Yoshifumi Itoh

Tohoku University, Miyagi, Japan

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Publications (37)79.55 Total impact

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    ABSTRACT: The xylanolytic bacterium Paenibacillus sp. strain W-61 encodes three extracellular xylanase genes, xyn1, xyn3, and xyn5. In this study, we identified a transcriptional activator required for transcription of the xyn3 gene in strain W-61. The activator, AxyR, contained the highly homologous AraC-type DNA binding domain and required xylobiose, xylotriose, or xylotetraose as cofactor for binding to the xyn3 promoter region.
    Bioscience Biotechnology and Biochemistry 05/2012; 76(5):1051-4. DOI:10.1271/bbb.120165 · 1.06 Impact Factor
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    Thi-Huyen Do · Yuki Suzuki · Naoki Abe · Jun Kaneko · Yoshifumi Itoh · Keitarou Kimura ·
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    ABSTRACT: The degQ gene of Bacillus subtilis (natto), encoding a small peptide of 46 amino acids, is essential for the synthesis of extracellular poly-gamma-glutamate (γPGA). To elucidate the role of DegQ in γPGA synthesis, we knocked out the degQ gene in Bacillus subtilis (natto) and screened for suppressor mutations that restored γPGA synthesis in the absence of DegQ. Suppressor mutations were found in degS, the receptor kinase gene of the DegS-DegU two-component system. Recombinant DegS-His6 mutant proteins were expressed in Escherichia coli cells and subjected to an in vitro phosphorylation assay. Compared with the wild type, mutant DegS-His6 proteins showed higher levels of autophosphorylation (R208Q, M195I, L248F, and D250N), reduced autodephosphorylation (D250N), reduced phosphatase activity toward DegU, or a reduced ability to stimulate the autodephosphorylation activity of DegU (R208Q, D249G, M195I, L248F, and D250N) and stabilized DegU in the phosphorylated form. These mutant DegS proteins mimic the effect of DegQ on wild-type DegSU in vitro. Interestingly, DegQ stabilizes phosphorylated DegS only in the presence of DegU, indicating a complex interaction of these three proteins.
    Applied and Environmental Microbiology 09/2011; 77(23):8249-58. DOI:10.1128/AEM.05827-11 · 3.67 Impact Factor
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    ABSTRACT: The peptidoglycan of Selenomonas ruminantium is covalently bound to cadaverine (PG-cadaverine), which likely plays a significant role in maintaining the integrity of the cell surface structure. The outer membrane of this bacterium contains a 45-kDa major protein (Mep45) that is a putative peptidoglycan-associated protein. In this report, we determined the nucleotide sequence of the mep45 gene and investigated the relationship between PG-cadaverine, Mep45, and the cell surface structure. Amino acid sequence analysis showed that Mep45 is comprised of an N-terminal S-layer-homologous (SLH) domain followed by α-helical coiled-coil region and a C-terminal β-strand-rich region. The N-terminal SLH domain was found to be protruding into the periplasmic space and was responsible for binding to peptidoglycan. It was determined that Mep45 binds to the peptidoglycan in a manner dependent on the presence of PG-cadaverine. Electron microscopy revealed that defective PG-cadaverine decreased the structural interactions between peptidoglycan and the outer membrane, consistent with the proposed role for PG-cadaverine. The C-terminal β-strand-rich region of Mep45 was predicted to be a membrane-bound unit of the 14-stranded β-barrel structure. Here we propose that PG-cadaverine possesses functional importance to facilitate the structural linkage between peptidoglycan and the outer membrane via specific interaction with the SLH domain of Mep45.
    Journal of bacteriology 11/2010; 192(22):5953-61. DOI:10.1128/JB.00417-10 · 2.81 Impact Factor
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    ABSTRACT: Paenibacillus sp. W-61 is capable of utilizing water-insoluble xylan for carbon and energy sources and has three xylanase genes, xyn1, xyn3, and xyn5. Xyn1, Xyn3, and Xyn5 are extracellular enzymes of the glycoside hydrolase (GH) families 11, 30, and 10, respectively. Xyn5 contains several domains including those of carbohydrate-binding modules (CBMs) similar to a surface-layer homologous (SLH) protein. This study focused on the role of Xyn5, localized on the cell surface, in water-insoluble xylan utilization. Electron microscopy using immunogold staining revealed Xyn5 clusters over the entire cell surface. Xyn5 was bound to cell wall fractions through its SLH domain. A Deltaxyn5 mutant grew poorly and produced minimal amounts of Xyn1 and Xyn3 on water-insoluble xylan. A Xyn5 mutant lacking the SLH domain (Xyn5DeltaSLH) grew poorly, secreting Xyn5DeltaSLH into the medium and producing minimal Xyn1 and Xyn3 on water-insoluble xylan. A mutant with an intact xyn5 produced Xyn5 on the cell surface, grew normally, and actively synthesized Xyn1 and Xyn3 on water-insoluble xylan. Quantitative reverse transcription-PCR showed that xylobiose, generated from water-insoluble xylan decomposition by Xyn5, is the most active inducer for xyn1 and xyn3. Luciferase assays using a Xyn5-luciferase fusion protein suggested that xylotriose is the best inducer for xyn5. The cell surface Xyn5 appears to play two essential roles in water-insoluble xylan utilization: (i) generation of the xylo-oligosaccharide inducers of all the xyn genes from water-insoluble xylan and (ii) attachment of the cells to the substrate so that the generated inducers can be immediately taken up by cells to activate expression of the xyn system.
    Journal of bacteriology 02/2010; 192(8):2210-9. DOI:10.1128/JB.01406-09 · 2.81 Impact Factor
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    Zui Fujimoto · Isao Shiga · Yoshifumi Itoh · Keitarou Kimura ·
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    ABSTRACT: Particular Bacillus subtilis strains produce a capsular polypeptide poly-γ-glutamate (γ-PGA) that functions as a physical barrier against bacteriophage infection. Bacteriophage φNIT1 can infect B. subtilis and produces a novel - PGA hydrolase PghP. PghP was overexpressed, purified and crystallized by the sitting-drop vapour-diffusion method. The crystals diffracted to a resolution of 2.4 Å using a synchrotron X-ray source and were found to belong to space group P3121 or P3 221. © 2009 International Union of Crystallography All rights reserved.
    Acta Crystallographica Section F Structural Biology and Crystallization Communications 10/2009; 65(Pt 9):913-6. DOI:10.1107/S1744309109029881 · 0.53 Impact Factor
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    Keitarou Kimura · Lam-Son Phan Tran · Thi-Huyen Do · Yoshifumi Itoh ·
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    ABSTRACT: An industrial strain of Bacillus subtilis (natto) was used to produce poly-gamma-DL-glutamate (gammaPGA), a polymer of DL-glutamate linked by a gamma-peptide bond. In spite of efforts to improve gammaPGA production by modifying the medium, little attention has been paid to the expression of the gammaPGA synthetase gene. In this study, we investigated the expression of the gammaPGA synthetic gene and the gammaPGA product under various conditions with the LacZ-fusion of the synthetic gene (pgsB-lacZ). The 5' upstream regulatory region of the pgsB gene was also investigated by constructing deletion mutations of lacZ-fusion. The pgsB-lacZ was clearly expressed in the early stationary phase and was abolished by degU gene disruption. The results showed that pgsB-lacZ expression was repressed in rich media, and that gammaPGA production was limited by the substrate supply rather than by the amount of synthetase. Adding D-glutamate to the medium reduced gammaPGA production and synthetic gene expression. The transcription start point was determined by primer extension, and it was found that up to -721 bp (translation start point = +1) of the 5' untranslated region (UTR) was required for optimal pgsB-lacZ fusion gene expression.
    Bioscience Biotechnology and Biochemistry 06/2009; 73(5):1149-55. DOI:10.1271/bbb.80913 · 1.06 Impact Factor
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    ABSTRACT: Paenibacillus sp. strain W-61, which can utilize xylan as the sole source of carbon and energy, produces extracellular xylanases 1 and 3 (Xyn1 and Xyn3) and cell surface xylanase 5. In this study we found that lppX, immediately downstream of xyn1, encodes a lipoprotein located on the outer layer of the cytoplasmic membrane and that the LppX lipoprotein is essential for the secretion of active Xyn1 across the cytoplasmic membranes. In Escherichia coli, wild-type LppX was destined for the inner layer of the outer membrane. Mutant LppX(C19A), in which Cys-19, a possible lipomodification residue, is replaced with Ala, was located in the periplasm without being anchored to the membranes. Another mutant, LppX(S20D S21D), with substitutions of Asp for Ser-20 and Ser-21 (conversion to an Asp-Asp signal for sorting to the inner membrane), resided on the outer layer of the inner membrane, demonstrating that LppX has the sorting property of a lipoprotein. E. coli harboring both xyn1 and lppX secreted active Xyn1 into the periplasm. In contrast, E. coli carrying xyn1 alone failed to do so, accumulating inactive Xyn1 in the cytoplasmic membranes. Exogenous LppX(C19A) liberated the inactive Xyn1, which had been stagnating in the inner membrane, into the medium as an active enzyme. Thus, we propose that LppX is a novel type of lipoprotein that assists Xyn1 in making the proper fold necessary for traveling across the cytoplasmic membranes to be secreted as an active enzyme.
    Journal of bacteriology 03/2009; 191(5):1641-9. DOI:10.1128/JB.01285-08 · 2.81 Impact Factor
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    ABSTRACT: Leukocidin (Luk), an exotoxin of Staphylococcus aureus consisting of LukF and LukS, is a hetero-oligomeric pore-forming cytolytic toxin toward human and rabbit polymorphonuclear leukocytes. However, it is uncertain how Luk affects the host immune response. In the present study, we investigated whether Luk has the ability to stimulate mouse bone marrow-derived myeloid dendritic cells (BM-DCs). LukF activated BM-DCs to generate IL-12p40 mRNA, induce intracellular expression and extracellular secretion of this cytokine and express CD40 on their surface, whereas LukS showed a much lower or marginal ability in the activation of BM-DCs than its counterpart component. Similarly, TNF-alpha was secreted by BM-DCs upon stimulation with these components. Combined addition of these components did not lead to a further increase in IL-12p40 secretion. IL-12p40 production caused by LukF was completely abrogated in BM-DCs from TLR4-deficient mice similarly to the response to lipopolysaccharide (LPS). Polymixin B did not affect the LukF-induced IL-12p40 production, although the same treatment completely inhibited the LPS-induced response. Boiling significantly inhibited the response caused by LukF, but not by LPS. Finally, in a luciferase reporter assay, LukF induced the activation of NF-kappaB in HEK293T cells transfected with TLR4, MD2 and CD14, whereas LukS did not show such activity. These results demonstrate that LukF caused the activation of BM-DCs by triggering a TLR4-dependent signaling pathway and suggests that Luk may affect the host inflammatory response as well as show a cytolytic effect on leukocytes.
    Microbes and Infection 02/2009; 11(2):245-53. DOI:10.1016/j.micinf.2008.11.013 · 2.86 Impact Factor
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    Kazuteru Yamada · Jun Kaneko · Yoshiyuki Kamio · Yoshifumi Itoh ·
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    ABSTRACT: Pectobacterium carotovorum subsp. carotovorum strain Er simultaneously produces the phage tail-like bacteriocin carotovoricin (Ctv) and pectin lyase (Pnl) in response to DNA-damaging agents. The regulatory protein RdgB of the Mor/C family of proteins activates transcription of pnl through binding to the promoter. However, the optimal temperature for the synthesis of Ctv (23 degrees C) differs from that for synthesis of Pnl (30 degrees C), raising the question of whether RdgB directly activates ctv transcription. Here we report that RdgB directly regulates Ctv synthesis. Gel mobility shift assays demonstrated RdgB binding to the P(0), P(1), and P(2) promoters of the ctv operons, and DNase I footprinting determined RdgB-binding sequences (RdgB boxes) on these and on the pnl promoters. The RdgB box of the pnl promoter included a perfect 7-bp inverted repeat with high binding affinity to the regulator (K(d) [dissociation constant] = 150 nM). In contrast, RdgB boxes of the ctv promoters contained an imperfect inverted repeat with two or three mismatches that consequently reduced binding affinity (K(d) = 250 to 350 nM). Transcription of the rdgB and ctv genes was about doubled at 23 degrees C compared with that at 30 degrees C. In contrast, the amount of pnl transcription tripled at 30 degrees C. Thus, the inverse synthesis of Ctv and Pnl as a function of temperature is apparently controlled at the transcriptional level, and reduced rdgB expression at 30 degrees C obviously affected transcription from the ctv promoters with low-affinity RdgB boxes. Pathogenicity toward potato tubers was reduced in an rdgB knockout mutant, suggesting that the RdgAB system contributes to the pathogenicity of this bacterium, probably by activating pnl expression.
    Applied and Environmental Microbiology 09/2008; 74(19):6017-25. DOI:10.1128/AEM.01297-08 · 3.67 Impact Factor
  • Keitarou Kimura · Yoshifumi Itoh ·
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    ABSTRACT: The insertion sequence IS4Bsu1 frequently causes Bacillus subtilis starters for the production of Japanese fermented soybean pasts (natto) to lose the ability to produce poly-gamma-glutamate, the viscous material characteristic of natto. Bacillus subtilis NAFM5, a derivative of a natto starter, has six IS4Bsu1 copies on its chromosome. In this study, we determined all six insertion loci of the insertion sequence (IS). One was located in the coding region of yktD, a putative gene involved in polyketide synthesis. Four were located in non-coding regions between iolR and iolA, between tuaA and lytC, between rapI and orf1 (a potential gene of unknown function), and between ynaE and orf3 (a putative gene similar to thiF), and one resided in an intergenic region between divergent possible orf4 and orf5 genes of unknown function. Here we describe the structural features of these loci and discuss the effects of the IS4Bsu1 insertions on the functions of the target gene and the expression of the downstream genes. In addition, we found that strain NAFM5 and commercial natto starters possess eight to 10 loci of another IS of the IS256 family (designated IS256Bsu1) on their chromosomes. IS256Bus1 appeared active in transposition, potentially causing phenotypic alterations in natto starters like those induced by IS4Bsu1.
    Bioscience Biotechnology and Biochemistry 11/2007; 71(10):2458-64. · 1.06 Impact Factor
  • Keitarou KIMURA · Yoshifumi ITOH ·

    Bioscience Biotechnology and Biochemistry 10/2007; 71(10):2458-2464. DOI:10.1271/bbb.70223 · 1.06 Impact Factor
  • Yoshifumi Itoh · Takayuki Nishijyo · Yuji Nakada ·
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    ABSTRACT: Nutritionally versatile Pseudomonads effectively utilize various nitrogenated compounds, including amino acids (such as glutamate, proline, arginine and histidine) as sources of carbon, nitrogen and energy. The histidine catabolic pathway of Pseudomonas was first established in Pseudomonas fluorescens followed by Pseudomonas putida and Pseudomonas aeruginosa. The genes for the pathway enzymes were then identified and characterized in P. putida. Expression of the P. aeruginosa and P. putida histidine catabolic enzymes absolutely requires the presence of histidine (or its degradation intermediate urocanate) and is subject to regulation by both carbon and nitrogen, as in Klebsiella aerogenes (formerly Aeromonas aerogenes) and Bacillus subtilis (for reviews, see refs [9,24,57,85]).
    Pseudomonas, 12/2006: pages 371-395;
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    ABSTRACT: Pseudomonas aeruginosa PAO1 has two possible catabolic pathways of spermidine and spermine; one includes the spuA and spuB products with unknown functions and the other involves spermidine dehydrogenase (SpdH; EC encoded by an unknown gene. The properties of SpdH in P. aeruginosa PAO1 were characterized and the corresponding spdH gene in this strain identified. The deduced SpdH (620 residues, calculated Mr of 68,861) had a signal sequence of 28 amino acids at the amino terminal and a potential transmembrane segment between residues 76 and 92, in accordance with membrane location of the enzyme. Purified SpdH oxidatively cleaved spermidine into 1,3-diaminopropane and 4-aminobutyraldehyde with a specific activity of 37 units (mg protein)(-1) and a Km value of 36 microM. The enzyme also hydrolysed spermine into spermidine and 3-aminopropanaldehyde with a specific activity of 25 units (mg protein)(-1) and a Km of 18 microM. Knockout of spdH had no apparent effect on the utilization of both polyamines, suggesting that this gene is minimally involved in polyamine catabolism. However, when spdH was fused to the polyamine-inducible promoter of spuA, it fully restored the ability of a spuA mutant to utilize spermidine. It is concluded that SpdH can perform a catabolic role in vivo, but P. aeruginosa PAO1 does not produce sufficient amounts of the enzyme to execute this function.
    Microbiology 09/2006; 152(Pt 8):2265-72. DOI:10.1099/mic.0.28920-0 · 2.56 Impact Factor
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    Yuji Nakada · Yoshifumi Itoh ·
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    ABSTRACT: Pseudomonas aeruginosa PAO1 utilizes 3-guanidinopropionate (3-GP) and 4-guanidinobutyrate (4-GB), which differ in one methylene group only, via distinct enzymes: guanidinopropionase (EC; the gpuA product) and guanidinobutyrase (EC; the gbuA product). The authors cloned and characterized the contiguous gpuPAR genes (in that order) responsible for 3-GP utilization, and compared the deduced sequences of their putative protein products, and the potential regulatory mechanisms of gpuPA, with those of the corresponding gbu genes encoding the 4-GB catabolic system. GpuA and GpuR have similarity to GbuA (49 % identity) and GbuR (a transcription activator of gbuA; 37 % identity), respectively. GpuP resembles PA1418 (58 % identity), which is a putative membrane protein encoded by a potential gene downstream of gbuA. These features of the GpuR and GpuP sequences, and the impaired growth of gpuR and gpuP knockout mutants on 3-GP, support the notion that GpuR and GpuP direct the 3-GP-inducible expression of gpuA, and the uptake of 3-GP, respectively. Northern blots of mRNA from 3-GP-induced PAO1 cells revealed three transcripts of gpuA, gpuP, and gpuP and gpuA together, suggesting that gpuP and gpuA each have a 3-GP-responsible promoter, and that some transcription from the gpuP promoter is terminated after gpuP, or proceeds into gpuA. Knockout of gpuR abolished 3-GP-dependent synthesis of the transcripts, confirming that GpuR activates transcription from these promoters, with 3-GP as a specific co-inducer. The sequence conservation between the three functional pairs of the Gpu and Gbu proteins, and the absence of gpuAPR in closely related species, imply that the triad gpu genes have co-ordinately evolved from origins common to the gbu counterparts, to establish an independent catabolic system of 3-GP in P. aeruginosa.
    Microbiology 01/2006; 151(Pt 12):4055-62. DOI:10.1099/mic.0.28258-0 · 2.56 Impact Factor
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    Keitarou Kimura · Lam-Son Phan Tran · Ikuo Uchida · Yoshifumi Itoh ·
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    ABSTRACT: During early stationary phase, Bacillus subtilis NAFM5 produces capsular poly(gamma-glutamic acid) (gammaPGA, 2x10(6) Da), which contains D- and L-glutamate, and then degrades it during late stationary phase. The gamma-glutamyltransferase (EC; GGT) of this strain successively hydrolysed gammaPGA from the amino-terminal end, to yield both D- and L-glutamate. This enzyme was specifically synthesized during the stationary phase through transcriptional activation of the corresponding ggt gene by the ComQXPA quorum-sensing system. A ggt knockout mutant degraded gammaPGA into 1x10(5) Da fragments, but not any further, indicating that the capsule gammaPGA is first internally degraded by an endo-type of gammaPGA hydrolase into 1x10(5) Da intermediates, then externally into glutamates via GGT. Due to its inability to generate the glutamates from the capsule, the ggt mutant sporulated more frequently than the wild-type strain. The results show that B. subtilis GGT has a powerful exo-gamma-glutamyl hydrolase activity that participates in capsule gammaPGA degradation to supply stationary-phase cells with constituent glutamates.
    Microbiology 01/2005; 150(Pt 12):4115-23. DOI:10.1099/mic.0.27467-0 · 2.56 Impact Factor
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    Keitarou Kimura · Lam-Son Phan Tran · Yoshifumi Itoh ·
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    ABSTRACT: Many bacteria, including Escherichia coli, have a unique gene that encodes glutamate racemase. This enzyme catalyses the formation of d-glutamate, which is necessary for cell wall peptidoglycan synthesis. However, Bacillus subtilis has two glutamate racemase genes, named racE and yrpC. Since racE appears to be indispensable for growth in rich medium, the role of yrpC in d-amino acid synthesis is vague. Experiments with racE- and yrpC-knockout mutants confirmed that racE is essential for growth in rich medium but showed that this gene was dispensable for growth in minimal medium, where yrpC executes the anaplerotic role of racE. LacZ fusion assays demonstrated that racE was expressed in both types of media but yrpC was expressed only in minimal medium, which accounted for the absence of yrpC function in rich medium. Neither racE nor yrpC was required for B. subtilis cells to synthesize poly-gamma-dl-glutamate (gamma-PGA), a capsule polypeptide of d- and l-glutamate linked through a gamma-carboxylamide bond. Wild-type cells degraded the capsule during the late stationary phase without accumulating the degradation products, d-glutamate and l-glutamate, in the medium. In contrast, racE or yrpC mutant cells accumulated significant amounts of d- but not l-glutamate. Exogenous d-glutamate utilization was somewhat defective in the mutants and the double mutation of race and yrpc severely impaired d-amino acid utilization. Thus, both racemase genes appear necessary to complete the catabolism of exogenous d-glutamate generated from gamma-PGA.
    Microbiology 10/2004; 150(Pt 9):2911-20. DOI:10.1099/mic.0.27045-0 · 2.56 Impact Factor
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    ABSTRACT: We identified four new family 19 chitinases in Oryza sativa L. cv. Nipponbare: one class I (OsChia1d), two class II (OsChia2a and OsChia2b), and one class IV (OsChia4a). OsChia2a resembled (about 60% identity) the catalytic domains of class I chitinases, but OsChia2b was almost identical (95% identity) to that of the class IV enzyme. OsChia1c, OsChia1c deltaCBD (a deletion of OsChia1c lacking a chitin-binding domain, CBD), and OsChia2b were separately expressed and purified in Pichia pastoris. OsChia1c inhibited fungal growth significantly more than OsChia1c deltaCBD or OsChia2b. The activities of these enzymes on chitin polymers were similar, but they acted differently on N-acetylchitooligosaccharides, (GlcNAC)n. OsChia1c slowly hydrolyzed (GlcNAC)6 and very poorly hydrolyzed (GlcNAC)4 and (GlcNAC)5. In contrast, OsChia2b efficiently hydrolyzed these oligosaccharides. The high antifungal activity and low hydrolytic activity of the class I enzyme towards (GlcNAC)n imply that it participates in the generation of N-acetylchitooligosaccharide elicitors from the cell walls of infecting fungi.
    Bioscience Biotechnology and Biochemistry 06/2003; 67(5):1063-70. DOI:10.1271/bbb.67.1063 · 1.06 Impact Factor
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    Keitarou Kimura · Yoshifumi Itoh ·
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    ABSTRACT: Some Bacillus subtilis strains, including natto (fermented soybeans) starter strains, produce a capsular polypeptide of glutamate with a gamma-linkage, called poly-gamma-glutamate (gamma-PGA). We identified and purified a monomeric 25-kDa degradation enzyme for gamma-PGA (designated gamma-PGA hydrolase, PghP) from bacteriophage PhiNIT1 in B. subtilis host cells. The monomeric PghP internally hydrolyzed gamma-PGA to oligopeptides, which were then specifically converted to tri-, tetra-, and penta-gamma-glutamates. Monoiodoacetate and EDTA both inhibited the PghP activity, but Zn(2+) or Mn(2+) ions fully restored the enzyme activity inhibited by the chelator, suggesting that a cysteine residue(s) and these metal ions participate in the catalytic mechanism of the enzyme. The corresponding pghP gene was cloned and sequenced from the phage genome. The deduced PghP sequence (208 amino acids) with a calculated M(r) of 22,939 was not significantly similar to any known enzyme. Thus, PghP is a novel gamma-glutamyl hydrolase. Whereas phage PhiNIT1 proliferated in B. subtilis cells encapsulated with gamma-PGA, phage BS5 lacking PghP did not survive well on such cells. Moreover, all nine phages that contaminated natto during fermentation produced PghP, supporting the notion that PghP is important in the infection of natto starters that produce gamma-PGA. Analogous to polysaccharide capsules, gamma-PGA appears to serve as a physical barrier to phage absorption. Phages break down the gamma-PGA barrier via PghP so that phage progenies can easily establish infection in encapsulated cells.
    Applied and Environmental Microbiology 06/2003; 69(5):2491-7. DOI:10.1128/AEM.69.5.2491-2497.2003 · 3.67 Impact Factor
  • Yuji Nakada · Yoshifumi Itoh ·
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    ABSTRACT: Putrescine can be synthesized either directly from ornithine by ornithine decarboxylase (ODC; the speC product) or indirectly from arginine via arginine decarboxylase (ADC; the speA product). The authors identified the speA and speC genes in Pseudomonas aeruginosa PAO1. The activities of the two decarboxylases were similar and each enzyme alone appeared to direct sufficient formation of the polyamine for normal growth. A mutant defective in both speA and speC was a putrescine auxotroph. In this strain, agmatine deiminase (the aguA product) and N-carbamoylputrescine amidohydrolase (the aguB product), which were initially identified as the catabolic enzymes of agmatine, biosynthetically convert agmatine to putrescine in the ADC pathway: a double mutant of aguAB and speC was a putrescine auxotroph. AguA was purified as a homodimer of 43 kDa subunits and AguB as a homohexamer of 33 kDa subunits. AguA specifically deiminated agmatine with K(m) and K(cat) values of 0.6 mM and 4.2 s(-1), respectively. AguB was specific to N-carbamoylputrescine and the K(m) and K(cat) values of the enzyme for the substrate were 0.5 mM and 3.3 s(-1), respectively. Whereas AguA has no structural relationship to any known C-N hydrolases, AguB is a protein of the nitrilase family that performs thiol-assisted catalysis. Inhibition by SH reagents and the conserved cysteine residue in AguA and its homologues suggested that this enzyme is also involved in thiol-mediated catalysis.
    Microbiology 04/2003; 149(Pt 3):707-14. DOI:10.1099/mic.0.26009-0 · 2.56 Impact Factor
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    Yuji Nakada · Takayuki Nishijyo · Yoshifumi Itoh ·
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    ABSTRACT: Pseudomonas aeruginosa PAO1 utilizes proline as the sole source of carbon and nitrogen via a bifunctional enzyme (the putA gene product) that has both proline dehydrogenase (EC and pyrroline 5-carboxylate dehydrogenase (EC activities. We characterized the pruR-putAP loci encoding the proline catabolic system of this strain. In contrast to the putA and putP (encoding proline permease) genes of other gram- negative bacteria, which are located at divergent or separate loci, Northern blotting demonstrated that the two genes form an operon in strain PAO1. While the phylogenetic lineage of the PutP protein of strain PAO1 was related to that of the origin (80% identity to the P. putida counterpart), PutA of PAO1 (PutAPAO) was rather distantly related (47% identity) to the P. putida counterpart. Moreover, unlike the PutA proteins of P. putida and enteric bacteria, PutAPAO appeared to lack a regulatory function. Upstream of the putAP operon, the divergent PA0781 gene specified a hypothetical outer membrane protein with a molecular weight of 74,202. This gene appeared to be dispensable for proline utilization as indicated by the normal growth of a knockout mutant of PA0781 on medium containing proline. The pruR (proline utilization regulator) gene immediately upstream of PA0781 encoded a transcriptional activator of the AraC/XylS protein family and mediated the proline-responsive expression of putAP. Primer extension studies identified a PruR-dependent promoter responsive to proline in the 5′-flanking region of putA. Thus, the proline utilization system of P. aeruginosa differs from that of P. putida with respect to putA structure, the organization of the putAP genes, and the regulatory mechanism of putA expression.
    Journal of Bacteriology 11/2002; 184(20):5633-40. DOI:10.1128/JB.184.20.5633-5640.2002 · 2.81 Impact Factor

Publication Stats

1k Citations
79.55 Total Impact Points


  • 2006-2012
    • Tohoku University
      • • Department of Microbial Biotechnology
      • • Graduate School of Agricultural Science
      Miyagi, Japan
    • National Research Institute of Brewing
      Edo, Tōkyō, Japan
  • 2010
    • Tohoku Gakuin University
  • 2009
    • Shokei Gakuin University
      Сендай, Miyagi, Japan
  • 2000-2009
    • National Food Research Institute
      Ibaragi, Ōsaka, Japan
  • 2002-2003
    • National Agriculture and Food Research Organization
      Tsukuba, Ibaraki, Japan
  • 1998-2001
    • Georgia State University
      • Department of Biology
      Atlanta, Georgia, United States
  • 1982-1989
    • Shinshu University
      Shonai, Nagano, Japan