 | SHIMIZU TetsuDepartment of Environmental Management Lecturer | ||
Last Updated :2024/05/15
Researcher Information
J-Global ID
Research Interests
- 紅色細菌 酵素 微生物
Academic & Professional Experience
- 2024/04 - Today Kindai UniversityFaculty of Agriculture Department of Environmental Management講師
- 2016/09 - 2024/03 地球環境産業技術研究機構バイオ研究グループ研究員
- 2013/08 - 2016/08 The University of TokyoBiotechnology Research Center特任研究員
Association Memberships
Published Papers
- Tetsu Shimizu; Kai Suzuki; Masayuki InuiApplied microbiology and biotechnology 108 (1) 1 - 11 2024/12Ethylene glycol is an industrially important diol in many manufacturing processes and a building block of polymers, such as poly(ethylene terephthalate). In this study, we found that a mycolic acid-containing bacterium Rhodococcus jostii RHA1 can grow with ethylene glycol as a sole source of carbon and energy. Deletion of a putative glycolate dehydrogenase gene (RHA1_ro03227) abolished growth with ethylene glycol, indicating that ethylene glycol is assimilated via glycolate in R. jostii RHA1. Transcriptome sequencing and gene deletion analyses revealed that a gene homologous to mycofactocin (MFT)-associated dehydrogenase (RHA1_ro06057), hereafter referred to as EgaA, is essential for ethylene glycol assimilation. Furthermore, egaA deletion also negatively affected the utilization of ethanol, 1-propanol, propylene glycol, and 1-butanol, suggesting that EgaA is involved in the utilization of various alcohols in R. jostii RHA1. Deletion of MFT biosynthetic genes abolished growth with ethylene glycol, indicating that MFT is the physiological electron acceptor of EgaA. Further genetic studies revealed that a putative aldehyde dehydrogenase (RHA1_ro06081) is a major aldehyde dehydrogenase in ethylene glycol metabolism by R. jostii RHA1. KEY POINTS: • Rhodococcus jostii RHA1 can assimilate ethylene glycol via glycolate • A mycofactocin-associated dehydrogenase is involved in the oxidation of ethylene glycol • An aldehyde dehydrogenase gene is important for the ethylene glycol assimilation.
- Tetsu Shimizu; Akira NakamuraExtremophiles : life under extreme conditions 26 (3) 37 - 37 2022/112-Keto-3-deoxy- D-gluconate (KDG) is an important intermediate found in various sugars, sugar acids and polysaccharide catabolic pathways. Here, we report that a functionally uncharacterized type-2 malate/L-lactate dehydrogenase family protein (TTHB078) from Thermus thermophilus HB8 catalyzes a novel reaction, NAD(P)H-dependent reductase activity on KDG. This enzyme, designated KdgG, utilizes both NADH and NADPH as electron donors, but higher activity was observed with NADH. Analysis of the reaction product revealed that KdgG catalyzes reversible reduction of KDG to form 3-deoxy-D-mannonate. Molecular phylogenetic analysis indicated that KdgG and its homologs distributed in the genus Thermus form a novel clade among type-2 malate/L-lactate dehydrogenase family proteins.
- Tetsu Shimizu; Haruhiko Teramoto; Masayuki InuiApplied and environmental microbiology 88 (12) e0050722 2022/06The purple nonsulfur phototrophic bacterium Rhodobacter sphaeroides produces hydrogen gas (H2) from acetate. An approach to improve the H2 production is preventing accumulation of an intracellular energy storage molecule known as poly(β-hydroxybutyrate) (PHB), which competes with H2 production for reducing power. However, disruption of PHB biosynthesis has been reported to severely impair the acetate assimilation depending on the genetic backgrounds and/or culture conditions. To solve this problem, we analyzed the relationship between PHB accumulation and acetate metabolism in R. sphaeroides. Gene deletion analyses based on the wild-type strain revealed that among the two polyhydroxyalkanoate synthase genes in the genome, phaC1, but not phaC2, is essential for PHB accumulation, and the phaC1 deletion mutant exhibited slow growth with acetate. On the other hand, a strain with the deletion of phaC1 together with phaR, which encodes a transcriptional regulator capable of sensing PHB accumulation, exhibited growth comparable to that of the wild-type strain despite no accumulation of PHB. These results suggest that PHB accumulation is required for normal growth with acetate by altering the expression of genes under the control of phaR. This hypothesis was supported by a transcriptome sequencing (RNA-seq) analysis revealing that phaR is involved in the regulation of the ethylmalonyl coenzyme A pathway for acetate assimilation. Consistent with these findings, deletion of phaC1 in a genetically engineered H2-producing strain resulted in lower H2 production from acetate due to growth defects, whereas deletion of phaR together with phaC1 restored growth with acetate and increased H2 production from acetate without PHB accumulation. IMPORTANCE This study provides a novel approach for increasing the yield of photofermentative H2 production from acetate by purple nonsulfur phototrophic bacteria. This study further suggests that polyhydroxyalkanoate is not only a storage substance for carbon and energy in bacteria, but may also act as a signaling molecule that mediates bacterial metabolic adaptations to specific environments. This notion will be helpful for understanding the physiology of polyhydroxyalkanoate-producing bacteria, as well as for their metabolic engineering via synthetic biology.
- Haruhiko Teramoto; Tetsu Shimizu; Masako Suda; Masayuki InuiInternational Journal of Hydrogen Energy 0360-3199 2022This study explored the genetic engineering of Escherichia coli for hydrogen (H2) production. In E. coli W3110, the introduction of NAD+-reducing [NiFe]-hydrogenase from Cupriavidus necator, combined with the inactivation of three endogenous [NiFe]-hydrogenases, exhibited not only H2 production but also H2 uptake based on exogenous hydrogenase. Although the H2 production ability was much lower than the H2 uptake ability, inactivation of the ethanol, lactate, and succinate production pathways resulted in a marked increase in H2 production, demonstrating the bidirectional hydrogenase function in vivo depending on NADH/NAD+. Unexpectedly, H2 production was completely repressed under conditions for high expression of exogenous hydrogenase. Furthermore, the introduction of the heterologous enzyme markedly repressed the endogenous H2 production ability of E. coli W3110 but not the HST02. These in vivo behaviors largely correlated with in vitro hydrogenase activity suggested complicated interactions between the native and nonnative functional expression of [NiFe]-hydrogenases.
- Masahiro Ito; Tetsu Shimizu; Akira NakamuraMicrobiology resource announcements 10 (10) 2021/03Kaistia sp. strain 32K, an aerobic Gram-negative bacterium, was isolated from soil in Japan. Here, we report the complete genome sequence of this bacterium, which has a 5.4-Mbp genome sequence, containing 4,919 protein-coding sequences.
- Yoshiaki Usui; Tetsu Shimizu; Akira Nakamura; Masahiro ItoBiology 9 (9) 2020/09Previously, we reported that the coculture of motile Methylobacterium sp. ME121 and non-motile Kaistia sp. 32K, isolated from the same soil sample, displayed accelerated motility of strain ME121 due to an extracellular polysaccharide (EPS) produced by strain 32K. Since EPS is a major component of biofilms, we aimed to investigate the biofilm formation in cocultures of the two strains. The extent of biofilm formation was measured by a microtiter dish assay with the dye crystal violet. A significant increase in the amount of biofilm was observed in the coculture of the two strains, as compared to that of the monocultures, which could be due to a metabolite produced by strain 32K. However, in the coculture with strain 32K, using Escherichia coli or Pseudomonas aeruginosa, there was no difference in the amount of biofilm formation as compared with the monoculture. Elevated biofilm formation was also observed in the coculture of strain ME121 with Kaistia adipata, which was isolated from a different soil sample. Methylobacterium radiotolerans, isolated from another soil sample, showed a significant increase in biofilm formation when cocultured with K. adipata, but not with strain 32K. We also found that the culture supernatants of strains 32K and K. adipata accelerated the motility of strains ME121 and M. radiotolerans, wherein culture supernatant of K. adipata significantly increased the motility of M. radiotolerans, as compared to that by the culture supernatant of strain 32K. These results indicated that there was a positive relationship between accelerated motility and increased biofilm formation in Methylobacterium spp. This is the first study to report that the metabolites from Kaistia spp. could specifically modulate the biofilm-forming ability of Methylobacterium spp. Methylobacterium spp. biofilms are capable of inhibiting the biofilm formation of mycobacteria, which are opportunistic pathogens that cause problems in infectious diseases. Thus, the metabolites from the culture supernatant of Kaistia spp. have the potential to contribute to the environment in which increased biofilm production of Methylobacterium is desired.
- Yoshiaki Usui; Yuu Wakabayashi; Tetsu Shimizu; Yuhei O Tahara; Makoto Miyata; Akira Nakamura; Masahiro ItoBiomolecules 10 (4) 2020/04 [Refereed]
Motile Methylobacterium sp. ME121 and non-motile Kaistia sp. 32K were isolated from the same soil sample. Interestingly, ME121 was significantly more motile in the coculture of ME121 and 32K than in the monoculture of ME121. This advanced motility of ME121 was also observed in the 32K culture supernatant. A swimming acceleration factor, which we named the K factor, was identified in the 32K culture supernatant, purified, characterized as an extracellular polysaccharide (5-10 kDa), and precipitated with 70% ethanol. These results suggest the possibility that the K factor was directly or indirectly sensed by the flagellar stator, accelerating the flagellar rotation of ME121. To the best of our knowledge, no reports describing an acceleration in motility due to coculture with two or more types of bacteria have been published. We propose a mechanism by which the increase in rotational force of the ME121 flagellar motor is caused by the introduction of the additional stator into the motor by the K factor. - Kei Sakaki; Keita Ohishi; Tetsu Shimizu; Ikki Kobayashi; Naoki Mori; Kenichi Matsuda; Takeo Tomita; Hidenori Watanabe; Kan Tanaka; Tomohisa Kuzuyama; Makoto NishiyamaNature chemical biology 16 (4) 415 - 422 2020/02 [Refereed]
In biotin biosynthesis, the conversion of pimeloyl intermediates to biotin is catalyzed by a universal set of four enzymes: BioF, BioA, BioD and BioB. We found that the gene homologous to bioA, the product of which is involved in the conversion of 8-amino-7-oxononanoate (AON) to 7,8-diaminononanoate (DAN), is missing in the genome of the cyanobacterium Synechocystis sp. PCC 6803. We provide structural and biochemical evidence showing that a novel dehydrogenase, BioU, is involved in biotin biosynthesis and functionally replaces BioA. This enzyme catalyzes three reactions: formation of covalent linkage with AON to yield a BioU-DAN conjugate at the ε-amino group of Lys124 of BioU using NAD(P)H, carboxylation of the conjugate to form BioU-DAN-carbamic acid, and release of DAN-carbamic acid using NAD(P)+. In this biosynthetic pathway, BioU is a suicide enzyme that loses the Lys124 amino group after a single round of reaction. - Shimizu T; Teramoto H; Inui MApplied microbiology and biotechnology 103 (23-24) 9739 - 9749 0175-7598 2019/11 [Refereed]
Purple non-sulfur photosynthetic bacteria such as Rhodobacter sphaeroides and Rhodopseudomonas palustris produce hydrogen gas (H2) via proton reduction, which is catalyzed by nitrogenase. Although the expression of nitrogenase is usually repressed under nitrogen-sufficient conditions, a partial deletion of nifA, which encodes a transcriptional activator of nitrogen-fixation genes, has been reported to enable the constitutive expression of nitrogenase in R. palustris. In this study, we evaluated the effects of a similar mutation (nifA* mutation) on H2 production during the photoheterotrophic growth of R. sphaeroides, based on the notion that H2 production by nitrogenase compensates for the loss of CO2 fixation via the Calvin cycle, thereby restoring the redox balance. The chromosomal nifA* mutation resulted in the slight restoration of the photoheterotrophic growth of a mutant strain lacking ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), the key enzyme of the Calvin cycle, when the strain was cultured in van Niel’s yeast medium. In addition, the strain with the nifA* mutation produced detectable levels of H2 during photoheterotrophic growth with acetate and ammonium; however, the H2 production was considerably lower than that observed during the photoheterotrophic growth of the strain with acetate and l-glutamate, where l-glutamate serves as a poor nitrogen source, thereby causing nitrogenase derepression. On the other hand, introduction of a multicopy plasmid harboring nifA* markedly restored the photoheterotrophic growth of the RubisCO-deletion mutant in van Niel’s yeast medium and resulted in efficient H2 production during the photoheterotrophic growth with acetate and ammonium. - Shimizu T; Teramoto H; Inui MApplied and environmental microbiology 85 (2) 1 - 17 0099-2240 2018/11 [Refereed]
Rhodobacter sphaeroides produces hydrogen gas (H2) from organic compounds via nitrogenase under anaerobic-light conditions in the presence of poor nitrogen sources, such as L-glutamate. R. sphaeroides utilizes the ethylmalonyl-coenzyme A (EMC) pathway for acetate assimilation, but its H2 yield from acetate in the presence of L-glutamate has been reported to be low. In this study, the deletion of ccr encoding crotonyl-coenzyme A (crotonyl-CoA) carboxylase/reductase, a key enzyme for the EMC pathway in R. sphaeroides, revealed that the EMC pathway is essential for H2 production from acetate and L-glutamate but not for growth and acetate consumption in the presence of L-glutamate. We introduced a plasmid expressing aceBA from Rhodobacter capsulatus encoding two key enzymes for the glyoxylate bypass into R. sphaeroides, which resulted in a 64% increase in H2 production. However, compared with the wild-type strain expressing heterologous aceBA genes, the strain with aceBA introduced in the genetic background of an EMC pathway-disrupted mutant showed a lower H2 yield. These results indicate that a combination of the endogenous EMC pathway and a heterologously expressed glyoxylate bypass is beneficial for H2 production. In addition, introduction of the glyoxylate bypass into a polyhydroxybutyrate (PHB) biosynthesis-disrupted mutant resulted in a delay in growth along with H2 production, although its H2 yield was comparable to that of the wild-type strain expressing heterologous aceBA genes. These results suggest that PHB production is important for fitness to the culture during H2 production from acetate and L-glutamate when both acetateassimilating pathways are present. IMPORTANCE As an alternative to fossil fuel, H2 is a promising renewable energy source. Although photofermentative H2 production from acetate is key to developing an effcient process of biohydrogen production from biomass-derived sugars, H2 yields from acetate and L-glutamate by R. sphaeroides have been reported to be low. In this study, we observed that in addition to the endogenous EMC pathway, heterologous expression of the glyoxylate bypass in R. sphaeroides markedly increased H2 yields from acetate and L-glutamate. Therefore, this study provides a novel strategy for improving H2 yields from acetate in the presence of L-glutamate and contributes to a clear understanding of acetate metabolism in R. sphaeroides during photofermentative H2 production. - Kazuhiro Fukano; Kunio Ozawa; Masaya Kokubu; Tetsu Shimizu; Shinsaku Ito; Yasuyuki Sasaki; Akira Nakamura; Shunsuke YajimaPLoS ONE Public Library of Science 13 (5) e0198010 1932-6203 2018/05 [Refereed]
For about 70 years, L-glucose had been considered non-metabolizable by either mammalian or bacterial cells. Recently, however, an L-glucose catabolic pathway has been discovered in Paracoccus laeviglucosivorans, and the genes responsible cloned. Scyllo-inositol dehydrogenase is involved in the first step in the pathway that oxidizes L-glucose to produce L-glucono-1,5-lactone with concomitant reduction of NAD+ dependent manner. Here, we report the crystal structure of the ternary complex of scyllo-inositol dehydrogenase with NAD+ and L-glucono-1,5-lactone at 1.8 Å resolution. The enzyme adopts a homo-tetrameric structure, similar to those of the inositol dehydrogenase family, and the electron densities of the bound sugar was clearly observed, allowing identification of the residues responsible for interaction with the substrate in the catalytic site. In addition to the conserved catalytic residues (Lys106, Asp191, and His195), another residue, His318, located in the loop region of the adjacent subunit, is involved in substrate recognition. Site-directed mutagenesis confirmed the role of these residues in catalytic activity. We also report the complex structures of the enzyme with myo-inositol and scyllo-inosose. The Arg178 residue located in the flexible loop at the entrance of the catalytic site is also involved in substrate recognition, and plays an important role in accepting both L-glucose and inositols as substrates. On the basis of these structural features, which have not been identified in the known inositol dehydrogenases, and a phylogenetic analysis of IDH family enzymes, we suggest a novel subfamily of the GFO/IDH/MocA family. Since many enzymes in this family have not biochemically characterized, our results could promote to find their activities with various substrates. - Tetsu Shimizu; Lulu Yin; Ayako Yoshida; Yuusuke Yokooji; Shin-ichi Hachisuka; Takaaki Sato; Takeo Tomita; Hiromi Nishida; Haruyuki Atomi; Tomohisa Kuzuyama; Makoto NishiyamaBIOCHEMICAL JOURNAL PORTLAND PRESS LTD 474 (1) 105 - 122 0264-6021 2017/01 [Refereed]
beta-Decarboxylating dehydrogenases, which are involved in central metabolism, are considered to have diverged from a common ancestor with broad substrate specificity. In a molecular phylogenetic analysis of 183 beta-decarboxylating dehydrogenase homologs from 84 species, TK0280 from Thermococcus kodakarensis was selected as a candidate for an ancestral-type beta-decarboxylating dehydrogenase. The biochemical characterization of recombinant TK0280 revealed that the enzyme exhibited dehydrogenase activities toward homoisocitrate, isocitrate, and 3-isopropylmalate, which correspond to key reactions involved in the lysine biosynthetic pathway, tricarboxylic acid cycle, and leucine biosynthetic pathway, respectively. In T. kodakarensis, the growth characteristics of the KUW1 host strain and a TK0280 deletion strain suggested that TK0280 is involved in lysine biosynthesis in this archaeon. On the other hand, gene complementation analyses using Thermus thermophilus as a host revealed that TK0280 functions as both an isocitrate dehydrogenase and homoisocitrate dehydrogenase in this organism, but not as a 3-isopropylmalate dehydrogenase, most probably reflecting its low catalytic efficiency toward 3-isopropylmalate. A crystallographic study on TK0280 binding each substrate indicated that Thr71 and Ser80 played important roles in the recognition of homoisocitrate and isocitrate while the hydrophobic region consisting of Ile82 and Leu83 was responsible for the recognition of 3-isopropylmalate. These analyses also suggested the importance of a water-mediated hydrogen bond network for the stabilization of the beta 3-alpha 4 loop, including the Thr71 residue, with respect to the promiscuity of the substrate specificity of TK0280. - Tetsu Shimizu; Takeo Tomita; Tomohisa Kuzuyama; Makoto NishiyamaJOURNAL OF BIOLOGICAL CHEMISTRY AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC 291 (19) 9948 - 9959 0021-9258 2016/05 [Refereed]
Several bacteria and archaea utilize the amino group-carrier protein, LysW, for lysine biosynthesis, in which an isopeptide bond is formed between the C-terminal Glu of LysW and an amino group of a-aminoadipate (AAA), The resulting LysW-gamma-AAA is phosphorylated by LysZ to form LysW-gamma-AAA phosphate, which is subsequently reduced to LysW-gamma-aminoadipic semialdehyde (LysW-gamma-AASA) through a reaction catalyzed by LysY. In this study, we determined the crystal structures of LysY from Thermus thermophilus HB27 (TtLysY) complexed with TtLysW-gamma-AASA and TtLysW-gamma-AAA, respectively. In both structures, the globular domain of TtLysW was recognized by positively charged residues on helix alpha 9 and the beta 11-alpha 10 loop of TtLysY through conformational changes. A mutational analysis confirmed that the interactions observed between TtLysY and LysW are important for the function of TtLysY. The extended LysW recognition loop and conserved arginine residue were identified as signatures to discriminate LysY from ArgC, which is involved in arginine biosynthesis. Combined with the previously determined TtLysZ.TtLysW complex structure, TtLysW may simultaneously bind TtLysZ and TtLysY. These structural insights suggest the formation of a TtLysWZY ternary complex, in which the flexible C-terminal extension of TtLysW promotes the efficient transfer of the labile intermediate from the active site of TtLysZ to that of TtLysY during the sequential reactions catalyzed by TtLysZY. - Aspartate kinase involved in 4-hydroxy-3-nitrosobenzamide biosynthesis in Streptomyces murayamaensisMai Tsujimoto; Ayako Yoshida; Tetsu Shimizu; Takeo Tomita; Yasuo Ohnishi; Tomohisa Kuzuyama; Makoto NishiyamaBIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY TAYLOR & FRANCIS LTD 80 (11) 2255 - 2263 0916-8451 2016 [Refereed]
Streptomyces murayamensis carries two aspartate kinase (AK) genes: one for the biosynthesis of lysine, threonine, and methionine, and the other (nspJ) contained in the biosynthetic gene cluster for the secondary metabolite, 4-hydroxy-3-nitrosobenzamide, for catalyzing the first reaction. AKs involved in the biosynthesis of amino acids are often regulated allosterically by the end products. In the present study, we characterized NspJ to investigate whether AKs involved in secondary metabolism were also allosterically regulated. NspJ was in (22) and ((22))(2) heterooligomeric forms, and was insensitive to all the compounds tested including lysine, threonine, and methionine. The reduction in the activity following the removal of ammonium sulfate, which induced subunit dissociation, suggests that the subunit may be involved in stabilizing the structure of the subunit in order to exhibit its activity. This study has provided the first example of a feedback-insensitive (22)-type AK, which is involved in the secondary metabolism. - Shun Fujinami; Kiyoko Takeda-Yano; Takefumi Onodera; Katsuya Satoh; Tetsu Shimizu; Yuu Wakabayashi; Issay Narumi; Akira Nakamura; Masahiro ItoGenome announcements 3 (5) 2015/09 [Refereed]
Methylobacterium sp. ME121 was isolated from soil as a mixed single colony with Kaistia sp. 32K, and its growth was enhanced by coculture. Here, we report the draft genome sequence of Methylobacterium sp. ME121, which may contribute to the study of the molecular mechanisms underlying this phenomenon. - Tetsu Shimizu; Akira NakamuraMICROBIOLOGY-SGM MICROBIOLOGY SOC 160 (Pt 3) 623 - 634 1350-0872 2014/03 [Refereed]
Five genes encoding enzymes required for L-gluconate catabolism, together with genes encoding components of putative ABC transporters, are located in a cluster in the genome of Paracoccus sp. 43P. A gene encoding a transcriptional regulator in the IcIR family, IgnR, is located in front of the cluster in the opposite direction. Reverse transcription PCR analysis indicated that the cluster was transcribed as an operon, termed the Ign operon. Two promoters, P-IgnA and P-IgnR, are divergently located in the intergenic region, and transcription from these promoters was induced by addition of L-gluconate or D-idonate, a catabolite of L-gluconate. Deletion of IgnR resulted in constitutive expression of IgnA, IgnH and IgnR, indicating that IgnR encodes a repressor protein for the expression of the Ign operon and IgnR itself. Electrophoretic mobility shift assay and DNase I footprinting analyses revealed that recombinant LgnR binds to both P-IgnA and P-IgnR, indicating that LgnR represses transcription from these promoters by competing with RNA polymerase for binding to these sequences. D-Idonate was identified as a candidate effector molecule for dissociation of LgnR from these promoters. Phylogenetic analysis revealed that LgnR formed a cluster with putative proteins from other genome sequences, which is distinct from those proteins of known regulatory functions, in the IcIR family of transcriptional regulators. Additionally, the phylogeny suggests an evolutionary linkage between the L-gluconate catabolic pathway and D-galactonate catabolic pathways distributed in Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Actinobacteria. - Tetsu Shimizu; Naoki Takaya; Akira NakamuraJOURNAL OF BIOLOGICAL CHEMISTRY AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC 287 (48) 40448 - 40456 0021-9258 2012/11 [Refereed]
AnL-glucose-utilizing bacterium, Paracoccus sp. 43P, was isolated from soil by enrichment cultivation in a minimal medium containing L-glucose as the sole carbon source. In cell-free extracts from this bacterium, NAD(+)-dependent L-glucose dehydrogenase was detected as having sole activity toward L-glucose. This enzyme, LgdA, was purified, and the lgdA gene was found to be located in a cluster of putative inositol catabolic genes. LgdA showed similar dehydrogenase activity toward scyllo-and myo-inositols. L-Gluconate dehydrogenase activity was also detected in cell-free extracts, which represents the reaction product of LgdA activity toward L-glucose. Enzyme purification and gene cloning revealed that the corresponding gene resides in a nine-gene cluster, the lgn cluster, which may participate in aldonate incorporation and assimilation. Kinetic and reaction product analysis of each gene product in the cluster indicated that they sequentially metabolize L-gluconate to glycolytic intermediates, D-glyceraldehyde-3-phosphate, and pyruvate through reactions of C-5 epimerization by dehydrogenase/reductase, dehydration, phosphorylation, and aldolase reaction, using a pathway similar to L-galactonate catabolism in Escherichia coli. Gene disruption studies indicated that the identified genes are responsible for L-glucose catabolism.
Awards & Honors
- 2023/06 Japan Association for Chemical Innovation 12th JACI Prize for Encouraging Young Researcher
酸素非発生型光合成細菌による糖からの高効率バイオ水素生産技術の開発受賞者: Tetsu Shimizu
Research Grants & Projects
- Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Early-Career ScientistsDate (from‐to) : 2020/04 -2023/03Author : 清水 哲1)前年度に実施したRNA-seq解析の結果、Rhodobacter sphaeroidesの酢酸資化経路であるエチルマロニルCoA経路を担う複数の遺伝子の転写量がphaRの破壊により増加していることが明らかとなった。そこで各遺伝子の上流配列を精査したところ、クロトニルCoAカルボキシラーゼ/レダクターゼ遺伝子(ccr)の上流に5'-CTGCN4GCAG-3'からなる既知のPhaR結合モチーフが存在することが判明し、PhaRがccrの発現を負に制御していることが強く示唆された。そこでPHB合成酵素遺伝子破壊株(ΔphaC)にccr発現用マルチコピープラスミドを導入したところ、対照株と比較して酢酸を炭素源とした生育が大きく回復することを見出した。以上の結果からΔphaC株ではPHB生産能の欠失にともないccrをはじめとしたPhaR制御下遺伝子の発現が抑制され、結果として酢酸を炭素源とした生育に異常をきたすことが予想された。
2)RNA-seq解析により同定されたphaRの破壊により転写量が増加する遺伝子のうちの10個について5'-RACE法により転写開始点を決定した。今後各遺伝子のプロモーター領域にPhaRが結合するか検討を行う。
3)R. sphaeroidesの近縁種であるR. capsulatusのPHB合成酵素遺伝子破壊株を構築した。今後この株の表現型について解析を行い、R. sphaeroidesと同様の制御がR. capsulatusにも存在するのか検証を行う。