Tomohisa Kuzuyama

The University of Tokyo, Tōkyō, Japan

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Publications (135)515.93 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Terpene cyclization reactions are fascinating owing to the precise control of connectivity and stereochemistry during the catalytic process. Cyclooctat-9-en-7-ol synthase (CotB2) synthesizes an unusual 5-8-5 fused-ring structure with six chiral centers from the universal diterpene precursor, the achiral C20 geranylgeranyl diphosphate substrate. An unusual new mechanism for the exquisite CotB2-catalyzed cyclization that involves a carbon–carbon backbone rearrangement and three long-range hydride shifts is proposed, based on a powerful combination of in vivo studies using uniformly 13C-labeled glucose and in vitro reactions of regiospecifically deuterium-substituted geranylgeranyl diphosphate substrates. This study shows that CotB2 elegantly demonstrates the synthetic virtuosity and stereochemical control that evolution has conferred on terpene synthases.
    Angewandte Chemie 02/2015; DOI:10.1002/ange.201411923
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    ABSTRACT: Terpene cyclization reactions are fascinating owing to the precise control of connectivity and stereochemistry during the catalytic process. Cyclooctat-9-en-7-ol synthase (CotB2) synthesizes an unusual 5-8-5 fused-ring structure with six chiral centers from the universal diterpene precursor, the achiral C20 geranylgeranyl diphosphate substrate. An unusual new mechanism for the exquisite CotB2-catalyzed cyclization that involves a carbon-carbon backbone rearrangement and three long-range hydride shifts is proposed, based on a powerful combination of in vivo studies using uniformly (13) C-labeled glucose and in vitro reactions of regiospecifically deuterium-substituted geranylgeranyl diphosphate substrates. This study shows that CotB2 elegantly demonstrates the synthetic virtuosity and stereochemical control that evolution has conferred on terpene synthases. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    Angewandte Chemie International Edition 02/2015; 54(14). DOI:10.1002/anie.201411923 · 11.34 Impact Factor
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    ABSTRACT: Odoriferous terpene metabolites of bacterial origin have been known for many years. In genome-sequenced Streptomycetaceae microorganisms, the vast majority produces the degraded sesquiterpene alcohol geosmin. Two minor groups of bacteria do not produce geosmin, with one of these groups instead producing other sesquiterpene alcohols, whereas members of the remaining group do not produce any detectable terpenoid metabolites. Because bacterial terpene synthases typically show no significant overall sequence similarity to any other known fungal or plant terpene synthases and usually exhibit relatively low levels of mutual sequence similarity with other bacterial synthases, simple correlation of protein sequence data with the structure of the cyclized terpene product has been precluded. We have previously described a powerful search method based on the use of hidden Markov models (HMMs) and protein families database (Pfam) search that has allowed the discovery of monoterpene synthases of bacterial origin. Using an enhanced set of HMM parameters generated using a training set of 140 previously identified bacterial terpene synthase sequences, a Pfam search of 8,759,463 predicted bacterial proteins from public databases and in-house draft genome data has now revealed 262 presumptive terpene synthases. The biochemical function of a considerable number of these presumptive terpene synthase genes could be determined by expression in a specially engineered heterologous Streptomyces host and spectroscopic identification of the resulting terpene products. In addition to a wide variety of terpenes that had been previously reported from fungal or plant sources, we have isolated and determined the complete structures of 13 previously unidentified cyclic sesquiterpenes and diterpenes.
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    ABSTRACT: Facile and stereoselective syntheses of three different kinds of deuterium-labelled geranylgeraniol analogs have been achieved. LiAlD4 is used as the deuterium source to ensure high deuterium incorporation. [8,8-d2]- and [9,9-d2]-geranylgeraniols have been prepared for the first time. [10-d]-geranylgeraniol was efficiently prepared with a high degree of deuterium incorporation.
    Bulletin of the Chemical Society of Japan 01/2015; 88(4). DOI:10.1246/bcsj.20140384 · 2.22 Impact Factor
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    ABSTRACT: Versipelostatin (VST) is an unusual 17-membered macrocyclic polyketide product that contains a spirotetronate skeleton. In this study, the entire VST biosynthetic gene cluster (vst) spanning 108 kb from Streptomyces versipellis 4083-SVS6 was identified by heterologous expression using a bacterial artificial chromosome vector. Here, we demonstrate that an enzyme VstJ catalyzes the stereoselective [4+2]-cycloaddition between the conjugated diene and the exocyclic olefin of a newly identified tetronate-containing intermediate to form the spirotetronate skeleton during VST biosynthesis.
    Journal of the American Chemical Society 12/2014; DOI:10.1021/ja510711x · 11.44 Impact Factor
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    ABSTRACT: In the biosynthesis of lysine by Thermus thermophilus, the metabolite α-ketoglutarate is converted to the intermediate α-aminoadipate (AAA), which is protected by the 54 amino acid acidic protein LysW. In the present study, we determined the crystal structure of LysZ from T. thermophilus (TtLysZ), an amino acid kinase that catalyzes the second step in the AAA to lysine conversion, which was in a complex with LysW at a resolution of 1.85 Å. A crystal analysis coupled with isothermal titration calorimetry of the TtLysZ mutants for TtLysW revealed tight interactions between LysZ and the globular and C-terminal extension domains of the LysW protein, which were mainly attributed to electrostatic forces. These results provided structural evidence for LysW acting as a protecting molecule for the α-amino group of AAA and also as a carrier protein to guarantee better recognition by biosynthetic enzymes for the efficient biosynthesis of lysine.
    Journal of Biological Chemistry 11/2014; 290(1). DOI:10.1074/jbc.M114.595983 · 4.60 Impact Factor
  • Jianwen Lin, Makoto Nishiyama, Tomohisa Kuzuyama
    The Journal of Antibiotics 10/2014; DOI:10.1038/ja.2014.149 · 2.04 Impact Factor
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    ABSTRACT: Cyclolavandulyl diphosphate synthase (CLDS; estimated molecular weight 23.1 kDa) from the soil bacterium Streptomyces sp. CL190 is an enzyme that catalyzes both the condensation of two molecules of C5 dimethylallyl diphosphate (DMAPP) and the subsequent cyclization. CLDS was crystallized in the absence and the presence of the substrate DMAPP. Diffraction data were collected at a synchrotron source and the crystals diffracted to 2.00 and 1.73 Å resolution, respectively. The crystal obtained in the absence of DMAPP belonged to space group P212121, with unit-cell parameters a = 39.0, b = 87.5, c = 113.6 Å. The crystal obtained in the presence of DMAPP belonged to space group P1, with unit-cell parameters a = 46.9, b = 61.7, c = 82.2 Å, α = 74.0, β = 84.5, γ = 86.0°.
    10/2014; 70(10). DOI:10.1107/S2053230X14018883
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    ABSTRACT: ArgR is known to serve as a repressor/activator of the metabolism of arginine. To elucidate the role of ArgR in the metabolism of Thermus thermophilus cells, comparative genome-wide comprehensive analysis was conducted for wild-type T. thermophilus and its mutant lacking the argR gene. Transcriptome analysis and chromatin affinity precipitation coupled with high-density tiling chip (ChAP-chip) analysis identified 34 genetic loci that are directly regulated by ArgR and indicated that ArgR decreases the expression of arginine biosynthesis and also regulates several other genes involved in amino acid metabolism, including lysine biosynthetic genes, as suggested by our previous study. Among genes whose expression was regulated by ArgR, the largest effect of argR knockout was observed in a putative operon, including genes TTHA0284, TTHA0283, and TTHA0282 involved in arginine biosynthesis. The promoter of this operon, argG, was repressed approximately 21-fold by ArgR. DNase I footprint analysis coupled with electrophoretic mobility shift assay suggested that high arginine-dependent repression was attributed to the fact that the promoter contains three operators for ArgR binding and ArgR is bound to the binding sites cooperatively, possibly forming a DNA loop, in the hexameric form stabilized by arginine binding.
    Extremophiles 07/2014; 18(6). DOI:10.1007/s00792-014-0669-2 · 2.17 Impact Factor
  • The Journal of Antibiotics 07/2014; DOI:10.1038/ja.2014.93 · 2.04 Impact Factor
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    ABSTRACT: Human Vγ2Vδ2 T cells monitor isoprenoid metabolism by recognizing foreign (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), a metabolite in the 2-C-methyl-d-erythritol-4-phosphate pathway used by most eubacteria and apicomplexan parasites, and self isopentenyl pyrophosphate, a metabolite in the mevalonate pathway used by humans. Whereas microbial infections elicit prolonged expansion of memory Vγ2Vδ2 T cells, immunization with prenyl pyrophosphates or aminobisphosphonates elicit short-term Vγ2Vδ2 expansion with rapid anergy and deletion upon subsequent immunizations. We hypothesized that a live, attenuated bacterial vaccine that overproduces HMBPP would elicit long-lasting Vγ2Vδ2 T cell immunity by mimicking a natural infection. Therefore, we metabolically engineered the avirulent aroA(-) Salmonella enterica serovar Typhimurium SL7207 strain by deleting the gene for LytB (the downstream enzyme from HMBPP) and functionally complementing for this loss with genes encoding mevalonate pathway enzymes. LytB(-) Salmonella SL7207 had high HMBPP levels, infected human cells as efficiently as did the wild-type bacteria, and stimulated large ex vivo expansions of Vγ2Vδ2 T cells from human donors. Importantly, vaccination of a rhesus monkey with live lytB(-) Salmonella SL7207 stimulated a prolonged expansion of Vγ2Vδ2 T cells without significant side effects or anergy induction. These studies provide proof-of-principle that metabolic engineering can be used to derive live bacterial vaccines that boost Vγ2Vδ2 T cell immunity. Similar engineering of metabolic pathways to produce lipid Ags or B vitamin metabolite Ags could be used to derive live bacterial vaccine for other unconventional T cells that recognize nonpeptide Ags.
    The Journal of Immunology 06/2014; 193(2). DOI:10.4049/jimmunol.1302746 · 5.36 Impact Factor
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    ABSTRACT: A cyclolavandulyl group is a C10 monoterpene with a branched and cyclized carbon skeleton. This monoterpene is rarely found in nature, and its biosynthesis is poorly understood. To determine the biosynthesis mechanism of this monoterpene, we sequenced the genome of Streptomyces sp. CL190, which produces lavanducyanin, a phenazine with an N-linked cyclolavandulyl structure. Sequencing and homology searches identified one candidate gene product that consists of only a cis-isoprenyl diphosphate synthase domain. Disruption of the gene and biochemical analysis of the recombinant enzyme demonstrated that the enzyme synthesized a cyclolavandulyl diphosphate essential for the biosynthesis of lavanducyanin. This enzyme is an unprecedented terpene synthase that catalyzes both the condensation of the C5 isoprene units and subsequent cyclization to form the cyclolavandulyl monoterpene structure.
    Journal of the American Chemical Society 03/2014; 136(13). DOI:10.1021/ja500270m · 11.44 Impact Factor
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    ABSTRACT: Two new acyloin compounds were isolated from the thermophilic bacterium Thermosporothrix hazakensis SK20-1(T) . Genome sequencing of the bacterium and biochemical studies identified the thiamine diphosphate (TPP)-dependent enzyme Thzk0150, which is involved in the formation of acyloin. Through extensive analysis of the Thzk0150-catalyzed reaction products, we propose a putative reaction mechanism involving two substrates: 4-methyl-2-oxovalerate as an acyl donor and phenyl pyruvate as an acyl acceptor.
    ChemBioChem 03/2014; 15(4). DOI:10.1002/cbic.201300690 · 3.06 Impact Factor
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    Dataset: b817312e
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    ABSTRACT: The cytochrome P450 RauA from Rhodococcus erythropolis JCM 6824 catalyzes the hydroxylation of a nitrogen atom in the quinolone ring of aurachin, thereby conferring strong antibiotic activity on the aurachin alkaloid. Here, we report the crystal structure of RauA in complex with its substrate, a biosynthetic intermediate of aurachin RE. Clear electron density showed that the quinolone ring is oriented parallel to the porphyrin plane of the heme cofactor, while the farnesyl chain curls into a U-shape topology and is buried inside the solvent-inaccessible hydrophobic interior of RauA. The nearest atom from the heme iron is the quinolone nitrogen (4.3 Å), which is consistent with RauA catalyzing the N-hydroxylation of the quinolone ring to produce mature aurachin RE.
    FEBS letters 11/2013; 588(1). DOI:10.1016/j.febslet.2013.11.016 · 3.34 Impact Factor
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    ABSTRACT: Thermus thermophilus exhibits hypersensitivity to a lysine analog, (S)-2-aminoethyl-cysteine (AEC). Cosmid libraries were constructed using genomes from two AEC-resistant mutants, AT10 and AT14, and the cosmids that conferred AEC resistance on the wild-type strain were isolated. When the cosmid library for mutant AT14 was screened, two independent cosmids conferring AEC resistance to the wild type were obtained. Two cosmids carried a common genomic region from TTC0795 to TTC0810. This region contains genes encoding two different ATP-binding cassette (ABC) transporters: one consisting of TTC0806/TTC0795 and the other consisting of TTC0967/TTC0968/TTC0969/TTC0970 using TTC0807 and TTC0966 as the periplasmic substrate-binding protein, respectively. Sequencing revealed that AT14 carries mutations in TTC0795 and TTC0969, causing decreases in the thermostability of the products. By similar screening for cosmids constructed for the mutant AT10, mutations were found at TTC0807 and TTC0969. Mutation in either of the transporter components gave partial resistance to AEC in the wild-type strain, while mutations of both transporters conferred complete AEC resistance. This result indicates that both transporters are involved in AEC uptake in T. thermophilus. To elucidate the mechanism of AEC uptake, crystal structures of TTC0807 were determined in several substrate-binding forms. The structures revealed that TTC0807 recognizes various basic amino acids by changing the side-chain conformation of Glu19, which interacts with the side-chain amino groups of the substrates.
    Journal of bacteriology 06/2013; DOI:10.1128/JB.00202-13 · 2.69 Impact Factor
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    ABSTRACT: Aurachin RE is a prenylated quinoline antibiotic that was first isolated from the genus Rhodococcus. It shows potent antibacterial activity against a variety of Gram-positive bacteria. Here we have identified a minimal biosynthesis gene cluster for aurachin RE in Rhodococcus erythropolis JCM 6824 by using random transposon mutagenesis and heterologous production. The Rhodococcus aurachin (rau) gene cluster consists of genes encoding cytochrome P450 (rauA), prenyltransferase, polyketide synthase, and farnesyl pyrophosphate synthase, as well as others including genes involved in regulation and transport. Markerless gene disruption of rauA resulted in the complete loss of aurachin RE production and in the accumulation of a new aurachin derivative lacking the N-hydroxy group. When the recombinant RauA was expressed in Escherichia coli, it catalyzed N-hydroxylation of the derivative to form aurachin RE. This study establishes the biosynthetic pathway of aurachin RE and provides experimental evidence for the role of P450 RauA in catalyzing N-hydroxylation of the quinoline ring, which is indispensable for the antibacterial activity of aurachin RE.
    ChemBioChem 06/2013; 14(9). DOI:10.1002/cbic.201300167 · 3.06 Impact Factor
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    ABSTRACT: N-(2-Chlorobenzyl)-substituted hydroxamate, readily produced by hydrolysis of ketoclomazone, was identified as an inhibitor of 1-deoxy-d-xylulose 5-phosphate synthase (DXS), with an IC50 value of 1.0 μM. The compound inhibited the growth of Haemophilus influenzae. A convenient spectroscopic method for assaying DXS using NADPH-lactate dehydrogenase (LDH) is also reported.
    Chemical Communications 03/2013; DOI:10.1039/c3cc40758f · 6.72 Impact Factor
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    ABSTRACT: LysW has been identified as a carrier protein in the lysine biosynthetic pathway that is active through the conversion of α-aminoadipate (AAA) to lysine. In this study, we found that the hyperthermophilic archaeon, Sulfolobus acidocaldarius, not only biosynthesizes lysine through LysW-mediated protection of AAA but also uses LysW to protect the amino group of glutamate in arginine biosynthesis. In this archaeon, after LysW modification, AAA and glutamate are converted to lysine and ornithine, respectively, by a single set of enzymes with dual functions. The crystal structure of ArgX, the enzyme responsible for modification and protection of the amino moiety of glutamate with LysW, was determined in complex with LysW. Structural comparison and enzymatic characterization using Sulfolobus LysX, Sulfolobus ArgX and Thermus LysX identify the amino acid motif responsible for substrate discrimination between AAA and glutamate. Phylogenetic analysis reveals that gene duplication events at different stages of evolution led to ArgX and LysX.
    Nature Chemical Biology 02/2013; DOI:10.1038/nchembio.1200 · 13.22 Impact Factor
  • Taro Ozaki, Makoto Nishiyama, Tomohisa Kuzuyama
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    ABSTRACT: The characterization of potential gene clusters is a promising strategy for the identification of novel natural products and the expansion of structural diversity. However, there are often difficulties in identifying potential metabolites because their biosynthetic genes are either silenced or expressed only at a low level. Here, we report the identification of a novel metabolite that is synthesized by a potential gene cluster containing an indole prenyltransferase gene (SCO7467) and a flavin-dependent monooxygenase (FMO) gene (SCO7468), which were mined from the genome of Streptomyces coelicolor A3(2). We introduced these two genes into the closely related Streptomyces lividans TK23 and analyzed the culture broths of the transformants. This process allowed us to identify a novel metabolite, 5-dimethylallylindole-3-acetonitrile (5-DMAIAN) that was overproduced in the transformant. Biochemical characterization of the recombinant SCO7467 and SCO7468 demonstrated the novel L-tryptophan metabolism leading to 5-DMAIAN. SCO7467 catalyzes the prenylation of L-tryptophan to form 5-dimethylallyl-L-tryptophan (5-DMAT). This enzyme is the first actinomycetes prenyltransferase known to catalyze the addition of a dimethylallyl group to the C-5 of tryptophan. SCO7468 then catalyzes the conversion of 5-DMAT into 5-dimethylallylindole-3-acetaldoxime (5-DMAIAOx). An aldoxime forming reaction catalyzed by the FMO enzyme was also identified for the first time in this study. Finally, dehydration of 5-DMAIAOx presumably occurs to yield 5-DMAIAN. This study provides insight into the biosynthesis of prenylated indoles that have been purified from actinomycetes.
    Journal of Biological Chemistry 02/2013; 288(14). DOI:10.1074/jbc.M112.436451 · 4.60 Impact Factor

Publication Stats

4k Citations
515.93 Total Impact Points

Institutions

  • 1993–2015
    • The University of Tokyo
      • • Center for Biotechnology Research
      • • Institute of Molecular and Cellular Biosciences
      Tōkyō, Japan
  • 2012
    • University of Illinois, Urbana-Champaign
      • Department of Chemistry
      Urbana, Illinois, United States
  • 2011
    • Hokkaido University
      • School of Engineering
      Sapporo, Hokkaidō, Japan
    • Japan Women's University
      Edo, Tōkyō, Japan
  • 2009
    • Seoul National University
      • Research Institute for Agriculture and Life Science
      Seoul, Seoul, South Korea
  • 2006
    • RIKEN
      Вако, Saitama, Japan
    • Kyung Hee University
      Sŏul, Seoul, South Korea
  • 2005
    • Juntendo University
      Edo, Tōkyō, Japan
    • Salk Institute
      La Jolla, California, United States
  • 2000–2004
    • Toyama Prefectural University
      • Biotechnology Research Center
      Toyama-shi, Toyama-ken, Japan
  • 2001
    • Tokyo Institute of Technology
      • Chemistry Department
      Tokyo, Tokyo-to, Japan
  • 1998
    • Harvard Medical School
      Boston, Massachusetts, United States