PUBLICATION

2024

Yoshidome D, Hidaka M, Miyanaga T, Ito Y, Kosono S, Nishiyama M.
Glutamate production from aerial nitrogen using the nitrogen-fixing bacterium Klebsiella oxytoca.
Commun Biol. 2024 Apr 11;7(1):443. doi: 10.1038/s42003-024-06147-z.

2023

Hibi G, Shiraishi T, Umemura T, Nemoto K, Ogura Y, Nishiyama M, Kuzuyama T.
Discovery of type II polyketide synthase-like enzymes for the biosynthesis of cispentacin.
Nat Commun. 2023 Dec 6;14(1):8065. doi: 10.1038/s41467-023-43731-z.
Morita Y, Yoshida A, Ye S, Tomita T, Yoshida M, Kosono S, Nishiyama M.
Protein-protein interaction-mediated regulation of lysine biosynthesis of Thermus thermophilus through the function-unknown protein LysV.
J Gen Appl Microbiol. 2023 Nov 15;69(2):91-101. doi: 10.2323/jgam.2023.06.003.
Kawai G, Sampei GI, Nishiyama M, Bessho Y.
Non-coding RNAs and functional RNA elements in Thermus thermophilus.
J Gen Appl Microbiol. 2023 Nov 15;69(2):131-134. doi: 10.2323/jgam.2023.05.001.
Nagata R, Nishiyama M, Kuzuyama T.
Substrate Recognition Mechanism of a Trichostatin A-Forming Hydroxyamidotransferase.
Biochemistry. 2023 Jun 20;62(12):1833-1837. doi: 10.1021/acs.biochem.3c00025.
Katoh T, Yamada C, Wallace MD, Yoshida A, Gotoh A, Arai M, Maeshibu T, Kashima T, Hagenbeek A, Ojima MN, Takada H, Sakanaka M, Shimizu H, Nishiyama K, Ashida H, Hirose J, Suarez-Diez M, Nishiyama M, Kimura I, Stubbs KA, Fushinobu S, Katayama T.
A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem.
Nat Chem Biol. 2023 Jun;19(6):778-789. doi: 10.1038/s41589-023-01272-y.
Kurosawa S, Okamura H, Yoshida A, Tomita T, Sone Y, Hasebe F, Shinada T, Takikawa H, Kosono S, Nishiyama M.
Mechanisms of Sugar Aminotransferase-like Enzymes to Synthesize Stereoisomers of Non-proteinogenic Amino Acids in Natural Product Biosynthesis.
ACS Chem Biol. 2023 Feb 17;18(2):385-395. doi: 10.1021/acschembio.2c00823.

2022

Zhu Y, Shiraishi T, Lin J, Inaba K, Ito A, Ogura Y, Nishiyama M, Kuzuyama T.
Complete Biosynthetic Pathway of the Phosphonate Phosphonothrixin: Two Distinct Thiamine Diphosphate-Dependent Enzymes Divide the Work to Form a C-C Bond.
J Am Chem Soc. 2022 Sep 21;144(37):16715-16719. doi: 10.1021/jacs.2c06546.
Kurosawa S, Hasebe F, Okamura H, Yoshida A, Matsuda K, Sone Y, Tomita T, Shinada T, Takikawa H, Kuzuyama T, Kosono S, Nishiyama M.
Molecular Basis for Enzymatic Aziridine Formation via Sulfate Elimination.
J Am Chem Soc. 2022 Sep 7;144(35):16164-16170. doi: 10.1021/jacs.2c07243.
Matsuda K, Arima K, Akiyama S, Yamada Y, Abe Y, Suenaga H, Hashimoto J, Shin-Ya K, Nishiyama M, Wakimoto T.
A Natural Dihydropyridazinone Scaffold Generated from a Unique Substrate for a Hydrazine-Forming Enzyme.
J Am Chem Soc. 2022 Jul 20;144(28):12954-12960. doi: 10.1021/jacs.2c05269.
Noguchi T, Isogai S, Terada T, Nishiyama M, Kuzuyama T.
Cryptic Oxidative Transamination of Hydroxynaphthoquinone in Natural Product Biosynthesis.
J Am Chem Soc. 2022 Mar 30;144(12):5435-5440. doi: 10.1021/jacs.1c13074.
Nagata R, Suemune H, Kobayashi M, Shinada T, Shin-Ya K, Nishiyama M, Hino T, Sato Y, Kuzuyama T, Nagano S.
Structural Basis for the Prenylation Reaction of Carbazole-Containing Natural Products Catalyzed by Squalene Synthase-Like Enzymes.
Angew Chem Int Ed Engl. 2022 May 9;61(20):e202117430. doi: 10.1002/anie.202117430.
Shimizu K, Suzuki H, Uemura T, Nozawa A, Desaki Y, Hoshino R, Yoshida A, Abe H, Nishiyama M, Nishiyama C, Sawasaki T, Arimura GI.
Immune gene activation by NPR and TGA transcriptional regulators in the model monocot Brachypodium distachyon.
Plant J. 2022 Apr;110(2):470-481. doi: 10.1111/tpj.15681.

2021

Fukase S, Ando T, Matsuzawa M, Kimura M, Sone Y, Izawa K, Kaitani A, Kamei A, Kojima M, Nakano N, Maeda K, Shimizu T, Ogawa H, Okumura K, Nishiyama M, Murakami A, Ebihara N, Kitaura J.
Pollen shells and soluble factors play non-redundant roles in the development of allergic conjunctivitis in mice.
Ocul Surf. 2021 Oct;22:152-162. doi: 10.1016/j.jtos.2021.08.009.
Komine-Abe A, Kondo N, Kubo S, Kawasaki H, Nishiyama M, Kosono S.
Characterization of lysine acetylation in the peripheral subunit-binding domain of the E2 subunit of the pyruvate dehydrogenase-2-oxoglutarate dehydrogenase hybrid complex from Corynebacterium glutamicum.
Biosci Biotechnol Biochem. 2021 Mar 24;85(4):874-881. doi: 10.1093/bbb/zbaa114.
Zhang J, Yuzawa S, Thong WL, Shinada T, Nishiyama M, Kuzuyama T.
Reconstitution of a Highly Reducing Type II PKS System Reveals 6π-Electrocyclization Is Required for o-Dialkylbenzene Biosynthesis.
J Am Chem Soc. 2021 Feb 24;143(7):2962-2969. doi: 10.1021/jacs.0c13378.
Hashimoto T, Hashimoto J, Kagaya N, Nishimura T, Suenaga H, Nishiyama M, Kuzuyama T, Shin-Ya K.
A novel oxazole-containing tetraene compound, JBIR-159, produced by heterologous expression of the cryptic trans-AT type polyketide synthase biosynthetic gene cluster.
J Antibiot (Tokyo). 2021 May;74(5):354-358. doi: 10.1038/s41429-021-00410-9.
Suzuki T, Tomita T, Hirayama K, Suzuki M, Kuzuyama T, Nishiyama M.
Involvement of subdomain II in the recognition of acetyl-CoA revealed by the crystal structure of homocitrate synthase from Sulfolobus acidocaldarius.
FEBS J. 2021 Mar;288(6):1975-1988. doi: 10.1111/febs.15527.

2020

Kinugawa H, Kondo N, Komine-Abe A, Tomita T, Nishiyama M, Kosono S.
In vitro reconstitution and characterization of pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase hybrid complex from Corynebacterium glutamicum.
Microbiologyopen. 2020 Aug 30:e1113. doi: 10.1002/mbo3.1113.
Kurosawa S, Matsuda K, Hasebe F, Shiraishi T, Shin-Ya K, Kuzuyama T, Nishiyama M.
Guanidyl modification of the 1-azabicyclo[3.1.0]hexane ring in ficellomycin essential for its biological activity.
Org Biomol Chem. 2020 Jun 25. doi: 10.1039/d0ob00339e.
Uemura T, Hachisu M, Desaki Y, Ito A, Hoshino R, Sano Y, Nozawa A, Mujiono K, Galis I, Yoshida A, Nemoto K, Miura S, Nishiyama M, Nishiyama C, Horito S, Sawasaki T, Arimura GI.
Soy and Arabidopsis receptor-like kinases respond to polysaccharide signals from Spodoptera species and mediate herbivore resistance.
Commun Biol. 2020 May 8;3(1):224. doi: 10.1038/s42003-020-0959-4.
Sakaki K, Ohishi K, Shimizu T, Kobayashi I, Mori N, Matsuda K, Tomita T, Watanabe H, Tanaka K, Kuzuyama T, Nishiyama M.
A suicide enzyme catalyzes multiple reactions for biotin biosynthesis in cyanobacteria.
Nat Chem Biol. 2020 Apr;16(4):415-422. doi: 10.1038/s41589-019-0461-9.

2019

Murai K, Lauterbach L, Teramoto K, Quan Z, Barra L, Yamamoto T, Nonaka K, Shiomi K, Nishiyama M, Kuzuyama T, Dickschat JS.
An Unusual Skeletal Rearrangement in the Biosynthesis of the Sesquiterpene Trichobrasilenol from Trichoderma.
Angew Chem Int Ed Engl. 2019 Oct 14;58(42):15046-15050. doi: 10.1002/anie.201907964.
Kobayashi M, Tomita T, Shin-Ya K, Nishiyama M, Kuzuyama T.
An Unprecedented Cyclization Mechanism in the Biosynthesis of Carbazole Alkaloids in Streptomyces.
Angew Chem Int Ed Engl. 2019 Sep 16;58(38):13349-13353. doi: 10.1002/anie.201906864.
Suzuki T, Akiyama N, Yoshida A, Tomita T, Lassak K, Haurat MF, Okada T, Takahashi K, Albers SV, Kuzuyama T, Nishiyama M.
Biochemical characterization of archaeal homocitrate synthase from Sulfolobus acidocaldarius.
FEBS Lett. 2019 Jul 22. doi: 10.1002/1873-3468.13550.
Kudo K, Koiwai H, Kagaya N, Nishiyama M, Kuzuyama T, Shin-Ya K, Ikeda H.
Comprehensive Derivatization of Thioviridamides by Heterologous Expression.
ACS Chem Biol. 2019 Jun 11. doi: 10.1021/acschembio.9b00330.
Romo AJ, Shiraishi T, Ikeuchi H, Lin GM, Geng Y, Lee YH, Liem PH, Ma T, Ogasawara Y, Shin-Ya K, Nishiyama M, Kuzuyama T, Liu HW.
The Amipurimycin and Miharamycin Biosynthetic Gene Clusters: Unraveling the Origins of 2-Aminopurinyl Peptidyl Nucleoside Antibiotics.
J Am Chem Soc. 2019 May 31. doi: 10.1021/jacs.9b03021.
Tomita T, Matsushita H, Yoshida A, Kosono S, Yoshida M, Kuzuyama T, Nishiyama M.
Glutamate dehydrogenase from Thermus thermophilus is activated by AMP and leucine as a complex with catalytically inactive adenine phosphoribosyltransferase homolog.
J Bacteriol. 2019 Apr 29. pii: JB.00710-18. doi: 10.1128/JB.00710-18.
Yoshida A, Yoshida M, Kuzuyama T, Nishiyama M, Kosono S.
Protein acetylation on 2-isopropylmalate synthase from Thermus thermophilus HB27.
Extremophiles. 2019 Jul;23(4):377-388. doi: 10.1007/s00792-019-01090-y.
Yashiro T, Sakata F, Sekimoto T, Shirai T, Hasebe F, Matsuda K, Kurosawa S, Suzuki S, Nagata K, Kasakura K, Nishiyama M, Nishiyama C.
Immunosuppressive Effect of a Non-Proteinogenic Amino Acid From Streptomyces Through Inhibiting Allogeneic T Cell Proliferation.
Biosci Biotechnol Biochem. 2019 Jun;83(6):1111-1116. doi: 10.1080/09168451.2019.1591262.
Shiraishi T, Nishiyama M, Kuzuyama T.
Biosynthesis of the uridine-derived nucleoside antibiotic A-94964: identification and characterization of the biosynthetic gene cluster provide insight into the biosynthetic pathway.
Org Biomol Chem. 2019 Jan 16;17(3):461-466. doi: 10.1039/c8ob02765j.
Chiba Y, Yoshida A, Shimamura S, Kameya M, Tomita T, Nishiyama M, Takai K.
Discovery and analysis of a novel type of the serine biosynthetic enzyme phosphoserine phosphatase in Thermus thermophilus.
FEBS J. 2019 Feb;286(4):726-736. doi: 10.1111/febs.14703.
Suzuki S, Kondo N, Yoshida M, Nishiyama M, Kosono S.
Dynamic changes in the acetylation and succinylation of the elongation factor Tu from Bacillus subtilis are dependent on the growth phase and nutrient conditions.
Microbiology. 2019 Jan 1;165(1):65-77. doi: 10.1099/mic.0.000737

2018

Umehara T, Kosono S, Söll D, Tamura K.
Lysine Acetylation Regulates Alanyl-tRNA Synthetase Activity in Escherichia coli.
Genes (Basel). 2018 Sep 28;9(10):473. doi: 10.3390/genes9100473.
Thong WL, Shin-ya K, Nishiyama M, Kuzuyama T.
Discovery of an antibacterial isoindolinone-containing tetracyclic polyketide by cryptic gene activation and characterization of its biosynthetic gene cluster.
ACS Chem Biol. 2018 Sep 21;13(9):2615-2622. doi: 10.1021/acschembio.8b00553.
Matsuda K, Tomita T, Shin-ya K, Wakimoto T, Kuzuyama T, Nishiyama M.
Discovery of unprecedented hydrazine-forming machinery in bacteria.
J Am Chem Soc. 2018 Jul 25;140(29):9083-9086. doi: 10.1021/jacs.8b05354.
Yoshida A, Kosono S, Nishiyama M.
Characterization of two 2-isopropylmalate synthase homologs from Thermus thermophilus HB27.
Biochem Biophys Res Commun. 2018 Jun 22;501(2):465-470. doi: 10.1016/j.bbrc.2018.05.013.
Vasileva D, Suzuki-Minakuchi C, Kosono S, Yoshida M, Okada K, Nojiri H.
Proteome and acylome analyses of the functional interaction network between the carbazole-degradative plasmid pCAR1 and host Pseudomonas putida KT2440.
Environ Microbiol Rep. 2018 Jun;10(3):299-309. doi: 10.1111/1758-2229.12639.
Zheng RC, Hachisuka SI, Tomita H, Imanaka T, Zheng YG, Nishiyama M, Atomi H.
An ornithine ω-aminotransferase required for growth in the absence of exogenous proline in the archaeon Thermococcus kodakarensis.
J Biol Chem. 2018 Mar 9;293(10):3625-3636. doi: 10.1074/jbc.RA117.001222.
Hossain TJ, Manabe S, Ito Y, Iida T, Kosono S, Ueda K, Hosomi A, Inoue D, Suzuki T.
Enrichment and characterization of a bacterial mixture capable of utilizing C-mannosyl tryptophan as a carbon source.
Glycoconj J. 2018 Apr;35(2):165-176. doi: 10.1007/s10719-017-9807-2.

2017

Tomita T, Kobayashi M, Karita Y, Yasuno Y, Shinada T, Nishiyama M, Kuzuyama T.
Structure and Mechanism of the Monoterpene Cyclolavandulyl Diphosphate Synthase that Catalyzes Consecutive Condensation and Cyclization.
Angew Chem Int Ed. 2017. Nov 20;56(47):14913-14917. doi: 10.1002/anie.201708474.
Komine-Abe A, Nagano-Shoji M, Kubo S, Kawasaki H, Yoshida M, Nishiyama M, Kosono S.
Effect of lysine succinylation on the regulation of 2-oxoglutarate dehydrogenase inhibitor, OdhI, involved in glutamate production in Corynebacterium glutamicum.
Biosci Biotechnol Biochem. 2017 Nov;81(11):2130-2138. doi: 10.1080/09168451.2017.1372182.
Cho SH, Kim SY, Tomita T, Shiraishi T, Park JS, Sato S, Kudo F, Eguchi T, Funa N, Nishiyama M, Kuzuyama T.
Fosfomycin Biosynthesis via Transient Cytidylylation of 2-Hydroxyethylphosphonate by the Bifunctional Fom1 Enzyme.
ACS Chem Biol. 2017. Aug 18;12(8):2209-2215. doi: 10.1021/acschembio.7b00419.
Fujita S, Cho SH, Yoshida A, Hasebe F, Tomita T, Kuzuyama T, Nishiyama M.
Crystal structure of LysK, an enzyme catalyzing the last step of lysine biosynthesis in Thermus thermophilus, in complex with lysine: Insight into the mechanism for recognition of the amino-group carrier protein, LysW.
Biochem Biophys Res Commun. 2017. Sep 16;491(2):409-415. doi: 10.1016/j.bbrc.2017.07.088.
Kudo K, Ozaki T, Shin-ya K, Nishiyama M, Kuzuyama T.
Biosynthetic Origin of the Hydroxamic Acid Moiety of Trichostatin A: Identification of Unprecedented Enzymatic Machinery Involved in Hydroxylamine Transfer.
J Am Chem Soc. 2017. May 24;139(20):6799-6802. doi: 10.1021/jacs.7b02071.
Yoshida M, Kudo N, Kosono S, Ito A. Chemical and structural biology of protein lysine deacetylases.
Proc Jpn Acad Ser B Phys Biol Sci. 2017;93(5):297-321. doi: 10.2183/pjab.93.019.
Tomita T, Yin L, Nakamura S, Kosono S, Kuzuyama T, Nishiyama M.
Crystal structure of the 2-iminoglutarate-bound complex of glutamate dehydrogenase from Corynebacterium glutamicum.
FEBS Lett. 2017. Jun;591(11):1611-1622. doi: 10.1002/1873-3468.12667.
Tomita T, Kim SY, Teramoto K, Meguro A, Ozaki T, Yoshida A, Motoyoshi Y, Mori N, Ishigami K, Watanabe H, Nishiyama M, Kuzuyama T.
Structural Insights into the CotB2-Catalyzed Cyclization of Geranylgeranyl Diphosphate to the Diterpene Cyclooctat-9-en-7-ol.
ACS Chem Biol. 2017. Jun 16;12(6):1621-1628. doi: 10.1021/acschembio.7b00154.
Yashiro T, Kasakura K, Oda Y, Kitamura N, Inoue A, Nakamura S, Yokoyama H, Fukuyama K, Hara M, Ogawa H, Okumura K, Nishiyama M, Nishiyama C.
The hematopoietic cell-specific transcription factor PU.1 is critical for expression of CD11c.
Int Immunol. 2017 Feb 1;29(2):87-94. doi: 10.1093/intimm/dxx009.
Nara A, Hashimoto T, Komatsu M, Nishiyama M, Kuzuyama T, Ikeda H.
Characterization of bafilomycin biosynthesis in Kitasatospora setae KM-6054 and comparative analysis of gene clusters in Actinomycetales microorganisms.
J Antibiot. 2017. May;70(5):616-624. doi: 10.1038/ja.2017.33.
Nagano-Shoji M, Hamamoto Y, Mizuno Y, Yamada A, Kikuchi M, Shirouzu M, Umehara T, Yoshida M, Nishiyama M, Kosono S.
Characterization of lysine acetylation of a phosphoenolpyruvate carboxylase involved in glutamate overproduction in Corynebacterium glutamicum.
Mol Microbiol. 2017 May;104(4):677-689. doi: 10.1111/mmi.13658.
Matsuda K, Hasebe F, Shiwa Y, Kanesaki Y, Tomita T, Yoshikawa H, Shin-ya K, Kuzuyama T, Nishiyama M.
Genome Mining of Amino Group Carrier Protein-Mediated Machinery: Discovery and Biosynthetic Characterization of a Natural Product with Unique Hydrazone Unit.
ACS Chem Biol. 2017. Jan 20;12(1):124-131. doi: 10.1021/acschembio.6b00818.
Ishigaki Y, Akanuma G, Yoshida M, Horinouchi S, Kosono S, Ohnishi Y.
Protein acetylation involved in streptomycin biosynthesis in Streptomyces griseus.
J Proteomics. 2017 Feb 23;155:63-72. doi: 10.1016/j.jprot.2016.12.006.
Shimizu T, Yin L, Yoshida A, Yokooji Y, Hachisuka SI, Sato T, Tomita T, Nishida H, Atomi H, Kuzuyama T, Nishiyama M.
Structure and function of an ancestral-type β-decarboxylating dehydrogenase from Thermococcus kodakarensis.
Biochem J. 2017. Jan 1;474(1):105-122. doi: 10.1042/BCJ20160699.
Kubota T, Matsushita H, Tomita T, Kosono S, Yoshida M, Kuzuyama T, Nishiyama M.
Novel stand-alone RAM domain protein-mediated catalytic control of anthranilate phosphoribosyltransferase in tryptophan biosynthesis in Thermus thermophilus.
Extremophiles. 2017. Jan;21(1):73-83. doi: 10.1007/s00792-016-0884-0.

2016

Hasebe F, Matsuda K, Shiraishi T, Futamura Y, Nakano T, Tomita T, Ishigami K, Taka H, Mineki R, Fujimura T, Osada H, Kuzuyama T & Nishiyama M. Amino-group carrier-protein-mediated secondary metabolite biosynthesis in Streptomyces. 2016. Nat Chem Biol. 12:967-972.
Takahashi K, Nakanishi F, Tomita T, Akiyama N, Lassak K, Albers SV, Kuzuyama T, Nishiyama M. Characterization of two β-decarboxylating dehydrogenases from Sulfolobus acidocaldarius. 2016. Extremophiles. 20(6):843-853.
Hashimoto T, Kuzuyama T. Mechanistic insights into Diels-Alder reactions in natural product biosynthesis. 2016. Curr Opin Chem Biol. 35:117-123.
Takahashi K, Tomita T, Kuzuyama T, Nishiyama M. Determinants of dual substrate specificity revealed by the crystal structure of homoisocitrate dehydrogenase from Thermus thermophilus in complex with homoisocitrate・Mg(2+)・NADH. 2016. Biochem Biophys Res Commun. 478(4):1688-93.
Yoshida A, Tomita T, Atomi H, Kuzuyama T, Nishiyama M. Lysine Biosynthesis of Thermococcus kodakarensis with the Capacity to Function as an Ornithine Biosynthetic System. 2016. J Biol Chem. 291(41):21630-21643.
Inahashi Y, Shiraishi T, Palm K, Takahashi Y, Omura S, Kuzuyama T, Nakashima T. Biosynthesis of Trehangelin in Polymorphospora rubra K07-0510: Identification of Metabolic Pathway to Angelyl-CoA. 2016. Chembiochem. 17(15):1442-7.
Shiraishi T, Hiro N, Igarashi M, Nishiyama M, Kuzuyama T. Biosynthesis of the antituberculous agent caprazamycin: Identification of caprazol-3"-phosphate, an unprecedented caprazamycin-related metabolite. 2016. J Gen Appl Microbiol. 62(3):164-6.
Shimizu T, Tomita T, Kuzuyama T, Nishiyama M. Crystal Structure of the LysY・LysW Complex from Thermus thermophilus. 2016. J Biol Chem. 291(19):9948-59.
Thong WL, Shin-ya K, Nishiyama M, Kuzuyama T. Methylbenzene-Containing Polyketides from a Streptomyces that Spontaneously Acquired Rifampicin Resistance: Structural Elucidation and Biosynthesis. 2016. J Nat Prod. 79(4):857-64.
Tanaka N, Kanazawa M, Tonosaki K, Yokoyama N, Kuzuyama T, Takahashi Y. Novel features of the ISC machinery revealed by characterization of Escherichia coli mutants that survive without iron-sulfur clusters. 2016. Mol Microbiol. 99(5):835-48.

2015

Medema MH et al. Minimum Information about a Biosynthetic Gene cluster. 2015. Nat Chem Biol 11(9):625-31.
Sato H, Teramoto K, Masumoto Y, Tezuka N, Sakai K, Ueda S, Totsuka Y, Shinada T, Nishiyama M, Wang C, Kuzuyama T, Uchiyama M. "Cation-Stitching Cascade": exquisite control of terpene cyclization in cyclooctatin biosynthesis. 2015. Sci Rep 5:18471.
Ye Y, Minami A, Mandi A, Liu C, Taniguchi T, Kuzuyama T, Monde K, Gomi K, Oikawa H. Genome Mining for Sesterterpenes Using Bifunctional Terpene Synthases Reveals a Unified Intermediate of Di/Sesterterpenes. 2015. J Am Chem Soc 137(36):11846-53.
Meguro, A., Motoyoshi, Y., Teramoto, K., Ueda, S., Totsuka, Y., Ando, Y., Tomita, T., Kim, S.Y., Kimura, T., Igarashi, M., Sawa, R., Shinada, T., Nishiyama, M., Kuzuyama, T. An unusual terpene cyclization mechanism involving a carbon-carbon bond rearrangement. 2015. Angew. Chem. Int. Ed. Engl. 27;54(14):4353-6.
Totsuka, Y., Ueda, S., Kuzuyama, T., Shinada, T. Facile Synthesis of Deuterium-labelled Geranylgeraniols. 2015. Bull. Chem. Soc. Jpn. 88, 575-7.
Hashimoto, T., Hashimoto, J., Teruya, K., Hirano, T., Shin-ya, K., Ikeda, H., Liu, H.W., Nishiyama, M., Kuzuyama, T. Biosynthesis of versipelostatin: identification of an enzyme-catalyzed [4+2]-cycloaddition required for macrocyclization of spirotetronate-containing polyketides. 2015. J. Am. Chem. Soc. 137(2):572-5.
Yamada, Y., Kuzuyama, T., Komatsu, M., Shin-Ya, K., Omura, S., Cane, D.E., Ikeda, H. Terpene synthases are widely distributed in bacteria. 2015. Proc. Natl. Acad. Sci. U. S. A. 112(3):857-62.
Yoshida, A., Tomita, T., Fujimura, T., Nishiyama, C., Kuzuyama, T., Nishiyama, M. Structural insight into amino group-carrier protein-mediated lysine biosynthesis: crystal structure of the LysZ・LysW complex from Thermus thermophilus. 2015. J. Biol. Chem. 290(1):435-47.

2014

Lin J, Nishiyama M, Kuzuyama T. Identification of the biosynthetic gene cluster for the herbicide phosphonothrixin in Saccharothrix sp. ST-888. 2014. J Antibiot. doi: 10.1038/ja.2014.149.
Tomita T, Ozaki T, Matsuda K, Nishiyama M, Kuzuyama T. Crystallization and preliminary X-ray diffraction analysis of cyclolavandulyl diphosphate synthase, a new member of the cis-isoprenyl diphosphate synthase superfamily. 2014. Acta Crystallogr F Struct Biol Commun. 70(Pt 10):1410-3.
Iwanaga N, Ide K, Nagashima T, Tomita T, Agari Y, Shinkai A, Kuramitsu S, Okada-Hatakeyema M, Kuzuyama T, Nishiyama M. Genome-wide comprehensive analysis of transcriptional regulation by ArgR in Thermus thermophilus. 2014. Extremophiles. 18(6):995-1008.
Park JS, Yabe S, Shin-Ya K, Nishiyama M, Kuzuyama T. New 2-(1'H-indole-3'-carbonyl)-thiazoles derived from the thermophilic bacterium Thermosporothrix hazakensis SK20-1^T. 2014. J Antibiot. doi: 10.1038/ja.2014.93.
Workalemahu G, Wang H, Puan KJ, Nada MH, Kuzuyama T, Jones BD, Jin C, Morita CT. 2014. Metabolic engineering of Salmonella vaccine bacteria to boost human Vγ2Vδ2 T cell immunity. J Immunol. 193(2):708-21.
Ozaki T, Zhao P, Shinada T, Nishiyama M, Kuzuyama T. 2014. Cyclolavandulyl skeleton biosynthesis via both condensation and cyclization catalyzed by an unprecedented member of the cis-isoprenyl diphosphate synthase superfamily. J Am Chem Soc. 136(13):4837-40.
Park JS, Kagaya N, Hashimoto J, Izumikawa M, Yabe S, Shin-Ya K, Nishiyama M, Kuzuyama T. 2014. Identification and Biosynthesis of New Acyloins from the Thermophilic Bacterium Thermosporothrix hazakensis SK20-1^T. Chembiochem. 15(4):527-32.

2013

Yasutake Y, Kitagawa W, Hata M, Nishioka T, Ozaki T, Nishiyama M, Kuzuyama T, Tamura T. 2013. Structure of the quinoline N-hydroxylating cytochrome P450 RauA, an essential enzyme that confers antibiotic activity on aurachin alkaloids. FEBS lett. 588(1):105-10.
Kanemaru Y, Hasebe F, Tomita T, Kuzuyama T, Nishiyama M. 2013. Two ATP-binding cassette transporters involved in (S)-2-aminoethyl-cysteine uptake in thermus thermophilus. J. Bacteriol. 195(17):3845-53.
Kitagawa W, Ozaki T, Nishioka T, Yasutake Y, Hata M, Nishiyama M, Kuzuyama T, Tamura T. 2013. Cloning and heterologous expression of the aurachin RE biosynthesis gene cluster afford a new cytochrome P450 for quinoline N-hydroxylation. Chembiochem 14(9):1085-93.
Hayashi D, Kato N, Kuzuyama T, Sato Y, Ohkanda J. 2013. Antimicrobial N-(2-chlorobenzyl)-substituted hydroxamate is an inhibitor of 1-deoxy-D-xylulose 5-phosphate synthase. Chem Commun. 49(49):5535-7.
Ouchi T, Tomita T, Horie A, Yoshida A, Takahashi K, Nishida H, Lassak K, Taka H, Mineki R, Fujimura T, Kosono S, Nishiyama C, Masui R, Kuramitsu S, Albers SV, Kuzuyama T, Nishiyama M. 2013. Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus. Nat Chem Biol. 9(4):277-83.
Ozaki T, Nishiyama M, Kuzuyama T. 2013. Novel Tryptophan Metabolism by a Potential Gene Cluster That Is Widely Distributed among Actinomycetes. J. Biol Chem 288(14):9946-56.
Meguro A, Tomita T, Nishiyama M, Kuzuyama T. 2013. Identification and characterization of bacterial diterpene cyclases that synthesize the cembrane skeleton. Chembiochem. 14(3):316-21.

2012

Isogai S, Nishiyama M, Kuzuyama T. 2012. Identification of 8-amino-2,5,7-trihydroxynaphthalene-1,4-dione, a novel intermediate in the biosynthesis of Streptomyces meroterpenoids. Bioorg Med Chem Lett. 22:5823-6.
Kim SY, Ju KS, Metcalf WW, Evans BS, Kuzuyama T, van der Donk WA. 2012. Different biosynthetic pathways to fosfomycin in Pseudomonas syringae and Streptomyces species. Antimicrob Agents Chemother.56:4175-83.
Kuzuyama T, Seto H. 2012. Two distinct pathways for essential metabolic precursors for isoprenoid biosynthesis. Proc Jpn Acad Ser B Phys Biol Sci. 88:41-52.
Matsushima D, Jenke-Kodama H, Sato Y, Fukunaga Y, Sumimoto K, Kuzuyama T, Matsunaga S, Okada S. 2012. The single cellular green microalga Botryococcus braunii, race B possesses three distinct 1-deoxy-D-xylulose 5-phosphate synthases. Plant Sci. 185-186:309-20.

2011

Tomita T, Kuzuyama T, Nishiyama M. 2011. Structural basis for leucine-induced allosteric activation of glutamate dehydrogenase. J Biol Chem. 286:37406-37413.
Sugiyama A, Linley PJ, Sasaki K, Kumano T, Yamamoto H, Shitan N, Ohara K, Takanashi K, Harada E, Hasegawa H, Terakawa T, Kuzuyama T, Yazaki K. 2011. Metabolic engineering for the production of prenylated polyphenols in transgenic legume plants using bacterial and plant prenyltransferases.Metab Eng. 13:629-637.
Dairi T, Kuzuyama T, Nishiyama M, Fujii I. 2011. Convergent strategies in biosynthesis. Nat Prod Rep. 28:1054-1086.
Shindo K, Tachibana A, Tanaka A, Toba S, Yuki E, Ozaki T, Kumano T, Nishiyama M, Misawa N, Kuzuyama T. 2011. Production of novel antioxidative prenyl naphthalen-ols by combinational bioconversion with dioxygenase PhnA1A2A3A4 and prenyltransferase NphB or SCO7190. Biosci Biotechnol Biochem.75: 505-510.
Koeduka, T., N. Shitan, T. Kumano, K. Sasaki, A. Sugiyama, P. Linley, T. Kawasaki, H. Ezura, T. Kuzuyama, and K. Yazaki. 2011. Production of prenylated flavonoids in tomato fruits expressing a prenyltransferase gene from Streptomyces coelicolor A3(2). Plant Biol. 13:411-415.
Matsumoto K, Yamada M, Leong CR, Jo SJ, Kuzuyama T, Taguchi S. 2011. A new pathway for poly(3-hydroxybutyrate) production in Escherichia coli and Corynebacterium glutamicum by functional expression of a new acetoacetyl-coenzyme A synthase. Biosci Biotechnol Biochem. 75:364-6.

2010

Ichikawa, N., A. Oguchi, H. Ikeda, J. Ishikawa, S. Kitani, Y. Watanabe, S. Nakamura, Y. Katano, E. Kishi, M. Sasagawa, A. Ankai, S. Fukui, Y. Hashimoto, S. Kamata, M. Otoguro, S. Tanikawa, T. Nihira, S. Horinouchi, Y. Ohnishi, M. Hayakawa, T. Kuzuyama, A. Arisawa, F. Nomoto, H. Miura, Y. Takahashi, and N. Fujita. 2010. Genome sequence of Kitasatospora setae NBRC 14216T: an evolutionary snapshot of the family Streptomycetaceae. DNA Res. 17:393-406.
Kumano, T., T. Tomita, M. Nishiyama, and T. Kuzuyama. 2010. Functional characterization of the promiscuous prenyltransferase responsible for furaquinocin biosynthesis: identification of a physiological polyketide substrate and its prenylated reaction products. J. Biol. Chem. 285: 39663-39671.
Matsue, Y., H. Mizuno, T. Tomita, T. Asami, M. Nishiyama, and T. Kuzuyama. 2010. The herbicide ketoclomazone inhibits 1-deoxy-D-xylulose 5-phosphate synthase in the 2-C-methyl-D-erythritol 4-phosphate pathway and shows antibacterial activity against Haemophilus influenzae. J. Antibiot. 63: 583-588.
Miyakoshi, S., S. Azami, and T. Kuzuyama. 2010. Microbial glucosylation of flavonols by Cunninghamella echinulata. J. Biosci. Bioeng. 110: 320-321.
Okada, T., T. Tomita, A. P. Wulandari, T. Kuzuyama, and M. Nishiyama. 2010. Mechanism of substrate recognition and insight into feedback inhibition of homocitrate synthase from Thermus thermophilus. J. Biol. Chem. 285: 4195-4205.
Suzuki, Y., K. Asada, J. Miyazaki, T. Tomita, T. Kuzuyama, and M. Nishiyama. 2010. Enhancement of the latent 3-isopropylmalate dehydrogenase activity of promiscuous homoisocitrate dehydrogenase by directed evolution. Biochem. J. 431:401-410.
Tomita, T., T. Miyazaki, J. Miyazaki, T. Kuzuyama, and M. Nishiyama. 2010. Hetero-oligomeric glutamate dehydrogenase from Thermus thermophilus. Microbiology 156:3801-13.
Yoshida, A., T. Tomita, T. Kuzuyama, and M. Nishiyama. 2010. Mechanism of concerted inhibition of alpha2beta2-type hetero-oligomeric aspartate kinase from Corynebacterium glutamicum. J. Biol. Chem. 285:27477-27486.
Okamura E, Tomita T, Sawa R, Nishiyama M, and Kuzuyama T. 2010. Unprecedented acetoacetyl-coenzyme A synthesizing enzyme of the thiolase superfamily involved in the mevalonate pathway. Proc. Natl. Acad. Sci. USA 107: 11265-11270.

2009

Xiao Y, Machacek M, Lee K, Kuzuyama T, Liu P. 2009. Prenyltransferase substrate binding pocket flexibility and its application in isoprenoid profiling. Mol Biosyst. 5: 913-917.
Kim SY, Zhao P, Igarashi M, Sawa R, Tomita T, Nishiyama M, Kuzuyama T. 2009. Cloning and heterologous expression of the cyclooctatin biosynthetic gene cluster afford a diterpene cyclase and two P450 hydroxylases. Chem Biol. 16: 736-743.
Ouchi T, Tomita T, Miyagawa T, Kuzuyama T, Nishiyama M. 2009. Dual roles of a conserved pair, Arg23 and Ser20, in recognition of multiple substrates in alpha-aminoadipate aminotransferase from Thermus thermophilus. Biochem Biophys Res Commun. 388: 21-27.
Horie A, Tomita T, Saiki A, Kono H, Taka H, Mineki R, Fujimura T, Nishiyama C, Kuzuyama T, Nishiyama M. 2009. Discovery of proteinaceous N-modification in lysine biosynthesis of Thermus thermophilus. Nat Chem Biol. 5: 673-679.
Ozaki T, Mishima S, Nishiyama M, Kuzuyama T. 2009. NovQ is a prenyltransferase capable of catalyzing the addition of a dimethylallyl group to both phenylpropanoids and flavonoids. J Antibiot. 62: 385-392.
Yoshida A, Tomita T, Kono H, Fushinobu S, Kuzuyama T, Nishiyama M. 2009. Crystal structures of the regulatory subunit of Thr-sensitive aspartate kinase from Thermus thermophilus. FEBS J. 276: 3124-3136.
Zhao P, Ueda JY, Kozone I, Chijiwa S, Takagi M, Kudo F, Nishiyama M, Shin-ya K, Kuzuyama T. 2009. New glycosylated derivatives of versipelostatin, the GRP78/Bip molecular chaperone down-regulator, from Streptomyces versipellis 4083-SVS6. Org Biomol Chem. 7: 1454-1460.
Kim YB, Kim SM, Kang MK, Kuzuyama T, Lee JK, Park SC, Shin SC, Kim SU. 2009. Regulation of resin acid synthesis in Pinus densiflora by differential transcription of genes encoding multiple 1-deoxy-D-xylulose 5-phosphate synthase and 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase genes. Tree Physiol. 29: 737-749.
Harada H, Yu F, Okamoto S, Kuzuyama T, Utsumi R, Misawa N. 2009. Efficient synthesis of functional isoprenoids from acetoacetate through metabolic pathway-engineered Escherichia coli. Appl Microbiol Biotechnol. 81: 915-925.
Tomita T, Miyagawa T, Miyazaki T, Fushinobu S, Kuzuyama T, Nishiyama M. 2009. Mechanism for multiple-substrates recognition of alpha-aminoadipate aminotransferase from Thermus thermophilus. Proteins. 75: 348-359.

2008

Sando T, Takeno S, Watanabe N, Okumoto H, Kuzuyama T, Yamashita A, Hattori M, Ogasawara N, Fukusaki E, Kobayashi A. 2008. Cloning and characterization of the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway genes of a natural-rubber producing plant, Hevea brasiliensis. Biosci Biotechnol Biochem. 72: 2903-2917.
Pakhomova S, Bartlett SG, Augustus A, Kuzuyama T, Newcomer ME. 2008. Crystal structure of fosfomycin resistance kinase FomA from Streptomyces wedmorensis. J Biol Chem. 283: 28518-28526.
Kumano T, Richard SB, Noel JP, Nishiyama M, Kuzuyama T. 2008. Chemoenzymatic syntheses of prenylated aromatic small molecules using Streptomyces prenyltransferases with relaxed substrate specificities. Bioorg Med Chem. 16: 8117-8126.
Kim SM, Kim YB, Kuzuyama T, Kim SU. 2008. Two copies of 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase (CMK) gene in Ginkgo biloba: molecular cloning and functional characterization. Planta. 228: 941-950.
Tello M, Kuzuyama T, Heide L, Noel JP, Richard SB. 2008. The ABBA family of aromatic prenyltransferases: broadening natural product diversity. Cell Mol Life Sci. 65: 1459-1463.
Kim SM, Kuzuyama T, Kobayashi A, Sando T, Chang YJ, Kim SU. 2008. 1-Hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase (IDS) is encoded by multicopy genes in gymnosperms Ginkgo biloba and Pinus taeda. Planta. 227: 287-298.

2007

Okada A, Shimizu T, Okada K, Kuzuyama T, Koga J, Shibuya N, Nojiri H, Yamane H. 2007. Elicitor induced activation of the methylerythritol phosphate pathway toward phytoalexins biosynthesis in rice. Plant Mol Biol. 65: 177-187.
Yajima S, Hara K, Iino D, Sasaki Y, Kuzuyama T, Ohsawa K, Seto H. 2007. Structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase in a quaternary complex with a magnesium ion, NADPH and the antimalarial drug fosmidomycin IActa Crystallogr Sect F Struct Biol Cryst Commun. 63: 466-470.
Puan, K. J., C. Jin, H. Wang, G. Sarikonda, A. M. Raker, H. K. Lee, M. I. Samuelson, E. Marker-Hermann, L. Pasa-Tolic, E. Nieves, J. L. Giner, T. Kuzuyama, and C. T. Morita. 2007. Preferential recognition of a microbial metabolite by human V{gamma}2V{delta}2 T cells. Int Immunol. 19: 657-673.
Yoshida, A., T. Tomita, T. Kurihara, S. Fushinobu, T. Kuzuyama, and M. Nishiyama. 2007. Structural Insight into Concerted Inhibition of alpha(2)beta(2)-Type Aspartate Kinase from Corynebacterium glutamicum. J Mol Biol. 368: 521-536.
Yoshida, A., T. Tomita, T. Kuzuyama, and M. Nishiyama. 2007. Purification, crystallization and preliminary X-ray analysis of regulatory subunit of aspartate kinase from Thermus thermophilus. Acta Crystallogr Sect F Struct Biol Cryst Commun. 63: 96-98.

2006

Tomita, T., S. Fushinobu, T. Kuzuyama, and M. Nishiyama. 2006. Structural basis for the alteration of coenzyme specificity in a malate dehydrogenase from Thermus flavus. Biochem. Biophys. Res. Commun. 347: 502-508.
Fujiwara, K., T. Tsubouchi, T. Kuzuyama, and M. Nishiyama. 2006. Involvement of arginine repressor in lysine biosynthesis of Thermus thermophilus. Microbiology. 152: 3585-3594.
Tomita, T., T. Kuzuyama, and M. Nishiyama. 2006. Alteration of coenzyme specificity of lactate dehydrogenase from Thermus thermophilus by introducing the loop region of NADP(H)-dependent malate dehydrogenase. Biosci. Biotechnol. Biochem. 70: 2230-2235.
Maeda, K., C. Nishiyama, T. Tokura, H. Nakano, S. Kanada, M. Nishiyama, K. Okumura, and H. Ogawa. 2006. FOG-1 represses GATA-1-dependent FceRI beta-chain transcription: transcriptional mechanism of mast cell-specific gene expression in mice. Blood. 108: 262-269.
Jia, Y., T. Tomita, K. Yamauchi, M. Nishiyama, and D. R. J. Palmer. 2006. Kinetics and product analysis of the reaction catalyzed by recombinant homoaconitase from Thermus thermophilus. Biochem. J. 396: 479-485.
Kawasaki, T., Y. Hayashi, T. Kuzuyama, K. Furihata, N. Itoh, H. Seto, and T. Dairi. 2006. Biosynthesis of a natural polyketide-isoprenoid hybrid compound furaquinocin A: Identification and heterologous expression of the gene cluster. J. Bacteriol. 188: 1236-1244.
Kim SM, T. Kuzuyama, YJ Chang, HJ Kwon, and SU Kim. 2006. Cloning and functional characterization of 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (GbMECT) gene from Ginkgo biloba. Phytochemistry. 67: 1435-1441.
Kim SM, T. Kuzuyama, YJ Chang, KS Song, and SU Kim. 2006. Identification of class 2 1-deoxy-D-xylulose 5-phosphate synthase and 1-deoxy-D-xylulose 5-phosphate reductoisomerase genes from Ginkgo biloba and their transcription in embryo culture with respect to ginkgolide biosynthesis. Planta Med. 72: 234-240.
Kim SM, T. Kuzuyama, YJ Chang, and SU Kim. Cloning and characterization of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (MECS) gene from Ginkgo biloba. Plant Cell Rep. 25: 829-35.

2005

Miyazaki, J., K. Asada, S. Fushinobu, T. Kuzuyama, and M. Nishiyama. 2005. Crystal structure of tetrameric homoisocitrate dehydrogenase from an extreme thermophile, Thermus thermophilus: involvement of hydrophobic dimer-dimer interaction in extremely high thermotolerance. J. Baceriol. 187: 6779-6788.
Tomita, T., S. Fushinobu, T. Kuzuyama, and M. Nishiyama. 2005. Crystal structure of NAD-dependent malate dehydrogenase complexed with NADP(H). Biochem. Biophys. Res. Commun. 334: 613-618.
Kuzuyama, T., J. P. Noel, and S. B. Richard. 2005. Structural basis for the promiscuous biosynthetic prenylation of aromatic natural products. Nature 435: 983-987.
Puan, K. J., H. Wang, T. Dairi, T. Kuzuyama, and C. T. Morita. 2005. fldA is an essential gene required in the 2-C-methyl-D-erythritol 4-phosphate pathway for isoprenoid biosynthesis. FEBS Lett. 579: 3802-3806.
Tsubouchi T., R. Mineki, H. Taka, N. Kaga, K. Murayama, C. Nishiyama, H. Yamane, T. Kuzuyama, and M. Nishiyama. 2005. Leader peptide-mediated transcriptional attenuation of lysine biosynthetic gene cluster in Thermus thermophilus. J. Biol. Chem. 280: 18511-18516.
Ito, T., C. Nishiyama, M. Nishiyama, H. Matsuda, K. Maeda, Y. Akizawa, Tsuboi, R, Okumura, and H. Ogawa. 2005. Mast cells acquire monocyte-specific gene expression and monocyte-like morphology by overproduction of PU.1. J. Immunol. 174: 376-383.
Nakano, N., C. Nishiyama, N. Masuoka, M. Nishiyama, H. Yamane, H. Okumura, and K. Ogawa. 2005. Analysis of PU.1/ICSBP (IRF-8) complex formation with various PU.1 mutants: Molecular cloning of rat Icsbp (Irf-8) cDNA. Immunogenetics. 56: 871-877.
Nishiyama, C., T. Ito, M. Nishiyama, S. Masaki, K. Maeda, N. Nakano, W. Ng, K. Fukuyama, M. Yamamoto, H. Okumura, and K. Ogawa. 2005. GATA-1 is required for expression of FceRI on mast cells: Analysis of mast cells derived from GATA-1 knockdown mouse bone marrow. Int. Immunol. 17: 847-856.
Eguchi, T., Y. Dekishima, H. Aizawa, H. Tamegai, K. Kakinuma, N. Misawa, T. Kuzuyama, and H. Seto. 2005. Preparation of highly deuterated zeaxanthin, lycopene, and b-carotene from fully deuterated mevalonate using engineered Escherichia coli. Tetrahedron 61: 2027-2035.

2004

Cho E.-M., A. Okada, H. Kenmoku, K. Otomo, T. Toyomasu, W. Mitsuhashi, T. Sassa, A. Yajima, G. Yabuta, K. Mori, H. Oikawa, H. Toshima, N. Shibuya, H. Nojiri, T. Omori, M. Nishiyama, and H. Yamane. 2004. Molecular cloning and characterization of a cDNA encoding ent-cassa-12,15-diene synthase, a putative diterpenoid phytoalexin biosynthetic enzyme, from suspension-cultured rice cells treated with a chitin elicitor. Plant J. 37: 1-8.
Nishiyama, C., M. Nishiyama, T. Ito, S. Masaki, K. Maeda, N. Masuoka, H. Yamane, T. 2004. Kitamura, H. Ogawa, and K. Okumura. Overproduction of PU.1 in mast cell progenitors: its effect on monocyte- and mast cell-specific gene expression. Biochem. Biophys. Res. Commun. 313: 516-521.
Nishiyama, C., M. Nishiyama, T. Ito, S. Masaki, N. Masuoka, H. Yamane, T. Kitamura, H. Ogawa, and K. Okumura. 2004. Functional analysis of PU.1 domains in monocyte-specific gene regulation. FEBS Lett. 561: 63-68.
Kato, C. T. Kurihara, N. Kobashi, H. Yamane, and M. Nishiyama. 2004. Conversion of feedback regulation in aspartate kinase by domain exchange. Biochem. Biophys. Res. Commun. 316: 802-808.
Lombo, T., N. Takaya, J. Miyazaki, K. Gotoh, M. Nishiyama, T. Kosuge, A. Nakamura, and T. Hoshino. 2004. Functional analysis of the small subunit of the putative homoaconitase from Pyrococcus horikoshii in the Thermus lysine pathway. FEMS Microbiol. Lett. 233: 315-324.
Jikumaru, Y., T. Asami, H. Seto, S. Yoshida, T. Yokoyama, N. Obara, M. Hasegawa, O. Kodama, M. Nishiyama, K. Okada, H. Nojiri, and H. Yamane. 2004. Preparation and biological activity of molecular probes to identify and analyze jasmonic acid-binding proteins. Biosci. Biotechnol. Biochem. 68: 1461-1466.
Miyazaki, T., J. Miyazaki, H. Yamane, and M. Nishiyama. 2004. a-Aminoadipate aminotransferase from an extremely thermophilic bacterium, Thermus thermophilus. Microbiology 150: 2327-2334.
Nemoto, T., E.-M. Cho, A. Okada, K. Okada, K. Otomo, Y. Kanno, T. Toyomasu, W. Mitsuhashi, T. Sassa, E. Minami, N. Shibuya, M. Nishiyama, H. Nojiri, and H. Yamane. 2004. Stemar-13-ene synthase, a diterpene cyclase involved in the biosynthesis of the phytoalexin oryzalexin S in rice. FEBS Lett. 571: 182-186.
Nishiyama, C., N. Masuoka, M. Nishiyama, T. Ito, H. Yamane, K. Okumura, and H. Ogawa. 2004. Evidence against requirement of Ser41 and Ser45 for function of PU.1 - Molecular cloning of rat PU.1. FEBS Lett. 572: 57-64.
Nishiyama, C., Y. Akizawa, M. Nishiyama, M. Hasegawa, T. Tokura, H. Kawada, K. Mitsuishi, T. Ito, N. Nakano, A. Okamoto, A. Takagi, H. Yagita, K. Okumura, and H. Ogawa. 2004. Polymorphisms in FceRIb promoter region affecting transcription activity: a possible promoter-dependent mechanism for association between FceRIb and atopy. J. Immunol. 173: 6458-6464.
Kiribuchi, K., M. Sugimori, M. Takeda, T. Otani, K. Okada, H. Onodera, M. Ugaki, Y. Tanaka, C. Tomiyama-Akimoto, T. Yamaguchi, E. Minami, N. Shibuya, T. Omori, M. Nishiyama, H. Nojiri, and H. Yamane. 2004. RERJ1, a jasmonic acid-responsive gene from rice, encodes a basic helix-loop-helix protein. Biochem. Biophys. Res. Commun. 325: 857-863.
Takagi, M., K. Kaneda, T. Shimizu, Y. Hayakawa, H. Seto, and T. Kuzuyama. 2004. Bacillus subtilis ypgA gene is fni, a nonessential gene encoding type 2 isopentenyl diphosphate isomerase. Biosci. Biotechnol. Biochem. 68: 132-137.
Kuzuyama, T., T. Dairi, H. Yamashita, Y. Shoji, and H. Seto. 2004. Hetereologous mevalonate production in Streptomyces lividans TK23. Biosci. Biotechnol. Biochem. 68: 931-934.
Kawasaki, T, T. Kuzuyama, Y. Kuwamori, N. Matsuura, N. Itoh, K. Furihata, H. Seto, and T. Dairi. 2004. Presence of copalyl diphosphate synthase gene in an actinomycete possessing the mevalonate pathway. J. Antibiot. 57: 739-747.

2003

Miyazaki, J., N. Kobashi, M. Nishiyama, and H. Yamane. 2003. Characterization of homoisocitrate dehydrogenase involved in lysine biosynthesis of an extremely thermophilic bacterium, Thermus thermophilus HB27, and evolutionary implication of beta-decarboxylating dehydrogenase. J. Biol. Chem. 278: 1864-1871.
Hasegawa, M., C. Nishiyama, Y. Akizawa, M. Nishiyama, K. Mitsuishi, T. Ito, S. Furukawa, C. Ra, K. Okumura, and H. Ogawa. 2003. A novel -66T/C polymorphism in FceRI a-chain promoter affecting the transcription activity: possible relationship to allergic diseases. J. Immunol. 171: 1927-1933.
Hasegawa, M., C. Nishiyama, M. Nishiyama, Y. Akizawa, K. Takahashi, T. Ito, S. Furukawa, C. Ra, K. Okumura, and H. Ogawa. 2003. Regulation of the human FceRI alpha-chain distal promoter. J. Immunol. 170: 3732-3738.
Maeda, K., C. Nishiyama, T. Tokura, Y. Akizawa, M. Nishiyama, H. Ogawa, K. Okumura, and C. Ra. 2003. Regulation of cell-type specific mouse FceRI beta-chain gene expression by GATA-I via four GATA motifs in the promoter. J. Immunol. 170: 334-340.
Nishiyama, C., T. Yokota, M. Nishiyama, C. Ra, K. Okumura, and H. Ogawa. 2003. Molecular cloning of rat YY1 transcription factor. Biosci. Biotechnol. Biochem. 67: 654-658.
Sakai, H., M. N. Vassylyeva, T. Matsuura, S.-i. Sekine, K. Gotoh, M. Nishiyama, T. Terada, M. Shirouzu, S. Kuramitsu, D. G. Vassylyev, and S. Yokoyama. 2003. Crystal structure of a lysine biosynthesis enzyme, LysX, from Thermus thermophilus HB8. J. Mol. Biol. 332: 729-740.
Vassylyeva, M. N., H. Sakai, T. Matsuura, S.-i. Sekine, M. Nishiyama, T. Terada, M. Shirouzu, S. Kuramitsu, D. G. Vassylyev, and S. Yokoyama. 2003. Cloning, expression, purification, crystallization and initial crystallographic analysis of lysine biosynthesis LysX protein from Thermus thermophilus HB8. Acta Crystallogr. D 59: 1651-1652.
Sobajima, H., M. Takeda, M. Sugimori, N. Kobashi, K. Kiribuchi, E. M. Cho, C. Akimoto, T. Yamaguchi, E. Minami, N. Shibuya, F. Schaller, E. W. Weiler, T. Yoshihara, H. Nishida, H. Nojiri, T. Omori, M. Nishiyama, and H. Yamane. 2003. Cloning and characterization of a jasmonic acid-responsive gene encoding 12-oxophytodienoic acid reductase in suspension-cultured rice cells. Planta 216: 692-698.