scientific journal

  • Geisa A. L. Goncalves, Yusaku Takasugi, Lili Jia, Yutaro Mori, Shuhei Noda, Tsutomu Tanaka, Hirofumi Ichinose, Noriho Kamiya
    Recently, the new trend in the second-generation ethanol industry is to use mild pretreatments, in order to reduce costs and to keep higher content of hemicellulose in the biomass. Nevertheless, a high enzyme dosage is still required in the conversion of (hemi)cellulose. The interaction between cellulases and xylanases seems to be an effective alternative to reduce enzyme loading in the saccharification process. At first, to evaluate the synergism of xylanases on bagasse degradation, we have produced two xylanases from glycoside hydrolase family 10 (GH10) and three xylanases from glycoside hydrolase family11 (GH11),from two thermophilic organisms, Thermobifida fusca and Clostridium thermocellum, and one mesophilic organism, Streptomyces lividans. Peracetic acid (PAA) pretreated bagasse was used as substrate. The combination of XynZ-C (GH10, from C. thermocellum), and XlnB (GH11, from S. lividans) presented the highest degree of synergy after 6 h (3,62). However, the combination of XynZ-C and Xyn11A (GH11, from T. fusca) resulted in the highest total yield of reducing sugars. To evaluate the synergism between xylanases and cellulases, commercial cellulase preparation from Trichoderma reesei was combined with the selected xylanases, XynZ-C and Xyn11A. About 2-fold increase was observed in the concentration of reducing sugars, when both xylanases, XynZ-C and Xyn11A, were added together with T. reesei cellulases in the reaction mixture. (C) 2015 Elsevier Inc. All rights reserved.
    ELSEVIER SCIENCE INC, May 2015, Enzyme and Microbial Technology, 72, 16 - 24, English
    [Refereed]
    Scientific journal

  • Shuhei Noda, Yoshifumi Kawai, Tsutomu Tanaka, Akihiko Kondo
    Streptomyces lividans was adopted as a host strain for 4-vinylphenol (4VPh) production directly from cellulose. In order to obtain novel phenolic acid decarboxylase (PAD) expressed in S. lividans, PADs distributed among Streptomyces species were screened. Three novel PADs, derived from Streptomyces sviceus, Streptomyces hygroscopicus, and Streptomyces cattleya, were successfully obtained and expressed in S. lividans. S. sviceus PAD (SsPAD) could convert p-hydroxycinnamic acid (pHCA) to 4VPh more efficiently than the others both in vitro and in vivo. For 4VPh production directly from cellulose, L-tyrosine ammonia lyase derived from Rhodobacter sphaeroides and SsPAD were introduced into endoglucanase-secreting S. lividans, and the 4VPh biosynthetic pathway was constructed therein. The created transformants successfully produced 4VPh directly from cellulose. (C) 2014 Elsevier Ltd. All rights reserved.
    Lead, ELSEVIER SCI LTD, Mar. 2015, Bioresource Technology, 180, 59 - 65, English
    [Refereed]
    Scientific journal

  • Shuhei Noda, Takuya Matsumoto, Tsutomu Tanaka, Akihiko Kondo
    Background: Streptavidin is a tetrameric protein derived from Streptomyces avidinii, and has tight and specific biotin binding affinity. Applications of the streptavidin-biotin system have been widely studied. Streptavidin is generally produced using protein expression in Escherichia coli. In the present study, the secretory production of streptavidin was carried out using Streptomyces lividans as a host. Results: In this study, we used the gene encoding native full-length streptavidin, whereas the core region is generally used for streptavidin production in Escherichia coli. Tetrameric streptavidin composed of native full-length streptavidin monomers was successfully secreted in the culture supernatant of Streptomyces lividans transformants, and had specific biotin binding affinity as strong as streptavidin produced by Escherichia coli. The amount of Sav using Streptomyces lividans was about 9 times higher than using Escherichia coli. Surprisingly, streptavidin produced by Streptomyces lividans exhibited affinity to biotin after boiling, despite the fact that tetrameric streptavidin is known to lose its biotin binding ability after brief boiling. Conclusion: We successfully produced a large amount of tetrameric streptavidin as a secretory-form protein with unique thermotolerance.
    Lead, BIOMED CENTRAL LTD, Jan. 2015, Microbial Cell Factories, 14, 5, English
    [Refereed]
    Scientific journal

  • Takaya Miyazaki, Shuhei Noda, Tsutomu Tanaka, Akihiko Kondo
    Background: Protein production as secretory-form is a powerful tool in industrial enzyme production due to the simple purification procedure. Streptomyces lividans is a versatile host for secretory production of useful proteins. In order to expand the amount of secreted protein, signal peptide sequences, which encourage protein secretion from inside cell to extracellular environment, are one of the most significant factors. In this study, we focused on Streptomyces lividans as a host strain to secrete useful proteins, and screened for signal peptides from the biomass-degradation enzymes derived from Thermobifida fusca YX and S. lividans. Results: Three candidate signal peptides were isolated and evaluated for their protein secretion ability using beta-glucosidase derived from T. fusca YX, which is a non-secreted protein, as a model protein. Using S. lividans xylanase C signal peptide, the amount of produced the beta-glucosidase reached 10 times as much as that when using Streptomyces cinnamoneus phospholipase D signal peptide, which was identified as a versatile signal peptide in our previous report. In addition, the introduction of the beta-glucosidase fused to xylanase C signal peptide using two kinds of plasmid, pUC702 and pTYM18, led to further protein secretion, and the maximal level of produced the beta-glucosidase increased up to 17 times (1.1 g/l) compared to using only pUC702 carrying the beta-glucosidase fused to S. cinnamoneus phospholipase D signal peptide. Conclusion: In the present study, we focused on signal peptide sequences derived from biomass degradation enzymes, which are usually secreted into the culture supernatant, and screened for signal peptides leading to effective protein secretion. Using the signal peptides, the hyper-protein secretion system was successfully demonstrated for the cytoplasmic beta-glucosidase.
    BIOMED CENTRAL LTD, Oct. 2013, Microbial Cell Factories, 12, 88, English
    [Refereed]
    Scientific journal

  • Shuhei Noda, Yoshifumi Kawai, Takaya Miyazaki, Tsutomu Tanaka, Akihiko Kondo
    We screened for high-activity endoglucanase (EG) as a first step toward the creation of cellulose-assimilating Streptomyces lividans transformants. EGs derived from Thermobifida fusca YX, Tfu0901, and S. lividans, cellulase B (CelB), were successfully expressed. Genes encoding Tfu0901 or CelB were introduced into S. lividans using the integrative vector pTYM18 and the high-copy-number vector pUC702, and EG activity was detected in the supernatant of each transformant. To achieve coexpression of EG and transglutaminase, the transglutaminase gene was introduced into EG-secreting S. lividans using pUC702. S. lividans coexpressing EG and transglutaminase effectively assimilated phosphoric acid swollen cellulose. The yield of Streptomyces cinnamoneus transglutaminase in the culture supernatant was 7.2 mg/L, which was 18 times higher than that of the control strain. To demonstrate the versatility of our system, we also created an EG-producing S. lividans transformant capable of coexpressing endoxylanase. The EG-secreting S. lividans transformants constructed here can be used to produce other useful compounds through cellulose fermentation.
    Lead, SPRINGER, Jul. 2013, Applied Microbiology and Biotechnology, 97(13) (13), 5711 - 5720, English
    [Refereed]
    Scientific journal

  • Yoshifumi Kawai, Shuhei Noda, Chiaki Ogino, Yasunobu Takeshima, Naoko Okai, Tsutomu Tanaka, Akihiko Kondo
    Background: p-Hydroxycinnamic acid (pHCA) is an aromatic compound that serves as a starting material for the production of many commercially valuable chemicals, such as fragrances and pharmaceuticals, and is also used in the synthesis of thermostable polymers. However, chemical synthesis of pHCA is both costly and harmful to the environment. Although pHCA production using microbes has been widely studied, there remains a need for more cost-effective methods, such as the use of biomass as a carbon source. In this study, we produced pHCA using tyrosine ammonia lyase-expressing Streptomyces lividans. In order to improve pHCA productivity from cellulose, we constructed a tyrosine ammonia lyase- and endoglucanase (EG)-expressing S. lividans transformant and used it to produce pHCA from cellulose.Results: A Streptomyces lividans transformant was constructed to express tyrosine ammonia lyase derived from Rhodobacter sphaeroides (RsTAL). The transformant produced 786 or 736 mg/L of pHCA after 7 days of cultivation in medium containing 1% glucose or cellobiose as the carbon source, respectively. To enhance pHCA production from phosphoric acid swollen cellulose (PASC), we introduced the gene encoding EG into RsTAL-expressing S. lividans. After 7 days of cultivation, this transformant produced 753, 743, or 500 mg/L of pHCA from 1% glucose, cellobiose, or PASC, respectively.Conclusions: RsTAL-expressing S. lividans can produce pHCA from glucose and cellobiose. Similarly, RsTAL- and EG-expressing S. lividans can produce pHCA from glucose and cellobiose with excess EG activity remaining in the supernatant. This transformant demonstrated improved pHCA production from cellulose. Further enhancements in the cellulose degradation capability of the transformant will be necessary in order to achieve further improvements in pHCA production from cellulose. © 2013 Kawai et al. licensee BioMed Central Ltd.
    May 2013, Microbial Cell Factories, 12(1) (1), 45, English
    [Refereed]
    Scientific journal

  • Shuhei Noda, Takaya Miyazaki, Tsutomu Tanaka, Ogino Chiaki, Akihiko Kondo
    Streptomyces mobaraensis transglutaminase (MTG) is one of the most useful transglutaminases due to its rather broad substrate specificity and independence of Ca2+. To achieve efficient production of active-form MTG using Streptomyces lividans as a host, we created three vector constructs consisting of the signal peptide sequence (pld signal) derived from the phospholipase D gene of Streptomyces cinnamoneus, prepro-domain of S. cinnamoneus transglutaminase, and the sequence encoding mature MTG, and then generated three over-expressing S. lividans strains. We successfully demonstrated that S. lividans can be used as a host for the efficient production of mature, active-form MTG. © 2013 Elsevier B.V.
    Lead, May 2013, Biochemical Engineering Journal, 74, 76 - 80, English
    [Refereed]
    Scientific journal

  • Yutaro Mori, Shiori Ozasa, Momoko Kitaoka, Shuhei Noda, Tsutomu Tanaka, Hirofumi Ichinose, Noriho Kamiya
    A novel multi-cellulase conjugate assembled on a double-stranded DNA scaffold, a DNA-(endoglucanase)(n) conjugate, exhibited unique hydrolytic activity toward crystalline cellulose (Avicel) depending on the cellulase/DNA ratio on the DNA-based artificial cellulosome.
    ROYAL SOC CHEMISTRY, 2013, Chemical Communications, 49(62) (62), 6971 - 6973, English
    [Refereed]
    Scientific journal

  • Shuhei Noda, Eiichi Kitazono, Tsutomu Tanaka, Chiaki Ogino, Akihiko Kondo
    Background: Benzoic acid is one of the most useful aromatic compounds. Despite its versatility and simple structure, benzoic acid production using microbes has not been reported previously. Streptomyces are aerobic, Gram-positive, mycelia-forming soil bacteria, and are known to produce various kinds of antibiotics composed of many aromatic residues. S. maritimus possess a complex amino acid modification pathway and can serve as a new platform microbe to produce aromatic building-block compounds. In this study, we carried out benzoate fermentation using S. maritimus. In order to enhance benzoate productivity using cellulose as the carbon source, we constructed endo-glucanase secreting S. maritimus. Results: After 4 days of cultivation using glucose, cellobiose, or starch as a carbon source, the maximal level of benzoate reached 257, 337, and 460 mg/l, respectively. S. maritimus expressed beta-glucosidase and high amylase-retaining activity compared to those of S. lividans and S. coelicolor. In addition, for effective benzoate production from cellulosic materials, we constructed endo-glucanase-secreting S. maritimus. This transformant efficiently degraded the phosphoric acid swollen cellulose (PASC) and then produced 125 mg/l benzoate. Conclusions: Wild-type S. maritimus produce benzoate via a plant-like beta-oxidation pathway and can assimilate various carbon sources for benzoate production. In order to encourage cellulose degradation and improve benzoate productivity from cellulose, we constructed endo-glucanase-secreting S. maritimus. Using this transformant, we also demonstrated the direct fermentation of benzoate from cellulose. To achieve further benzoate productivity, the L-phenylalanine availability needs to be improved in future.
    Lead, BIOMED CENTRAL LTD, Apr. 2012, MICROBIAL CELL FACTORIES, 11, 49, English
    [Refereed]
    Scientific journal

  • Shuhei Noda, Takaya Miyazaki, Tsutomu Tanaka, Chiaki Ogino, Akihiko Kondo
    Transglutaminase from Streptoverticillium cinnamoneum (StvcMTG) was produced using recombinant Streptomyces lividans. When grown on glycerol and xylose as sole carbon sources, S. lividans/StvcMTG produced 360 and 530 mg of StvcMTG per liter, respectively. With starch and xylan, the strain produced 230 and 400 mg of StvcMTG per liter, respectively. Recombinant S. lividans/encP, which expresses phenylalanine ammonia lyase from Streptomyces maritimus, produced 160 mg/L of cinnamic acid from cellulose. These results show that S. lividans can assimilate various carbon sources and produce useful compounds in desirable quantities. (C) 2011 Elsevier Ltd. All rights reserved.
    Lead, ELSEVIER SCI LTD, Jan. 2012, Bioresource Technology, 104, 648 - 651, English
    [Refereed]
    Scientific journal

  • Shuhei Noda, Takaya Miyazaki, Takanori Miyoshi, Michiru Miyake, Naoko Okai, Tsutomu Tanaka, Chiaki Ogino, Akihiko Kondo
    Cinnamic acid production was demonstrated using Streptomyces as a host. A gene encoding phenylalanine ammonia lyase (PAL) from Streptomyces maritimus was introduced into Streptomyces lividans, and its expression was confirmed by Western blot analysis. After 4 days cultivation using glucose as carbon source, the maximal level of cinnamic acid reached 210 mg/L. When glycerol (30 g/L) was used as carbon source, the maximal level of produced cinnamic acid reached 450 mg/L. In addition, using raw starch, xylose or xylan as carbon source, the maximal level of cinnamic acid reached 460, 300, and 130 mg/L, respectively. We demonstrated that S. lividans has great potential to produce cinnamic acid as well as other aromatic compounds.
    Lead, SPRINGER HEIDELBERG, May 2011, Journal of Industrial Microbiology and Biotechnology, 38(5) (5), 643 - 648, English
    [Refereed]
    Scientific journal

  • Shuhei Noda, Yuko Ito, Nobuaki Shimizu, Tsutomu Tanaka, Chiaki Ogino, Akihiko Kondo
    Streptomyces lividans is known to produce large amounts of proteins in culture supernatants. In this report, to expand the secretory expression system with a strong promoter derived from phospholipase D of Streptoverticillium cinnamoneum, we expressed three kinds of proteins: transglutaminase from Sty. cinnamoneum (StvcMTG) and beta-1,4-endoglucanase and beta-glucosidase from Thermobifida fusca YX. The StvcMTG gene was introduced into S. lividans using the shuttle vector pUC702 for Escherichia coli and S. lividans, and high level secretory production of StvcMTG (230 mu g/ml in the culture supernatant) was achieved. The other prokaryotic proteins, beta-1,4-endoglucanase and beta-glucosidase, were also expressed in (His)(6)-tag fused form into culture supernatants and retained high activity. Furthermore, complete purification was achieved by conventional column or affinity column chromatography for each recombinant protein with 1 mg/ml over protein concentration. Three independent proteins were thus successfully expressed and purified, and we expect to use this system for the expression of other valuable heterologous proteins. (C) 2010 Elsevier Inc. All rights reserved.
    Lead, ACADEMIC PRESS INC ELSEVIER SCIENCE, Oct. 2010, Protein Expression and Purification, 73(2) (2), 198 - 202, English
    [Refereed]
    Scientific journal

■ MISC
  • 人工的な共培養空間デザイン
    野田修平
    Mar. 2024, 生物工学会誌 バイオミディア, 102(3) (3), 124 - 124

  • 代謝工学的アプローチによる微生物共培養の技術革新及び最新の研究動向
    野田修平
    Feb. 2024, 化学工学 トピックス, 88(2) (2), 88 - 88

  • 大腸菌ペリプラズムでのグルコース-6-リン酸の捕捉は芳香族アミノ酸合成を促進する
    藤原良介, 野田修平, 田中勉
    Nov. 2022, バイオサイエンスとインダストリー, 80(6) (6), 474 - 475

  • 糖の使い分け技術 ・ 代謝制御添加剤を駆使した 微生物発酵生産
    藤原良介, 野田修平, 田中勉
    Oct. 2022, 化学工業, 73(10) (10)

  • 糖の使い分け技術・“代謝スパイス”を駆使した微生物発酵生産
    藤原良介, 野田修平, 田中勉
    Dec. 2021, バイオインダストリー, 38(12) (12), 9 - 16

  • 物質生産とエネルギー獲得を独立させるパラレル型代謝工学技術
    藤原良介, 野田修平, 田中勉
    Jul. 2020, バイオサイエンスとインダストリー(B&I), 78(4) (4), 316 - 317

  • 微生物に糖を目的別に使い分けさせる新技術によるポリマー原料の生産性向上
    藤原良介, 田中勉, 野田修平
    May 2020, クリーンエネルギー 2, 29(5) (5), 20 - 25

  • Gut microbes become tiny industrial chemical factories
    Shuhei Noda
    2018, RIKEN research, Fall, 26 - 28

  • 大腸菌を用いたポリマー原料としてのマレイン酸生産
    野田修平, 白井智量, 近藤昭彦
    2018, バイオサイエンスとインダストリー(B&I), 76(4) (4), 294 - 295, Japanese
    Introduction other

  • 大腸菌を用いたマレイン酸合成法の開発
    野田 修平
    Dec. 2017, フジサンケイビジネスアイ, 13 - 13

■ Lectures, oral presentations, etc.
  • 代謝経路の大規模改変から発想する有用化合物生産プラットホーム
    野田 修平
    第12回日本生物工学会東日本支部コロキウム「微生物代謝工学の研究最前線」, Feb. 2024
    [Invited]

  • 有用バルクケミカル合成大腸菌プラットホーム開発における質量分析機器の活用
    野田 修平
    質量分析インフォマティクス研究会ワークショップ, Mar. 2019, Japanese, Domestic conference
    [Invited]
    Invited oral presentation

  • 芳香族化合物合成プラットホームの開発~芳香族モノマー合成に理想的な大腸菌代謝デザイン~
    野田 修平
    第70回 日本生物工学会大 シンポジウム「新時代の物質生産宿主開発の方法論:ゲノムを大規模に編集する。代謝計測から設計図を書く」, Sep. 2018, Japanese, Domestic conference
    Oral presentation

  • Metabolic design of a platform Escherichia coli strain producing various chorismate derivatives
    Shuhei Noda
    2nd Korea-Japan Smart Biodesign Workshop: Technology exchange for green biotechnology, Feb. 2017, English, International conference
    [Invited]
    Oral presentation

  • Metabolic design of a platform Escherichia coli strain producing various chorismate derivatives
    Shuhei Noda
    YABEC 2016 : 22nd Symposium of Young Asian Biological Engineers' Community, Oct. 2016, English, International conference
    [Invited]
    Oral presentation

  • Metabolic design of a platform Escherichia coli strain producing various chorismate derivatives
    Shuhei Noda
    The 6th iBioK Asian Workshop, Dec. 2015, English, International conference
    [Invited]
    Oral presentation

■ Affiliated Academic Society
  • 日本生物物理学会

  • Japanese Society of Enzyme Engineering

  • The Society for Biotechnology, Japan

  • THE SOCIETY OF CHEMICAL ENGINEERS, JAPAN

■ Research Themes
  • 剛直成分含有ポリマーの完全バイオ循環空間デザイン
    国立研究開発法人科学技術振興機構, 戦略的創造研究推進事業(さきがけ)「持続可能な材料設計に向けた確実な結合とやさしい分解」領域, Oct. 2022 - Mar. 2026, Principal investigator

  • 炭素をつなぐ:SAMT自在制御基盤の確立
    野田 修平
    日本学術振興会, 科学研究費助成事業, 学術変革領域研究(A), 神戸大学, Apr. 2023 - Mar. 2025, Principal investigator

  • 代謝ブラックボックスの可視化から紐解く遺伝子導入パターン最適化手法の確立
    野田 修平
    日本学術振興会, 基盤研究(B), Apr. 2022 - Mar. 2025, Principal investigator

  • 革新的CO2利用に向けたC1完全バイオ循環空間デザイン
    野田 修平
    一般財団法人 カーボンリサイクルファンド, 2022年度 CRF研究助成活動(一般公募枠), Aug. 2022 - Jul. 2024, Principal investigator

  • 新奇酵素の合理的デザインによる芳香族化合物合成プラットホームの拡張
    野田 修平
    日本学術振興会, 若手研究, Apr. 2019 - Mar. 2023, Principal investigator
    Competitive research funding

  • 【未来社会】 細胞表層工学と代謝工学を用いたPEP蓄積シャーシ株の創製
    田中 勉
    国立研究開発法人科学技術振興機構, 未来社会創造事業(探索加速型), 2017 - Mar. 2022
    Competitive research funding

  • ピルビン酸バイパス/リサイクル技術を拡張した芳香族化合物合成プラットホームの開発
    野田 修平
    日本学術振興会, 若手研究(B), Apr. 2017 - Mar. 2019, Principal investigator
    Competitive research funding

  • Non-Conventional酵母によるテーラーメイド芳香族化合物合成法の開発
    野田 修平
    日本学術振興会, 研究活動スタート支援, Aug. 2013 - Mar. 2015, Principal investigator
    Competitive research funding

  • 放射菌の抗生物質生産における素反応を応用した芳香族化合物生産経路の合理的構築
    野田 修平
    日本学術振興会, 科学研究費助成事業, 特別研究員奨励費, 神戸大学, 2012 - 2013
    近年、化石資源の枯渇・地球温暖化等の環境問題が顕在化している。温室効果ガスの削減、持続可能な社会形成のため、石油依存社会から、エネルギーや化成品を再生可能なバイオマス資源に依存したバイオリファイナリー社会への変革が求められている。特に、芳香族系の化成品原料生産は、その生合成経路が複雑であること、また酵母や大腸菌等の微生物にとって毒性を示すため、バイオプロセスに置き換えるのが困難であり、石油資源からの生産に完全に依存している。本研究では、既存化成品原料生産のケミカルプロセスからバイオプロセスへの変換を目指した。本研究においては、放線菌Atreptomyces属に注目し、バイオマス資源からの芳香族化合物生産、バイオマス資源からの高効率な物質生産のための基盤の開発を行った。 放線菌Streptomyces maritimusの2次代謝経路の一部を利用することにより、微生物を用いて初めて安息香酸の生産に成功した。3%デンプンから最大で460mg/Lの安息香酸生産に成功した。また、セルロースからの安息香酸生産を目指し、木質系バイオマス糖化酵素の一種であるエンドグルカナーゼ導入株を創製した。創製した株を用い、1%セルロースから最大で120mg/Lの安息香酸生産に成功した。本研究における報告は、微生物発酵によるバイオマス資源からの芳香族化合物生産に関する初めての報告であり、その収率もグルコースを用いた他の微生物による他の芳香族化合物生産における報告に匹敵するものである。しかしながら、セルロースからの安息香酸収率は、同仕込み量のグルコースの場合と比較して不十分であった。そこでバイオマス糖化効率を高めるためにバイオマス糖化酵素生産量の増強を検討し、バイオマス糖化酵素分泌生産量を10倍に向上させることに成功した。 以上より、セルロース資化性安息香酸生産菌とバイオマス糖化酵素大量生産技術を組み合わせることにより、セルロースから効率的に芳香族化合物を生産可能な技術の確立が期待される。

■ Industrial Property Rights
  • グルコース6リン酸を捕捉する物質を用いた芳香族化合物の製造方法
    田中勉, 野田修平, 藤原良介
    特願2019-123262, 01 Jul. 2019, 国立大学法人神戸大学・特定国立研究開発法人理化学研究所, 特開2021-7388
    Patent right

  • 糖代謝経路が改変された微生物
    田中勉, 野田修平, 藤原良介
    特願2019-089294, 13 May 2019, 国立大学法人神戸大学・特定国立研究開発法人理化学研究所, 特開2020-184993
    Patent right

  • Method for producing aromatic compound and derivative thereof
    Shuhei Noda, Tomokazu Shirai
    PCT/JP2016/074649, 24 Aug. 2016, 02 Mar. 2017
    Patent right

  • サリチル酸の製造方法
    白井 智量, 野田 修平
    特願2014-222462, 31 Oct. 2014, 国立研究開発法人理化学研究所, 特開2016-086688, 23 May 2016
    Patent right

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