SEARCH

Search Details

HIDESE Ryota
Graduate School of Science, Technology and Innovation / Department of Science, Technology and Innovation
Professor

Researcher basic information

■ Research news
  • 10 Mar. 2020, Successful method yielding high rate of D-lactate using cyanobacteria could revolutionize bioplastic production
    Link to Kobe Univ. HP
■ Research Areas
  • Life sciences / Molecular biology
  • Life sciences / Applied microbiology

Research activity information

■ Award
  • 2019 日本生物工学会, 生物工学論文賞, Leucine responsive regulatory protein is involved in methionine metabolism and polyamine homeostasis in acetic acid bacterium Komagataeibacter europaeus
    Yuri Ishii, Naoki Akasaka, Hisao Sakoda, Ryota Hidese, Shinsuke Fujiwara

  • 2018 日本生物工学会, 2018年度 第26回 生物工学論文賞
    秀瀨 涼太

  • 2018 長瀬科学技術振興財団, 平成30年度 長瀬研究振興賞
    秀瀨 涼太

  • 2018 極限環境生物学会, 研究奨励賞
    秀瀨 涼太

■ Paper
  • Ryota Hidese, Kanae Sakai, Musashi Takenaka, Keiji Fushimi, Hisashi Kudo, Kenya Tanaka, Ryo Nasuno, Christopher J. Vavricka, Akihiko Kondo, Tomohisa Hasunuma
    Jun. 2025, ACS Catalysis, 15, 11931 - 11943
    [Refereed]

  • Keiji Fushimi, Yusuke Nakai, Akiko Nishi, Ryo Suzuki, Masahiro Ikegami, Risa Nimura, Taichi Tomono, Ryota Hidese, Hisashi Yasueda, Yusuke Tagawa, Tomohisa Hasunuma
    In this study, we developed the autonomous lab (ANL), which is a system based on robotics and artificial intelligence (AI) to conduct biotechnology experiments and formulate scientific hypotheses. This system was designed with modular devices and Bayesian optimization algorithms, allowing it to effectively run a closed loop from culturing to preprocessing, measurement, analysis, and hypothesis formulation. As a case study, we used the ANL to optimize medium conditions for a recombinant Escherichia coli strain, which overproduces glutamic acid. The results demonstrated that our autonomous system successfully replicated the experimental techniques, such as sample preparation and data measurement, and improved both the cell growth rate and the maximum cell growth. The ANL offers a versatile and scalable solution for various applications in the field of bioproduction, with the potential to improve efficiency and reliability of experimental processes in the future.
    Feb. 2025, Scientific reports, 15(1) (1), 6648 - 6648, English, International magazine
    Scientific journal
    Link to Kobe Univ. Repository (Kernel)

  • Kosuke Inabe, Ryota Hidese, Yuichi Kato, Mami Matsuda, Takanobu Yoshida, Keiji Matsumoto, Akihiko Kondo, Shunsuke Sato, Tomohisa Hasunuma
    Polyhydroxyalkanoate (PHA) is an attractive bio-degradable plastic alternative to petrochemical plastics. Photosynthetic cyanobacteria accumulate biomass by fixing atmospheric CO2, making them promising hosts for sustainable PHA production. Conventional PHA production in cyanobacteria requires prolonged cultivation under nutrient limitation to accumulate cellular PHA. In this study, we developed a system for growth-coupled production of the PHA poly-hydroxybutyrate (PHB), using the marine cyanobacterium Synechococcus sp. PCC 7002. A recombinant strain termed KB1 expressing a set of heterologous PHB biosynthesis genes (phaA/phaB from Cupriavidus necator H16 and phaE/phaC from Synechocystis sp. PCC 6803) accumulated substantial PHB during growth (11.4% of dry cell weight). To improve PHB accumulation, we introduced the Pseudomonas aeruginosa phosphoketolase gene (pk) into strain KB1, rewiring intermediates of the Calvin-Benson-Bassham (CBB) cycle (xyluose-5-phosphate, sedoheptulose 7-phosphate, and fructose-6-phosphate) to acetyl-CoA. The pk-expressing strain, KB15, accumulated 2.1-fold enhanced levels of PHB (23.8% of dried cell weight), relative to the parent strain, KB1. The highest PHB titer of KB15 strain supplemented with acetate was about 1.1 g L-1 and the yield was further enhanced by 2.6-fold following growth at 38 °C (0.21 g L-1 d-1), relative to growth at 30 °C. Metabolome analysis revealed that pool sizes of CBB intermediates decreased, while levels of acetyl-CoA increased in strain KB15 compared with strain KB1, and this increase was further enhanced following growth at 38 °C. Our data demonstrate that acetyl-phosphate generated by Pk was converted into acetyl-CoA via acetate by hitherto unidentified enzymes. In conclusion, expression of heterologous PHB biosynthesis genes enabled growth-coupled PHB production in strain PCC 7002, which was increased through acetyl-CoA supplementation by bypassing acetyl-phosphate and elevating culture temperature.
    Jan. 2025, Metabolic engineering, 88, 228 - 239, English, International magazine
    Scientific journal
    Link to Kobe Univ. Repository (Kernel)

  • Ayaka Tsuji, Kosuke Inabe, Ryota Hidese, Yuichi Kato, Lucília Domingues, Akihiko Kondo, Tomohisa Hasunuma
    Marine cyanobacteria such as Picosynechococcus sp. (formerly called Synechococcus sp.) PCC 7002 are promising chassis for photosynthetic production of commodity chemicals with low environmental burdens. Genetic engineering of cyanobacteria conventionally employs antibiotic resistance markers. However, limited availability of antibiotic-resistant markers is a problem for highly multigenic strain engineering. Although several markerless genetic manipulation methods have been developed for PCC 7002, they often lack versatility due to the requirement of gene disruption in the host strain. To achieve markerless transformation in Synechococcus sp. with no requirements for the host strain, this study developed a method in which temporarily introduces a mutated phenylalanyl-tRNA synthetase gene (pheS) into the genome for counter selection. Amino acid substitutions in the PheS that cause high susceptibility of PCC 7002 to the phenylalanine analog p-chlorophenylalanine were examined, and the combination of T261A and A303G was determined as the most suitable mutation. The mutated PheS-based selection was utilized for the markerless knockout of the nblA gene in PCC 7002. In addition, the genetic construct containing the lldD and lldP genes from Escherichia coli was introduced into the ldhA gene site using the counter selection strategy, resulting in a markerless recombinant strain. The repeatability of this method was demonstrated by the double markerless knockin recombinant strain, suggesting it will be a powerful tool for multigenic strain engineering of cyanobacteria.
    Oct. 2024, Microbial cell factories, 23(1) (1), 268 - 268, English, International magazine
    Scientific journal
    Link to Kobe Univ. Repository (Kernel)

  • Ryota Hidese, Takayuki Ohira, Satsuki Sakakibara, Tsutomu Suzuki, Naoki Shigi, Shinsuke Fujiwara
    Ubiquitin-like proteins (Ubls) in eukaryotes and bacteria mediate sulfur transfer for the biosynthesis of sulfur-containing biomolecules and form conjugates with specific protein targets to regulate their functions. Here, we investigated the functions and physiological importance of Ubls in a hyperthermophilic archaeon by constructing a series of deletion mutants. We found that the Ubls (TK1065, TK1093, and TK2118) in Thermococcus kodakarensis are conjugated to their specific target proteins, and all three are involved in varying degrees in the biosynthesis of sulfur-containing biomolecules such as tungsten cofactor (Wco) and tRNA thiouridines. TK2118 (named UblB) is involved in the biosynthesis of Wco in a glyceraldehyde 3-phosphate:ferredoxin oxidoreductase, which is required for glycolytic growth, whereas TK1093 (named UblA) plays a key role in the efficient thiolation of tRNAs, which contributes to cellular thermotolerance. Intriguingly, in the presence of elemental sulfur (S0) in the culture medium, defective synthesis of these sulfur-containing molecules in Ubl mutants was restored, indicating that T. kodakarensis can use S0 as an alternative sulfur source without Ubls. Our analysis indicates that the Ubl-mediated sulfur-transfer system in T. kodakarensis is important for efficient sulfur assimilation, especially under low S0 conditions, which may allow this organism to survive in a low sulfur environment.IMPORTANCESulfur is a crucial element in living organisms, occurring in various sulfur-containing biomolecules including iron-sulfur clusters, vitamins, and RNA thionucleosides, as well as the amino acids cysteine and methionine. In archaea, the biosynthesis routes and sulfur donors of sulfur-containing biomolecules are largely unknown. Here, we explored the functions of Ubls in the deep-blanched hyperthermophilic archaeon, Thermococcus kodakarensis. We demonstrated functional redundancy of these proteins in the biosynthesis of tungsten cofactor and tRNA thiouridines and the significance of these sulfur-carrier functions, especially in low sulfur environments. We propose that acquisition of a Ubl sulfur-transfer system, in addition to an ancient inorganic sulfur assimilation pathway, enabled the primordial archaeon to advance into lower-sulfur environments and expand their habitable zone.
    Aug. 2024, mBio, 15(8) (8), e0053424, English, International magazine
    Scientific journal
    Link to Kobe Univ. Repository (Kernel)

  • Hiroki Mori, Misato Matsui, Takahiro Bamba, Yoshimi Hori, Sayaka Kitamura, Yoshihiro Toya, Ryota Hidese, Hisashi Yasueda, Tomohisa Hasunuma, Hiroshi Shimizu, Naoaki Taoka, Shingo Kobayashi
    Elsevier BV, Jul. 2024, Metabolic Engineering, 84, 180 - 190
    Scientific journal

  • Yuichi Kato, Ryota Hidese, Mami Matsuda, Ryudo Ohbayashi, Hiroki Ashida, Akihiko Kondo, Tomohisa Hasunuma
    Glycogen serves as a metabolic sink in cyanobacteria. Glycogen deficiency causes the extracellular release of distinctive metabolites such as pyruvate and 2-oxoglutarate upon nitrogen depletion; however, the mechanism has not been fully elucidated. This study aimed to elucidate the mechanism of carbon partitioning in glycogen-deficient cyanobacteria. Extracellular and intracellular metabolites in a glycogen-deficient ΔglgC mutant of Synechococcus elongatus PCC 7942 were comprehensively analyzed. In the presence of a nitrogen source, the ΔglgC mutant released extracellular glutamate rather than pyruvate and 2-oxoglutarate, whereas its intracellular glutamate level was lower than that in the wild-type strain. The de novo synthesis of glutamate increased in the ΔglgC mutant, suggesting that glycogen deficiency enhanced carbon partitioning into glutamate and extracellular excretion through an unidentified transport system. This study proposes a model in which glutamate serves as the prime extracellular metabolic sink alternative to glycogen when nitrogen is available.
    Feb. 2024, Communications biology, 7(1) (1), 233 - 233, English, International magazine
    Scientific journal
    Link to Kobe Univ. Repository (Kernel)

  • Ryota Hidese, Ryudo Ohbayashi, Yuichi Kato, Mami Matsuda, Kan Tanaka, Sousuke Imamura, Hiroki Ashida, Akihiko Kondo, Tomohisa Hasunuma
    Abstract The cyanobacterium Synechococcus elongatus PCC 7942 accumulates alarmone guanosine tetraphosphate (ppGpp) under stress conditions, such as darkness. A previous study observed that artificial ppGpp accumulation under photosynthetic conditions led to the downregulation of genes involved in the nitrogen assimilation system, which is activated by the global nitrogen regulator NtcA, suggesting that ppGpp regulates NtcA activity. However, the details of this mechanism have not been elucidated. Here, we investigate the metabolic responses associated with ppGpp accumulation by heterologous expression of the ppGpp synthetase RelQ. The pool size of 2-oxoglutarate (2-OG), which activates NtcA, is significantly decreased upon ppGpp accumulation. De novo 13C-labeled CO2 assimilation into the Calvin-Benson-Bassham cycle and glycolytic intermediates continues irrespective of ppGpp accumulation, whereas the labeling of 2-OG is significantly decreased under ppGpp accumulation. The low 2-OG levels in the RelQ overexpression cells could be because of the inhibition of metabolic enzymes, including aconitase, which are responsible for 2-OG biosynthesis. We propose a metabolic rearrangement by ppGpp accumulation, which negatively regulates 2-OG levels to maintain carbon and nitrogen balance.
    Springer Science and Business Media LLC, Dec. 2023, Communications Biology, 6(1) (1)
    Scientific journal
    Link to Kobe Univ. Repository (Kernel)

  • Ryota Hidese, Mami Matsuda, Mamiko Kajikawa, Takashi Osanai, Akihiko Kondo, Tomohisa Hasunuma
    The four-carbon (C4) dicarboxylic acids, fumarate, malate, and succinate, are the most valuable targets that must be exploited for CO2-based chemical production in the move to a sustainable low-carbon future. Cyanobacteria excrete high amounts of C4 dicarboxylic acids through glycogen fermentation in a dark anoxic environment. The enhancement of metabolic flux in the reductive TCA branch in the Cyanobacterium Synechocystis sp. PCC6803 is a key issue in the C4 dicarboxylic acid production. To improve metabolic flux through the anaplerotic pathway, we have created the recombinant strain PCCK, which expresses foreign ATP-forming phosphoenolpyruvate carboxykinase (PEPck) concurrent with intrinsic phosphoenolpyruvate carboxylase (Ppc) overexpression. Expression of PEPck concurrent with Ppc led to an increase in C4 dicarboxylic acids by autofermentation. Metabolome analysis revealed that PEPck contributed to an increase in carbon flux from hexose and pentose phosphates into the TCA reductive branch. To enhance the metabolic flux in the reductive TCA branch, we examined the effect of corn-steep liquor (CSL) as a nutritional supplement on C4 dicarboxylic acid production. Surprisingly, the addition of sterilized CSL enhanced the malate production in the PCCK strain. Thereafter, the malate and fumarate excreted by the PCCK strain are converted into succinate by the CSL-settling microorganisms. Finally, high-density cultivation of cells lacking the acetate kinase gene showed the highest production of malate and fumarate (3.2 and 2.4 g/L with sterilized CSL) and succinate (5.7 g/L with non-sterile CSL) after 72 h cultivation. The present microbial community engineering is useful for succinate production by one-pot fermentation under dark anoxic conditions.
    American Chemical Society (ACS), Nov. 2022, ACS synthetic biology, 11(12) (12), 4054 - 4064, English, International magazine
    [Refereed]
    Scientific journal
    Link to Kobe Univ. Repository (Kernel)

  • Tomoki Oyama, Yuichi Kato, Ryota Hidese, Mami Matsuda, Minenosuke Matsutani, Satoru Watanabe, Akihiko Kondo, Tomohisa Hasunuma
    Abstract Background Microalgal lipid production has attracted global attention in next-generation biofuel research. Nitrogen starvation, which drastically suppresses cell growth, is a common and strong trigger for lipid accumulation in microalgae. We previously developed a mutant Chlamydomonas sp. KAC1801, which can accumulate lipids irrespective of the presence or absence of nitrates. This study aimed to develop a feasible strategy for stable and continuous lipid production through semi-continuous culture of KAC1801. Results KAC1801 continuously accumulated > 20% lipid throughout the subculture (five generations) when inoculated with a dry cell weight of 0.8–0.9 g L−1 and cultured in a medium containing 18.7 mM nitrate, whereas the parent strain KOR1 accumulated only 9% lipid. Under these conditions, KAC1801 continuously produced biomass and consumed nitrates. Lipid productivity of 116.9 mg L−1 day−1 was achieved by semi-continuous cultivation of KAC1801, which was 2.3-fold higher than that of KOR1 (50.5 mg L−1 day−1). Metabolome and transcriptome analyses revealed a depression in photosynthesis and activation of nitrogen assimilation in KAC1801, which are the typical phenotypes of microalgae under nitrogen starvation. Conclusions By optimizing nitrate supply and cell density, a one-step cultivation system for Chlamydomonas sp. KAC1801 under nitrate-replete conditions was successfully developed. KAC1801 achieved a lipid productivity comparable to previously reported levels under nitrogen-limiting conditions. In the culture system of this study, metabolome and transcriptome analyses revealed a nitrogen starvation-like response in KAC1801.
    Springer Science and Business Media LLC, Sep. 2022, Biotechnology for Biofuels and Bioproducts, 15(1) (1), English
    [Refereed]
    Scientific journal
    Link to Kobe Univ. Repository (Kernel)

  • Wakao Fukuda, Mamoru Osaki, Yusuke Yasuda, Ryota Hidese, Tsunehiko Higuchi, Naoki Umezawa, Shinsuke Fujiwara, Eiichi Mizohata
    May 2022, Catalysts, 12(5) (5), 567, English
    [Refereed]
    Scientific journal

  • Yuichi Kato, Kosuke Inabe, Ryota Hidese, Akihiko Kondo, Tomohisa Hasunuma
    Elsevier BV, Jan. 2022, Bioresource Technology, 344, 126196 - 126196, English
    Scientific journal
    Link to Kobe Univ. Repository (Kernel)

  • Kosuke Inabe, Ayaka Miichi, Mami Matsuda, Takanobu Yoshida, Yuichi Kato, Ryota Hidese, Akihiko Kondo, Tomohisa Hasunuma
    Nitrogen is essential for the biosynthesis of various molecules in cells, such as amino acids and nucleotides, as well as several types of lipids and sugars. Cyanobacteria can assimilate several forms of nitrogen, including nitrate, ammonium, and urea, and the physiological and genetic responses to these nitrogen sources have been studied previously. However, the metabolic changes in cyanobacteria caused by different nitrogen sources have not yet been characterized. This study aimed to elucidate the influence of nitrate and ammonium on the metabolic profiles of the cyanobacterium Synechocystis sp. strain PCC 6803. When supplemented with NaNO3 or NH4Cl as the nitrogen source, Synechocystis sp. PCC 6803 grew faster in NH4Cl medium than in NaNO3 medium. Metabolome analysis indicated that some metabolites in the CBB cycle, glycolysis, and TCA cycle, and amino acids were more abundant when grown in NH4Cl medium than NaNO3 medium. 15N turnover rate analysis revealed that the nitrogen assimilation rate in NH4Cl medium was higher than in NaNO3 medium. These results indicate that the mechanism of nitrogen assimilation in the GS-GOGAT cycle differs between NaNO3 and NH4Cl. We conclude that the amounts and biosynthetic rate of cyanobacterial metabolites varies depending on the type of nitrogen.
    MDPI AG, Dec. 2021, Metabolites, 11(12) (12), 867 - 867
    Scientific journal
    Link to Kobe Univ. Repository (Kernel)

  • Yuichi Kato, Tomoki Oyama, Kentaro Inokuma, Christopher J. Vavricka, Mami Matsuda, Ryota Hidese, Katsuya Satoh, Yutaka Oono, Jo-Shu Chang, Tomohisa Hasunuma, Akihiko Kondo
    AbstractLight/dark cycling is an inherent condition of outdoor microalgae cultivation, but is often unfavorable for lipid accumulation. This study aims to identify promising targets for metabolic engineering of improved lipid accumulation under outdoor conditions. Consequently, the lipid-rich mutant Chlamydomonas sp. KOR1 was developed through light/dark-conditioned screening. During dark periods with depressed CO2 fixation, KOR1 shows rapid carbohydrate degradation together with increased lipid and carotenoid contents. KOR1 was subsequently characterized with extensive mutation of the ISA1 gene encoding a starch debranching enzyme (DBE). Dynamic time-course profiling and metabolomics reveal dramatic changes in KOR1 metabolism throughout light/dark cycles. During light periods, increased flux from CO2 through glycolytic intermediates is directly observed to accompany enhanced formation of small starch-like particles, which are then efficiently repartitioned in the next dark cycle. This study demonstrates that disruption of DBE can improve biofuel production under light/dark conditions, through accelerated carbohydrate repartitioning into lipid and carotenoid.
    Springer Science and Business Media LLC, Dec. 2021, Communications Biology, 4(1) (1)
    Scientific journal
    Link to Kobe Univ. Repository (Kernel)

  • Ryota Hidese, Mami Matsuda, Takashi Osanai, Tomohisa Hasunuma, Akihiko Kondo
    d-Lactate is one of the most valuable compounds for manufacturing biobased polymers. Here, we have investigated the significance of endogenous malate dehydrogenase (decarboxylating) (malic enzyme, ME), which catalyzes the oxidative decarboxylation of malate to pyruvate, in d-lactate biosynthesis in the cyanobacterium Synechocystis sp. PCC6803. d-Lactate levels were increased by 2-fold in ME-overexpressing strains, while levels in ME-deficient strains were almost equivalent to those in the host strain. Dynamic metabolomics revealed that overexpression of ME led to increased turnover rates in malate and pyruvate metabolism; in contrast, deletion of ME resulted in increased pool sizes of glycolytic intermediates, probably due to sequential feedback inhibition, initially triggered by malate accumulation. Finally, both the loss of the acetate kinase gene and overexpression of endogenous d-lactate dehydrogenase, concurrent with ME overexpression, resulted in the highest production of d-lactate (26.6 g/L) with an initial cell concentration of 75 g-DCW/L after 72 h fermentation.
    Feb. 2020, ACS synthetic biology, 9(2) (2), 260 - 268, English, International magazine
    [Refereed]
    Link to Kobe Univ. Repository (Kernel)

  • Wakao Fukuda, Yuka Yamori, Masafumi Hamakawa, Mamoru Osaki, Moeko Fukuda, Ryota Hidese, Yu Kanesaki, Akiko Okamoto-Kainuma, Satoru Kato, Shinsuke Fujiwara
    Branched-chain polyamine (BCPA) synthase (BpsA), encoded by the bpsA gene, is responsible for the biosynthesis of BCPA in the hyperthermophilic archaeon Thermococcus kodakarensis, which produces N4-bis(aminopropyl)spermidine and spermidine. Here, next-generation DNA sequencing and liquid chromatography-mass spectrometry (LC-MS) were used to perform transcriptomic and proteomic analyses of a T. kodakarensis strain (DBP1) lacking bpsA. Subsequently, the contributions of BCPA to gene transcription (or transcript stabilization) and translation (or protein stabilization) were analyzed. Compared with those in the wild-type strain (KU216) cultivated at 90 °C, the transcript levels of 424 and 21 genes were up- and downregulated in the DBP1 strain, respectively. The expression levels of 12 frequently-used tRNAs were lower in DBP1 cells than KU216 cells, suggesting that BCPA affects translation efficiency in T. kodakarensis. LC-MS analyses of cells grown at 90 °C detected 50 proteins in KU216 cells only, 109 proteins in DBP1 cells only, and 499 proteins in both strains. Notably, the transcript levels of some genes did not correlate with those of the proteins. RNA-seq and RT-qPCR analyses of ten proteins that were detected in KU216 cells only, including three flagellin-related proteins (FlaB2-4) and cytosolic NiFe-hydrogenase subunit alpha (HyhL), revealed that the corresponding transcripts were expressed at higher levels in DBP1 cells than KU216 cells. Electron microscopy analyses showed that flagella formation was disrupted in DBP1 cells at 90 °C, and western blotting confirmed that HyhL expression was eliminated in the DBP1 strain. These results suggest that BCPA plays a regulatory role in gene expression in T. kodakarensis.
    Springer Science and Business Media LLC, Feb. 2020, Amino acids, 52(2) (2), 287 - 299, English, International magazine
    [Refereed]
    Scientific journal

  • Ryota Hidese, Masataka Toyoda, Ken-ichi Yoshino, Wakao Fukuda, Gita Adhirani Wihardja, Seigo Kimura, Junso Fujita, Masaru Niitsu, Tairo Oshima, Tadayuki Imanaka, Eiichi Mizohata, Shinsuke Fujiwara
    Branched-chain polyamine synthase (BpsA) catalyzes sequential aminopropyl transfer from the donor, decarboxylated S-adenosylmethionine (dcSAM), to the acceptor, linear-chain polyamine, resulting in the production of a quaternary-branched polyamine via tertiary branched polyamine intermediates. Here, we analyzed the catalytic properties and X-ray crystal structure of Tth-BpsA from Thermus thermophilus and compared them with those of Tk-BpsA from Thermococcus kodakarensis, which revealed differences in acceptor substrate specificity and C-terminal structure between these two enzymes. To investigate the role of the C-terminal flexible region in acceptor recognition, a region (QDEEATTY) in Tth-BpsA was replaced with that in Tk-BpsA (YDDEESSTT) to create chimeric Tth-BpsA C9, which showed a severe reduction in catalytic efficiency toward N4 -aminopropylnorspermidine, but not toward N4 -aminopropylspermidine, mimicking Tk-BpsA substrate specificity. Tth-BpsA C9 Tyr346 and Thr354 contributed to discrimination between tertiary branched-chain polyamine substrates, suggesting that the C-terminal region of BpsA recognizes acceptor substrates. Liquid chromatography-tandem mass spectrometry analysis on a Tk-BpsA reaction mixture with dcSAM revealed two aminopropyl groups bound to two of five aspartate/glutamate residues (Glu339 , Asp342 , Asp343 , Glu344 , and Glu345 ) in the C-terminal flexible region. Mutating each of these five amino acid residues to asparagine/glutamine resulted in a slight decrease in activity. The quadruple mutant D342N/D343N/E344Q/E345Q exhibited a severe reduction in catalytic efficiency, suggesting that these aspartate/glutamate residues function to receive aminopropyl chains. In addition, the X-ray crystal structure of the Tk-BpsA ternary complex bound to N4 -bis(aminopropyl)spermidine revealed that Asp126 and Glu259 interacted with the aminopropyl moiety in N4 -aminopropylspermidine.
    Oct. 2019, The FEBS Journal, 286(19) (19), 3926 - 3940, English, International magazine
    [Refereed]
    Scientific journal

  • Branched-chain polyamine stabilizes RNA polymerase at elevated temperatures in hyperthermophiles
    YAMORI Yuka, HAMAKAWA Masafumi, HIDESE Ryota, FUKUDA Moeko, ATOMI Haruyuki, FUKUDA Wakao, FUJIWARA Shinsuke
    May 2019, Amino Acids, 1 - 11, English
    [Refereed]
    Scientific journal

  • SAKIHAMA Yuri, HIDESE Ryota, HASUNUMA Tomohisa, KONDO Akihiko
    Yeasts are extremely useful, not only for fermentation but also for a wide spectrum of fuel and chemical productions. We analyzed the overall metabolic turnover and transcript dynamics in glycolysis and the TCA cycle, revealing the difference in adaptive pyruvate metabolic response between a Crabtree-negative species, Kluyveromyces marxianus, and a Crabtree-positive species, Saccharomyces cerevisiae, during aerobic growth. Pyruvate metabolism was inclined toward ethanol production under aerobic conditions in S. cerevisiae, while increased transcript abundances of the genes involved in ethanol metabolism and those encoding pyruvate dehydrogenase were seen in K. marxianus, indicating the augmentation of acetyl-CoA synthesis. Furthermore, different metabolic turnover in the TCA cycle was observed in the two species: malate and fumarate production in S. cerevisiae was higher than in K. marxianus, irrespective of aeration; however, fluxes of both the reductive and oxidative TCA cycles were enhanced in K. marxianus by aeration, implying both the cycles contribute to efficient electron flux without producing ethanol. Additionally, decreased hexokinase activity under aerobic conditions is expected to be important for maintenance of suitable carbon flux. These findings demonstrate differences in the key metabolic trait of yeasts employing respiration or fermentation, and provide important insight into the metabolic engineering of yeasts.
    Mar. 2019, Scientific Reports, 9(1) (1), 5319 - 5319, English, International magazine
    [Refereed]
    Scientific journal
    Link to Kobe Univ. Repository (Kernel)

  • Hiroyuki Okano, Misato Baba, Ryota Hidese, Kei Iida, Tongyang Li, Kenji Kojima, Teisuke Takita, Itaru Yanagihara, Shinsuke Fujiwara, Kiyoshi Yasukawa
    We evaluated fidelity of various reverse transcriptases (RTs) by a novel method with modified next-generation sequencing (NGS). In the optimized condition, one NGS run could handle cDNA products from multiple cDNA synthesis reactions performed at different conditions. This was achieved using a primer containing not only the tag of 14 randomized bases to label each cDNA molecule but also a tag of five bases to label each reaction condition. With this method, we quantitated the error rates of 44 cDNA synthesis reactions by retroviral RTs or genetically engineered DNA polymerases with RT activity under different conditions. The results indicated that high concentrations of MgCl2, Mn(OCOCH3)2, and dNTP decrease the fidelity and that these effects are more pronounced in reactions using RT from human immunodeficiency virus type 1. This is the first report about a precise fidelity monitoring of various RTs by a direct sequence determination.
    Aug. 2018, Enzyme and microbial technology, 115, 81 - 85, English, International magazine
    [Refereed]
    Scientific journal

  • Agmatine Production by Aspergillus oryzae Is Elevated by Low pH during Solid-State Cultivation
    AKASAKA Naoki, KATO Saori, KATO Saya, HIDESE Ryota, WAGU Yutaka, SAKODA Hisao, FUJIWARA Shinsuke
    Jul. 2018, Applied and Environmental Microbiology, 17(84) (84), 15, English
    [Refereed]
    Scientific journal

  • Hiroyuki Okano, Misato Baba, Katsuhiro Kawato, Ryota Hidese, Itaru Yanagihara, Kenji Kojima, Teisuke Takita, Shinsuke Fujiwara, Kiyoshi Yasukawa
    One-step RT-PCR has not been widely used even though some thermostable DNA polymerases with reverse transcriptase (RT) activity were developed from bacterial and archaeal polymerases, which is owing to low cDNA synthesis activity from RNA. In the present study, we developed highly-sensitive one-step RT-PCR using the single variant of family A DNA polymerase with RT activity, K4polL329A (L329A), from the hyperthermophilic bacterium Thermotoga petrophila K4 or the 16-tuple variant of family B DNA polymerase with RT activity, RTX, from the hyperthermophilic archaeon Thermococcus kodakarensis. Optimization of reaction condition revealed that the activities for cDNA synthesis and PCR of K4polL329A and RTX were highly affected by the concentrations of MgCl2 and Mn(OCOCH3)2 as well as those of K4polL329A or RTX. Under the optimized condition, 300 copies/μl of target RNA in 10 μl reaction volumes were successfully detected by the one-step RT-PCR with K4polL329A or RTX, which was almost equally sensitive enough compared with the current RT-PCR condition using retroviral RT and thermostable DNA polymerase. Considering that K4polL329A and RTX are stable even at 90-100°C, our results suggest that the one-step RT-PCR with K4polL329A or RTX is more advantageous than the current one.
    Mar. 2018, Journal of bioscience and bioengineering, 125(3) (3), 275 - 281, English, Domestic magazine
    [Refereed]
    Scientific journal

  • Thermostable DNA helicase improves the sensitivity of digital PCR
    HIDESE Ryota, KAWATO Katsuhiro, NAKURA Yukiko, FUJIWARA Ayako, YASUKAWA Kiyoshi, YANAGIHARA Itaru, FUJIWARA Shinsuke
    Jan. 2018, Biochemical and Biophysical Research Communications, 495(3) (3), 2189 - 2194, English
    [Refereed]
    Scientific journal

  • Yuri Ishii, Naoki Akasaka, Hisao Sakoda, Ryota Hidese, Shinsuke Fujiwara
    Elsevier B.V., Jan. 2018, Journal of Bioscience and Bioengineering, 125(1) (1), 67 - 75, English
    [Refereed]
    Scientific journal

  • Ryota Hidese, Ka Man Tse, Seigo Kimura, Eiichi Mizohata, Junso Fujita, Yuhei Horai, Naoki Umezawa, Tsunehiko Higuchi, Masaru Niitsu, Tairo Oshima, Tadayuki Imanaka, Tsuyoshi Inoue, Shinsuke Fujiwara
    Nov. 2017, FEBS JOURNAL, 284(21) (21), 3684 - 3701, English
    [Refereed]
    Scientific journal

  • Kiyoshi Yasukawa, Kei Iida, Hiroyuki Okano, Ryota Hidese, Misato Baba, Itaru Yanagihara, Kenji Kojima, Teisuke Takita, Shinsuke Fujiwara
    Oct. 2017, BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 492(2) (2), 147 - 153, English
    [Refereed]
    Scientific journal

  • Ryota Hidese, Keita Yamashita, Kohei Kawazuma, Tamotsu Kanai, Haruyuki Atomi, Tadayuki Imanaka, Shinsuke Fujiwara
    Sep. 2017, EXTREMOPHILES, 21(5) (5), 903 - 917, English
    [Refereed]
    Scientific journal

  • Le Gao, Ryota Hidese, Shinsuke Fujiwara
    Sep. 2017, JOURNAL OF BIOSCIENCE AND BIOENGINEERING, 124(3) (3), 283 - 288, English
    [Refereed]
    Scientific journal

  • Hiroyuki Okano, Misato Baba, Tomomi Yamasaki, Ryota Hidese, Shinsuke Fujiwara, Itaru Yanagihara, Takeshi Ujiiye, Tsukasa Hayashi, Kenji Kojima, Teisuke Takita, Kiyoshi Yasukawa
    May 2017, BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 487(1) (1), 128 - 133, English
    [Refereed]
    Scientific journal

  • Hiroyuki Okano, Yuta Katano, Misato Baba, Ayako Fujiwara, Ryota Hidese, Shinsuke Fujiwara, Itaru Yanagihara, Tsukasa Hayashi, Kenji Kojima, Teisuke Takita, Kiyoshi Yasukawa
    Jan. 2017, ENZYME AND MICROBIAL TECHNOLOGY, 96, 111 - 120, English
    [Refereed]
    Scientific journal

  • Ryota Hidese, Ki-Hwan Im, Masaki Kobayashi, Masaru Niitsu, Takemitsu Furuchi, Shinsuke Fujiwara
    2017, BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, 81(9) (9), 1845 - 1849, English
    [Refereed]
    Scientific journal

  • Application of a Euryarchaeota-Specific Helicase from Thermococcus kodakarensis for Noise Reduction in PCR
    Ayako Fujiwara, Katsuhiro Kawato, Saori Kato, Kiyoshi Yasukawa, Ryota Hidese, Shinsuke Fujiwara
    May 2016, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 82(10) (10), 3022 - 3031, English
    [Refereed]
    Scientific journal

  • CuI and H2O2 Inactivate and FeII Inhibits [Fe]-Hydrogenase at very low Concentrations
    HIDESE Ryota, ATAKA Kenichi, BILL Eckhard, SHIMA Seigo
    Jul. 2015, ChemBioChem, 16(13) (13), 1861 - 1865, English
    [Refereed]
    Scientific journal

  • Naoki Akasaka, Wiwik Astuti, Yuri Ishii, Ryota Hidese, Hisao Sakoda, Shinsuke Fujiwara
    Jun. 2015, JOURNAL OF BIOSCIENCE AND BIOENGINEERING, 119(6) (6), 661 - 668, English
    [Refereed]
    Scientific journal

  • Naoki Akasaka, Yuri Ishii, Ryota Hidese, Hisao Sakoda, Shinsuke Fujiwara
    Dec. 2014, JOURNAL OF BIOSCIENCE AND BIOENGINEERING, 118(6) (6), 607 - 615, English
    [Refereed]
    Scientific journal

  • Ryota Hidese, Takahiro Inoue, Tadayuki Imanaka, Shinsuke Fujiwara
    Jul. 2014, MOLECULAR MICROBIOLOGY, 93(2) (2), 331 - 345, English
    [Refereed]
    Scientific journal

  • Kazuma Okada, Ryota Hidese, Wakao Fukuda, Masaru Niitsu, Koichi Takao, Yuhei Horai, Naoki Umezawa, Tsunehiko Higuchi, Tairo Oshima, Yuko Yoshikawa, Tadayuki Imanaka, Shinsuke Fujiwara
    May 2014, JOURNAL OF BACTERIOLOGY, 196(10) (10), 1866 - 1876, English
    [Refereed]
    Scientific journal

  • Ryota Hidese, Ryo Nishikawa, Le Gao, Masahiro Katano, Tomohiro Imai, Satoru Kato, Tamotsu Kanai, Haruyuki Atomi, Tadayuki Imanaka, Shinsuke Fujiwara
    May 2014, EXTREMOPHILES, 18(3) (3), 573 - 588, English
    [Refereed]
    Scientific journal

  • Ryota Hidese, Hisaaki Mihara, Tatsuo Kurihara, Nobuyoshi Esaki
    Mar. 2014, JOURNAL OF BACTERIOLOGY, 196(6) (6), 1238 - 1249, English
    [Refereed]
    Scientific journal

  • Naoki Akasaka, Hisao Sakoda, Ryota Hidese, Yuri Ishii, Shinsuke Fujiwara
    Dec. 2013, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 79(23) (23), 7334 - 7342, English
    [Refereed]
    Scientific journal

  • Eriko Nagaoka, Ryota Hidese, Tadayuki Imanaka, Shinsuke Fujiwara
    Aug. 2013, JOURNAL OF BACTERIOLOGY, 195(15) (15), 3442 - 3450, English
    [Refereed]
    Scientific journal

  • Ryota Hidese, Hisaaki Mihara, Tatsuo Kurihara, Nobuyoshi Esaki
    Oct. 2012, JOURNAL OF BIOCHEMISTRY, 152(4) (4), 341 - 346, English
    [Refereed]
    Scientific journal

  • Ryota Hidese, Hisaaki Mihara, Nobuyoshi Esaki
    Jul. 2011, APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 91(1) (1), 47 - 61, English
    [Refereed]
    Scientific journal

  • Ryota Hidese, Hisaaki Mihara, Tatsuo Kurihara, Nobuyoshi Esaki
    Feb. 2011, JOURNAL OF BACTERIOLOGY, 193(4) (4), 989 - 993, English
    [Refereed]
    Scientific journal

  • Functional analysis of a novel NADH-dependent dihydropyrimidine dehydrogenase from Escherichia coli
    HIDESE Ryota, MIHARA Hisaaki, ESAKI Nobuyoshi
    Sep. 2009, Vitamins, 83(9) (9), 528 - 532, English
    [Refereed]
    Scientific journal

  • Hisaaki Mihara, Ryota Hidese, Masahiro Yamane, Tatsuo Kurihara, Nobuyoshi Esaki
    Aug. 2008, BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 372(3) (3), 407 - 411, English
    [Refereed]
    Scientific journal

■ MISC
  • 第3章 生物工学の研究100年 育種技術 -突然変異から代謝工学へ-
    近藤昭彦, 蓮沼誠久, 秀瀬涼太
    Oct. 2022, 日本生物工学会100年史, 29 - 31, Japanese
    Introduction scientific journal

  • 微生物の高速育種を実現するスマートセル創出プラットフォーム
    蓮沼誠久, 秀瀬涼太, 番場崇弘
    Apr. 2022, 化学工学 [特集]「生物機能を利用したモノづくり」に貢献するプロセス強化, 86(4) (4), 157 - 160, Japanese
    Introduction scientific journal

  • 光合成メタボロミクスの物質生産への応用
    加藤悠一, 秀瀬涼太, 蓮沼誠久
    Sep. 2021, 生物工学会誌, 99(9) (9), 456 - 460, Japanese

  • 耐熱性ヘリカーゼを利用した高精度核酸検出技術の開発
    FUJIWARA SHINSUKE, FUJIWARA AYAKO, HIDESE RYOTA
    Jul. 2017, 生物工学会誌, 95(7) (7), 383 - 387, Japanese
    Introduction scientific journal

  • 超好熱性アーキアThermococcus kodakarensis由来分岐鎖ポリアミン合成酵素の構造と機能
    HIDESE RYOTA, FUJIWARA SHINSUKE
    Apr. 2016, 酵素工学ニュース, 75, Japanese
    Introduction scientific journal

  • 進化は長い目で見て
    HIDESE RYOTA
    Mar. 2016, 生物工学会誌, 94(3) (3), 131, Japanese
    Introduction scientific journal

  • 好熱菌の低温ストレス耐性
    HIDESE RYOTA, FUJIWARA SHINSUKE
    Aug. 2015, 生物工学会誌, 93(8) (8), 464 - 467, Japanese
    Introduction scientific journal

  • 耐熱性タンパク質を利用したビスフェノールAの吸着
    HIDESE RYOTA, 今岡 進, 藤原 伸介
    Apr. 2014, ケミカルエンジニヤリング, 59(4) (4), 17 - 21, Japanese
    Introduction scientific journal

  • 高温において翻訳活性化作用を持つポリアミン
    HIDESE RYOTA, FUJIWARA SHINSUKE
    May 2012, バイオサイエンスとインダストリー, 70(3) (3), 211 - 212, Japanese
    Introduction scientific journal

  • シャペロニンと生物進化
    HIDESE RYOTA
    Jan. 2012, 生物工学会誌, 90(1) (1), 39, Japanese
    Introduction scientific journal

■ Books And Other Publications
  • 微生物を活用した有用物質の製造技術 （第5章 CO2からの有用物質生産, 第2節「水素酸化細菌によるCO2吸収」)
    秀瀬涼太, 蓮沼誠久
    Joint work, シーエムシー出版, May 2023, ISBN: 9784781317403
    Scholarly book

  • スマートセルインダストリー –微生物細胞を用いた物質生産の展望–（第1編 ハイスループット合成・分析・評価技術，第2章 ハイスループット微生物構築・評価技術，第1節 「微生物を用いた物質生産とハイスループット微生物構築技術」）
    ISHII JUN, 西 晶子, 北野 美保, 中村 朋美, SHOUJI SHINICHIROU, HIDESE RYOTA, HASUNUMA TOMOHISA, KONDO AKIHIKO
    Joint work, シーエムシー出版, Jun. 2018, Japanese
    Scholarly book

  • Identification of branched-chain polyamines in hyperthermophiles, In Methods in Molecular Biology
    HIDESE Ryota, FUKUDA Wakao, NIITSU Masaru, FUJIWARA Shinsuke
    Joint work, Springer, 2018, English
    Scholarly book

  • Protein synthesis and polyamines in thermophiles: Effect of polyamines on nucleic acid maintenance and gene expression, In Polyamines, a universal molecular nexus for growth, survival and specialized metabolism
    FUJIWARA Shinsuke, HIDESE Ryota, INOUE Takahiro, FUKUDA Wakao
    Joint work, Springer, Nov. 2015, English
    Scholarly book

  • Long-chain and branched polyamines in thermophilic microbes. In Polyamines, a universal molecular nexus for growth, survival and specialized metabolism
    FUKUDA Wakao, HIDESE Ryota, FUJIWARA Shinsuke
    Joint work, Springer, 2015, English
    Scholarly book

■ Lectures, oral presentations, etc.
  • Physiological roles of Thermococcus kodakarensis ubiquitin-like proteins in the biosynthesis of sulfur-containing biomolecules.
    Ryota Hidese, Satsuki Sakakibara, Takayuki Ohira, Tsutomu Suzuki, Naoki Shigi, Shinsuke Fujiwara
    Thermophiles2019, Sep. 2019, English, International conference
    Poster presentation

  • 分岐鎖ポリアミンが超好熱菌のRNA ポリメラーゼ複合体に及ぼす影響
    福田 萌子, 家森 優佳, 濱川 匡史, HIDESE RYOTA, 福田 青郎, 藤原 伸介
    第71回日本生物工学会大会, Sep. 2019, Japanese, 岡山大学, Domestic conference
    Oral presentation

  • カチオンの構造に依存した負電荷脂質膜の相分離
    永田 佳嗣, 引地 啓太, HIDESE RYOTA, 藤原 伸介, 下川 直史, 高木 昌宏
    第71回日本生物工学会大会, Sep. 2019, Japanese, 岡山大学, Domestic conference
    Oral presentation

  • 微生物代謝経路の解析と生物生産への応用
    HIDESE RYOTA
    第5回 生物資源セミナー, Jan. 2019, Japanese, 立命館大学びわこくさつキャンパス, Domestic conference
    Oral presentation

  • 硫黄転移関連タンパク質から紐解く生命の進化
    HIDESE RYOTA
    極限環境生物学会2018年度(第19回)年会, Dec. 2018, Japanese, 松江コンベンションセンター, Domestic conference
    [Invited]
    Invited oral presentation

  • 超好熱性アーキアにおけるユビキチン様タンパク質の機能解析
    榊原 早津季, HIDESE RYOTA, 藤原 伸介
    第70回日本生物工学会大会, Sep. 2018, Japanese, 関西大学 千里山キャンパス, Domestic conference
    Poster presentation

  • ハイスループット微生物構築・評価技術の開発
    ISHII JUN, 西 晶子, 北野 美保, 中村 朋美, KATO HIROKO, SHOUJI SHINICHIROU, HIDESE RYOTA, 梅野 太輔
    第20回 新産業技術促進検討会, Jul. 2018, Japanese, モノづくり日本会議/日刊工業新聞社, Domestic conference
    Poster presentation

  • 超好熱性アーキアのモリブドプテリン生合成における硫黄転移系
    HIDESE RYOTA
    第65回 日本生化学会 近畿支部例会, May 2018, Japanese, 兵庫医科大学, Domestic conference
    Oral presentation

TOP