研究業績

2024　｜2023　｜　 2022　｜2021　｜　 2020　｜2019　｜　 2018　｜2017　｜　 2016　｜2015　｜　 2014　｜2013　｜　 2012　｜2011　｜　 2010　｜2009　｜　 2008　｜2007　｜　 2006　｜2005　｜　 2004　｜2003　｜

2024

ORIGINAL ARTICLES

• Suzuki-Minakuchi C, Yamamoto N, Takahira S, Yamaguchi M, Takeda Y, Okada K, Shigeto S, Nojiri H. Transcriptional heterogeneity of catabolic genes on the plasmid pCAR1 causes host-specific carbazole degradation. Appl Environ Microbiol. 2024 Jan 30:e0124723. doi: 10.1128/aem.01247-23. Epub ahead of print. PMID: 38289097. Format:
• Zhang D, Lin R, Yamamoto N, Wang Z, Lin H, Okada K, Liu Y, Xiang X, Zheng T, Zheng H, Yi X, Noutoshi Y, Zheng A. Mitochondrial-targeting effector RsIA_CtaG/Cox11 in Rhizoctonia solani AG-1 IA has two functions: plant immunity suppression and cell death induction mediated by a rice cytochrome c oxidase subunit. Mol Plant Pathol. 2024 Jan;25(1):e13397. doi: 10.1111/mpp.13397. Epub 2023 Oct 30. PMID: 37902589; PMCID: PMC10799210.

2023

ORIGINAL ARTICLES

• Shimada T, Minato S, Hasegawa Y, Miyamoto K, Minato Y, Shenton MR, Okada K, Kawaide H, Toyomasu T. Characterization of diterpene synthase genes in Brachypodium distachyon, a monocotyledonous model plant, provides evolutionary insight into their multiple homologs in cereals. Biosci Biotechnol Biochem. 2023 Dec 19;88(1):8-15. doi: 10.1093/bbb/zbad146. PMID: 37833097.
• Okamoto K, Inoue T, Nagano T, Miyazaki S, Takahashi I, Asami T, Okada K, Okada K, Nakajima M. Chemical screening of inhibitors specific for MdDOX-Co that cause an apple columnar tree-shape. Biosci Biotechnol Biochem. 2023 Dec 19;88(1):63-69. doi: 10.1093/bbb/zbad142. PMID: 37791963.

2022

ORIGINAL ARTICLES

• Zhang D, Wang Z, Yamamoto N, Wang M, Yi X, Li P, Lin R, Nasimi Z, Okada K, Mochida K, Noutoshi Y, Zheng A. Secreted Glycosyltransferase RsIA_GT of Rhizoctonia solani AG-1 IA Inhibits Defense Responses in Nicotiana benthamiana. Pathogens (2022) 11(9):1026. [PubMed]
• Knoch E, Kovács J, Deiber S, Tomita K, Shanmuganathan R, Serra Serra N, Okada K, Becker C, Schandry N. Transcriptional response of a target plant to benzoxazinoid and diterpene allelochemicals highlights commonalities in detoxification. BMC Plant Biol. (2022) A22(1):402. doi: 10.1186/s12870-022-03780-w. [PubMed]
• Wu D, Hu Y, Akashi S, Nojiri H, Guo L, Ye C, Zhu Q. H, Okada K, Fan L. Lateral transfers lead to the birth of momilactone biosynthetic gene clusters in grass. Plant Journal (2022) 111, 1354–1367[PubMed]
• Pi-Cheng Tsai, Joydeep Chakraborty, Chiho Suzuki-Minakuchi, Tohru Terada, Tatsurou Kotake, Jun Matsuzawa,Kazunori Okada, and Hideaki Nojiri The α- and β-Subunit Boundary at the Stem of the Mushroom-Like α 3 β 3 -Type Oxygenase Component of Rieske Non-heme Iron Oxygenases is the Rieske-Type Ferredoxin-Binding Site. AEM (2022) 88(15):e0083522.doi: 10.1128/aem.00835-22.[PubMed]
• Naloka K, Jaroonrunganan J, Woratecha N, Khondee N, Nojiri H, Pinyakong O. Physiological changes in Rhodococcus ruber S103 immobilized on biobooms using low-cost media enhance stress tolerance and crude oil-degrading activity. Sci Rep. 2022 Jun 21;12(1):10474. doi: 10.1038/s41598-022-14488-0. PMID: 35729341; PMCID: PMC9213463.[PubMed]
• Fukuda K, Uefune M, Fukaki H, Yamauchi Y, Hara-Nishimura I, Ozawa R, Matsui K, Sugimoto K, Okada K, Imai R, Takahashi K, Enami S, Wurst R, Takabayashi J. Aerial (+)-borneol modulates root morphology, auxin signalling and meristematic activity in Arabidopsis roots. Biol Lett. (2022) May;18(5):20210629. doi: 10.1098/rsbl.2021.0629. Epub (2022) May 4. PMID: 35506238; PMCID: PMC9065954.[PubMed]
• Chongyang Y., Ning H., Chihiro I., Yu-Liang Y., Hideaki N., Ying-Ning H., Mei-Fang C., (2022) "Rhizospheric plant-microbe synergistic interactions achieve efficient arsenic phytoextraction by Pteris vittata." Journal of Hazardous Materials, 128870. doi: 10.1016/j.jhazmat.2022.128870. [PubMed]

2021

ORIGINAL ARTICLES

• Valea I, Motegi A, Kawamura N, Kawamoto K, Miyao A, Ozawa R, Takabayashi J, Gomi K, Nemoto K, Nozawa A, Sawasaki T, Shinya T, Galis I, Miyamoto K, Nojiri H, Okada K. (2021)"The rice wound-inducible transcription factor RERJ1 sharing same signal transduction pathway with OsMYC2 is necessary for defense response to herbivory and bacterial blight." Plant Mol Biol. (in press) doi: 10.1007/s11103-021-01186-0. [PubMed]
• Tomonori Shinya, Koji Miyamoto, Kenichi Uchida, Yuko Hojo, Emi Yumoto, Kazunori Okada, Hisakazu Yamane, Ivan Galis (2021) "Chitooligosaccharide elicitor and oxylipins synergistically elevate phytoalexin production 2 in rice " Plant Mol Biol. [PubMed]
• Inagaki H, Miyamoto K, Ando N, Murakami K, Sugisawa K, Morita S, Yumoto E, Teruya M, Uchida K, Kato N, Kaji T, Takaoka Y, Hojo Y, Shinya T, Galis I, Nozawa A, Sawasaki T, Nojiri N, Ueda M, Okada K (2021) "Deciphering OPDA signaling components in the momilactone- producing moss Calohypnum plumiforme" Frontiers in Plant Science, section Plant Metabolism and Chemodiversity [PubMed]
• Tomita K, Yashiroda Y, Matsuo Y, Piotrowski J, Li S, Okamoto R, Yoshimura M, Kimura H, Kawamura Y, Kawamukai M, Boone C, Yoshida M, Nojiri H, Okada K (2021) "Genome-wide Screening of Genes Associated with Momilactone B Sensitivity in the Fission Yeast." G3_Genes Genomes Genetics. 11(8): jkab156. DOI: 10.1093/g3journal/jkab156 [PubMed]
• Laothamteep, N., Kawano, H., Vejarano, F., Suzuki-Minakuchi, C., Shintani, M., Nojiri, H., Pinyakong, O. (2021) "Effects of environmental factors and coexisting substrates on PAH degradation and transcriptomic responses of the defined bacterial consortium OPK." Environ. Pollut., 116769. https://doi.org/10.1016/j.envpol.2021.116769 .
• Chakraborty J, Suzuki-Minakuchi C, Tomita T, Okada K, and Nojiri H (2021). A novel gene cluster is involved in the degradation of lignin-derived onoaromatics in Thermus oshimai JL-2. Appl. Environ. Microbiol. 87(11):e01589-20. doi: 10.1128/AEM.01589-20. [PubMed]
• Mpofu E, Alias A, Tomita K, Suzuki-Minakuchi C, Tomita K, Chakraborty J, Malon M, Ogura Y, Takikawa H, Okada K, Kimura T, Nojiri H. (2021) " Azoxystrobin amine: A novel azoxystrobin degradation product from Bacillus licheniformis strain TAB7." Chemosphere. 2021 Jan 18;273:129663. doi: 10.1016/j.chemosphere.2021.129663. [PubMed]
• Ogawa D, Suzuki Y, Yokoo T, Katoh E,Teruya M, Muramatsu M, Ma F.J., Yoshida Y, Isaji S, Ogo Y, Miyao M, Kim J.M., Kojima M, Takebayashi Y, Sakakibara H, Takeda S, Okada K, Mori N, Seki M, Habu Y (2021) "Acetic-acid-induced jasmonate signaling in root enhances drought avoidance in rice." Scientific Reports. [PubMed]

2020

ORIGINAL ARTICLES

• Kawano H, Suzuki-Minakuchi C, Sugiyama D, Watanabe N, Takahashi Y, Okada K, Nojiri H. (2020) "A novel small RNA on the Pseudomonas putida KT2440 chromosome is involved in the fitness cost imposed by IncP-1 plasmid RP4." Frontiers in Microbiology. doi: 10.3389/fmicb.2020.01328[PubMed]
• Nakamura T, Suzuki-Minakuchi C, Kawano H, Kanesaki Y, Kawasaki S, Okada K and Nojiri H (2020) "H-NS Family Proteins Drastically Change Their Targets in Response to the Horizontal Transfer of the Catabolic Plasmid pCAR1." Front. Microbiol. 11:1099. doi: 10.3389/fmicb.2020.01099[PubMed]
• Mao L, Kawaide H, Higuchi T, Chen M, Miyamoto K, Hirata Y, Kimura H, Miyazaki S, Teruya M, Fujiwara K, Tomita K, Yamane H, Hayashi K, Nojiri H, Jia L, Qiu J, Ye C, Timko MP, Fan L, Okada K (2020) "Genomic evidence for convergent evolution of gene clusters for momilactone biosynthesis in land plants. Proc Natl Acad Sci U S A. 2020;117(22):12472‐12480. doi:10.1073/pnas.1914373117[PubMed]

REVIEW ARTICLES

• Toyomasu T, Shenton MR, Okada K. (2020) "Evolution of Labdane-Related Diterpene Synthases in Cereals." Plant & Cell Physiology. doi: 10.1093/pcp/pcaa106. Online ahead of print.[PubMed]

2019

ORIGINAL ARTICLES

• Devanadera A, Vejarano F, Zhai Y, Suzuki-Minakuchi C, Ohtsubo Y, Tsuda M, Kasai Y, Takahata Y, Okada K, Nojiri H (2019) "Complete Genome Sequence of an Anaerobic Benzene-Degrading Bacterium, Azoarcus sp. Strain DN11." Microbiol Resour Announc. 8: e01699-18 [PubMed]
• Watahiki S, Kimura N, Yamazoe A, Miura T, Sekiguchi Y, Noda N, Matsukura S, Kasai D, Takahata Y, Nojiri H, Fukuda M (2019) "Ecological impact assessment of a bioaugmentation site on remediation of chlorinated ethylenes by multi-omics analysis." J Gen Appl Microbiol. [Epub ahead of print] [PubMed]
• Mpofu E, Vejarano F, Suzuki-Minakuchi C, Ohtsubo Y, Tsuda M, Chakraborty J, Nakajima M, Okada K, Tada N, Kimura T, Nojiri H (2019) "Complete genome sequence of Bacillus licheniformis TAB7, a compost deodorizing strain with potential for plant-growth promotion." Microbiol Resour Announc. 8: e01659-18 [PubMed]
• Vejarano F, Suzuki-Minakuchi C, Ohtsubo Y, Tsuda M, Okada K, Nojiri H. (2019) "Complete Genome Sequence of Thalassococcus sp. Strain S3, a Marine Roseobacter Clade Member Capable of Degrading Carbazole." Microbiol Resour Announc. 8:e00231-19.[PubMed]

BOOKS

• Suzuki-Minakuchi C and Navarre WW: "Xenogeneic Silencing and Horizontal Gene Transfer" in "DNA Traffic in the Environment", eds. Nishida H and Oshima T (2019) Springer Verlag, Singapore, Singapore, 1-27

AWARDS

• 王 翌霞 （PD）：Poster award for the Protein Research Conference in China

2018

ORIGINAL ARTICLES

• Sakuda A, Suzuki-Minakuchi C, Okada K, Nojiri H. (2018) "Conjugative selectivity of plasmids is affected by coexisting recipient candidates." mSphere. 3: e00490-18 [PubMed]
• Vejarano F, Suzuki-Minakuchi C, Ohtsubo Y, Tsuda M, Okada K, Nojiri H. (2018) "Complete genome sequence of the marine carbazole-degrading bacterium Erythrobacter sp. strain KY5." Microbiol Resour Announc. 7:e00935-18. [PubMed]
• Toyomasu T, Goda C, Sakai A, Miyamoto K, Shenton MR, Tomiyama S, Mitsuhashi W, Yamane H, Kurata N, Okada K. (2018) "Characterization of diterpene synthase genes in the wild rice species Oryza brachyatha provides evolutionary insight into rice phytoalexin biosynthesis." Biochem Biophys Res Commun. 503(3):1221-1227.[PubMed]
• Sun Z, Vasileva D, Suzuki-Minakuchi C, Okada K, Luo F, Igarashi Y, Nojiri H. (2018) "Differential protein-protein binding affinities of H-NS family proteins encoded on the chromosome of Pseudomonas putida KT2440 and IncP-7 plasmid pCAR1." Biosci Biotechnol Biochem. 82(9):1640-1646.[PubMed]
• Salvador-Guirao R, Baldrich P, Tomiyama S, Hsing YI, Okada K, San Segundo B. (2018) "OsDCL1a activation impairs phytoalexin biosynthesis and compromises disease resistance in rice." Ann Bot. Jul 18. doi: 10.1093/aob/mcy141. [Epub ahead of print][PubMed]
• Vasileva D, Suzuki-Minakuchi C, Kosono S, Yoshida M, Okada K, Nojiri H (2018). "Proteome and acylome analyses of the functional interaction network between the carbazole-degradative plasmid pCAR1 and host Pseudomonas putida KT2440" Environmental Microbiology Reports. 10(3):299-309.[PubMed]
• Yamamoto T, Yoshida Y, Nakajima K, Tominaga M, Gyohda A, Suzuki,a Okamoto T, Nishimura T, Yokotani N, Minami E, Nishizawa Y, Miyamoto K, Yamane H, Okada K, Koshiba T (2018) "Antagonistic Regulation of RSOsPR10 Expression by Jasmonate/Ethylene and Salicylate Pathways is Mediated by OsERF87 Activator and OsWRKY76 Repressor, respectively, in Rice Roots" Plant Direct [in press]

AWARDS

• 冨山　詩歩（M2）：Poster award for the International Symposium on Rice Functional Genomics 2018
• 河野　響（M2）：東京大学大学院農学生命科学研究科　研究科長賞

2017

ORIGINAL ARTICLES

• Sakuda A, Suzuki-Minakuchi C, Matsui K, Takahashi Y, Okada K, Yamane H, Masaki Shintani M, Hideaki N (2018) "Divalent cations increase the conjugation efficiency of the incompatibility P-7 group plasmid pCAR1 among different Pseudomonas hosts" Microbiology. 164(1):20-27. [PubMed]
• Ye Z, Nakagawa K, Natsume M, Nojiri H, Kawaide H, Okada K. (2018) "In planta functions of cytochrome P450 monooxygenase genes in the phytocassane biosynthetic gene cluster on rice chromosome 2" Biosci. Biotech. Biochem. 82(6):1021-1030. [PubMed]
• Valea I, Motegi A, Kawamura N, Shimizu T, Miyamoto K, Yamane H, Nojiri H, Okada K. (2017) "Biological roles of the rice bHLH factor RERJ1 on stress responses via jsmonate signaling" Acta Horticulture. Proc. of the II international Symposium on Pyrethrum. 1169:133-137
• Zongping Sun, Delyana Vasileva, Chiho Suzuki-Minakuchi, Kazunori Okada, Feng Luo, Yasuo Igarashi and Hideaki Nojir (2017) “Growth phase-dependent expression profiles of three vital H-NS family proteins encoded on the chromosome of Pseudomonas putida KT2440 and on the pCAR1 plasmid” BMC Microbiology [PubMed]
• Yoshida Y, Miyamoto K, Yamane H, Nishizawa Y, Minami E, Nojiri H, Okada K (2017) “OsTGAP1 is responsible for JA-inducible diterpenoid phytoalexin biosynthesis in rice roots with biological impacts on allelopathic interaction.” Physiol Plant. Aug 30. doi: 10.1111/ppl.12638.[PubMed]
• Pagakrong Wanapaisan, Natthariga Laothamteep, Felipe Vejarano, Joydeep Chakraborty, Masaki Shintani, Chanokporn Muangchinda, Tomomi Morita, Chiho Suzuki-Minakuchi, Kengo Inouee, Hideaki Nojiri (2017) “Synergistic degradation of pyrene by five culturable bacteria in a mangrove sediment-derived bacterial consortium” Journal of Hazardous Materials [PubMed]
• Guo L, Qiu J, Ye C, Jin G, Mao L, Zhang H, Yang X, Peng Q, Wang Y, Jia L, Lin Z, Li G, Fu F, Liu C, Chen L, Shen E, Wang W, Wu S, Xia C, Zhang Y, Zhou X, Wang L, Wu L, Song W, Wang Y, Shu Q, Aoki D, Yumoto E, Yokota T, Miyamoto M, Okada K, Kim DC, Cai D, Zhang C, Lou Y, Qian Q, Yamaguchi H, Yamane H, Kong CH,Timko MP, Bai L, Fan L (2017) "Barnyardgrass (Echinochloa crus-galli) genome analysis provides insight into its adaptation and invasiveness as a weed." Nature Communications. 8(1):1031. doi: 10.1038/s41467-017-01067-5.[PubMed]
• Ogawa S, Kawahara-Miki R, Miyamoto K, Yamane H, Nojiri H, Tsujii Y, Okada K. (2017) "OsMYC2 mediates numerous defence-related transcriptional changes via jasmonic acid signalling in rice."
  Biochem Biophys Res Commun. 486(3):796-803. doi: 10.1016/j.bbrc.2017.03.125. Epub 2017 Mar 25.[PubMed]
• Chakraborty J, Suzuki-Minakuchi C, Okada K, Nojiri H. (2017) "Thermophilic bacteria are potential sources of novel Rieske non-heme iron oxygenases."AMB Express 7(1):17. doi: 10.1186/s13568-016-0318-5.[PubMed]
• Ogawa S, Miyamoto K, Nemoto K, Sawasaki T, Yamane H, Nojiri H, Okada K. (2017) "OsMYC2, an essential factor for JA-inductive sakuranetin production in rice, interacts with MYC2-like proteins that enhance its transactivation ability." Sci Rep. Jan 9;7:40175. doi: 10.1038/srep40175.[PubMed]
• Ye Z, Nakagawa K, Natsume M, Nojiri H, Kawaide H, Okada K. (2017) "Biochemical synthesis of uniformly 13C-labeled diterpene hydrocarbons and their bioconversion to diterpenoid phytoalexins in planta" Biosci. Biotech. Biochem. [PubMed]

2016

ORIGINAL ARTICLES

• Shinya T, Hojo Y, Desaki Y, Christeller JT, Okada K, Shibuya N, Galis I (2016) "Modulation of plant defense responses to herbivores by simultaneous recognition of different herbivore-associated elicitors in rice."Sci Rep. doi: 10.1038/srep32537.[PubMed]
• Suzuki-Minakuchi C, Kawazuma K, Matsuzawa J, Vasileva D, Fujimoto Z, Terada T, Okada K, Nojiri H. (2016) "Structural similarities and differences in H-NS family proteins revealed by the N-terminal structure of TurB in Pseudomonas putida KT2440" FEBS Lett. [Epub ahead of print] [PubMed]
• Takeuchi, Hasegawa H, Gyohda A, Komatsu S, Okamoto T, Okada K, Terakawa T, Koshiba T. "Overexpression of RSOsPR10, a root-specific rice PR10 gene, confers tolerance against drought stress in rice and drought and salt stresses in bentgrass" [in press] [PubMed]
• Toyomasu T, Miyamoto K, Shenton MR, Sakai A, Sugawara C, Horie K, Kawaide H, Hasegawa M, Chuba M, Mitsuhashi W, Yamane H, Kurata N, Okada K. (2016) "Characterization and evolutionary analysis of ent-kaurene synthase like genes from the wild rice species Oryza rufipogon. " Biochem Biophys Res Commun. 18;480(3):402-408 [PubMed]
• Nishimura T, Mochizuki S, Ishii-Minami N, Fujisawa Y, Kawahara Y, Yoshida Y, Okada K, Ando S, Matsumura H, Terauchi R, Minami E, Nishizawa Y. (2016)"Magnaporthe oryzae Glycine-Rich Secretion Protein, Rbf1 Critically Participates in Pathogenicity through the Focal Formation of the Biotrophic Interfacial Complex." PLoS Pathog. 6;12(10):e1005921. [PubMed]
• Okada K, Kawaide H, Miyamoto K, Miyazaki S, Kainuma R, Kimura H, Fujiwara K, Natsume M, Nojiri H, Nakajima M, Yamane H, Hatano Y, Nozaki H, Hayashi K. HpDTC1, a Stress-Inducible Bifunctional Diterpene Cyclase Involved in Momilactone Biosynthesis, Functions in Chemical Defence in the Moss Hypnum plumaeforme. Sci Rep. 2016 May 3;6:25316. doi: 10.1038/srep25316. [PubMed]
• Miyamoto K, Fujita M, Shenton MR, Akashi S, Sugawara C, Sakai A, Horie K, Hasegawa M, Kawaide H, Mitsuhashi W, Nojiri H, Yamane H, Kurata N, Okada K, Toyomasu T. Evolutionary trajectory of phytoalexin biosynthetic gene clusters in rice. Plant J. 2016 May 1. doi: 10.1111/tpj.13200. [PubMed]
• Miyamoto K, Enda I, Okada T, Sato Y, Watanabe K, Sakazawa T, Yumoto E, Shibata K, Asahina M, Iino M, Yokota T, Okada K, Yamane H. Jasmonoyl-L-isoleucine is required for the production of a flavonoid phytoalexin but not diterpenoid phytoalexins in ultraviolet-irradiated rice leaves. Biosci Biotechnol Biochem. 2016 Oct;80(10):1934-8. [PubMed]
• Lee S, Takahashi Y, Oura H, Suzuki-Minakuchi C, Okada K, Yamane H, Nomura N, Nojiri H "Effects of carbazole-degradative plasmid pCAR1 on biofilm morphology in Pseudomonas putida KT2440" Environ Microbiol Rep.2016 Apr;8(2):261-71. [PubMed]
• Yanagida K, Sakuda A, Suzuki-MinakuchiI C, Shintani M, Matsui K, Okada K, Nojiri H. "Comparisons of the transferability of plasmids pCAR1, pB10, R388, and NAH7 among Pseudomonas putida at different cell densities" Biosci Biotechnol Biochem. Jan 25:1-4. [Epub ahead of print] [PubMed]
• Kotake T, Matsuzawa J, Suzuki-MinakuchiI C, Okada K, Nojiri H, Iwata K. "Purification and partial characterization of the extradiol dioxygenase, 2'-carboxy-2,3-dihydroxybiphenyl 1,2-dioxy genase, in the fluorene degradation pathway from Rhodococcus sp. strain DFA3" 2016 Jan 21:1-7. [Epub ahead of print] [PubMed]

AWARDS

• 河野響（M1）：「環境バイオテクノロジー学会2016年度大会」ポスター賞
• Ayako Sakuda (M2): Poster Award for the Kanto branch of JSBBA
• Zongping SUN (D3): Poster Award for the 19th Chinese National Symposium on Environmental Microbiology
• Tomomi Ueda (B4): Poster Award for the 17th Symposium on the Japanese Society for Extremophiles

2015

ORIGINAL ARTICLES

• Yun CS, Takahashi Y, Shintani M, Takeda T, Suzuki-Minakuchi C, Okada K, Yamane H, Nojiri H. "MvaT family proteins encoded on IncP-7 plasmid pCAR1 and the host chromosome regulate host transcriptome cooperatively but differently." (2015) Appl Environ Microbiol. 2015 Nov 20. pii: AEM.03071-15. [PubMed]
• Yamamura C, Mizutani E, Okada K, Nakagawa H, Fukushima S, Tanaka A, Maeda S, Kamakura T, Yamane H, Takatsuji H, Mori M. Diterpenoid Phytoalexin Factor, a bHLH Transcription Factor, Plays a Central Role in the Biosynthesis of Diterpenoid Phytoalexins in Rice. Plant J. 2015 Oct 27. doi: 10.1111/tpj.13065. [PubMed]
• Chiho Suzuki-Minakuchi, Ryusuke Hirotani, Masaki Shintani, Toshiharu Takeda, Yurika Takahashi, Kazuhiro Matsui, Delyana Vasileva, Choong-Soo Yun, Kazunori Okada, Hisakazu Yamane, and Hideaki Nojiri　(2015) "Effects of three different nucleoid-associated proteins encoded on the IncP-7 plasmid pCAR1 on the host Pseudomonas putida KT2440" Appl Environ Microbiol, 81(8):2869-80 [PubMed]
• Takahash Y*, Shintani M*, Takase N, Kazo Y, Kawamura F, Hara H, Nishida H, Okada K, Yamane H, Nojiri H "Modulation of primary cell function of host Pseudomonas bacteria by the conjugative plasmid pCAR1" (2015) Environmental Microbiology. Jan;17(1):134-55. doi: 10.1111/1462-2920.12515.[PubMed]

REVIEW ARTICLES

• Inoue, K.*, Pinyakong, O., Kasuga, K., and H. Nojiri. . A basic introduction to aerobic biodegradation of petroleum aromatic compounds. In "Manual of Environmental Microbiology, 4th ed.", eds. M. V. Yates, C. H. Nakatsu, R. V. Miller, and S. D. Pillai, ASM Press, Washington, DC. in press.
• Okada K, Abe H, Arimura GI (2015) "Jasmonates Induce Both Defense Responses and Communication in Monocotyledonous and Dicotyledonous Plants." Plant Cell Physiol. 2015 Jan;56(1):16-27. Epub 2014 Nov 4.[PubMed]
• Masaki Shintani, Chiho Suzuki-Minakuchi, Hideaki Nojiri (2015) " Nucleoid-associated proteins encoded on plasmids: Occurrence and mode of function" Plasmid 80:32-44. [PubMed]

AWARDS

• 松澤 淳(D2)： 第3回「物構研サイエンスフェスタ」ポスター賞

2014

ORIGINAL ARTICLES

• Hasegawa M, Mitsuhara I, Seo S, Okada K, Yamane H, Iwai T, Ohashi Y (2014) "Analysis on blast fungus-responsive characters of a flavonoid phytoalexin sakuranetin; accumulation in infected rice leaves, antifungal activity and detoxification by fungus." Molecules. Aug 4;19(8):11404-18. doi: 10.3390/molecules190811404.[PubMed]
• Toyomasu T, Usui M, Sugawara C, Kanno Y, Sakai A,Takahashi H, Nakazono M, Kuroda M, Miyamoto K, Morimoto Y, Mitsuhashi W, Okada K, Yamaguchi S, Yamane H "Transcripts of two ent-copalyl diphosphate synthase genes differentially localize in rice plants according to their distinct biological roles" (2014) Journal of Experimental Botany 66(1):369-76[PubMed]
• Miyamoto K, Nishizawa Y, Minami E, Nojiri H, Yamane H, Okada K "Overexpression of the bZIP transcription factor OsbZIP79 suppresses the production of diterpenoid phytoalexin in rice cells" (2014) Journal of Plant Physiology Sep 16;173C:19-27[PubMed]
• Matsuzawa J, Aikawa H, Umeda T, Ashikawa Y, Suzuki-Minakuchi C,Kawano Y, Fujimoto Z, Okada K, Yamane H, Nojiri H "Crystallization and preliminary X-ray diffraction analyses of the redox-controlled complex of terminal oxygenase and ferredoxincomponents in the Rieske nonhaem iron oxygenase, carbazole 1,9a-dioxygenase" (2014) Acta F Oct;70(Pt 10):1406-9. doi:
  10.1107/S2053230X14018779. Epub 2014 Sep 25.[PubMed]
• Suzuki C, Kawazuma K, Horita S, Terada T, Tanokura M, Okada K, Yamane H, Nojiri H. "Oligomerization mechanisms of an H-NS family protein, Pmr, encoded on the plasmid pCAR1 provide a molecular basis for functions of H-NS family members"(2014) PLOS ONE Aug 19;9(8):e105656.[PubMed]
• Miyamoto K, Matsumoto T, Okada A, Komiyama K, Chujo T, Yoshikawa H, Nojiri H, Yamane H, Okada K "Identification of target genes of the bZIP transcription factor OsTGAP1, whose overexpression causes elicitor-induced hyperaccumulation of diterpenoid phytoalexins in rice cells" (2014) PLOS ONE Aug 26;9(8):e105823[PubMed]
• Akagi A, Fukushima S, Okada K, Jiang C.J, Yoshida R, Nakayama A, Shimono M, Sugano S, Yamane H, Takatsuji H "WRKY45-dependent priming of diterpenoid phytoalexin biosynthesis in rice and the role of cytokinin in triggering the reaction" (2014) Plant Molecular Biology 86(1-2):171-83.[PubMed]
• Chujo T, Miyamoto K, Masuda Y, Ogawa S, Shimizu T, Kishi-Kaboshi M, Takahashi A, Nishizawa N, Minami E, Nojiri H, Yamane H, Okada K "Overexpression of phosphomimic mutated OsWRKY53 leads to enhanced blast resistance in rice" (2014) PLOS ONE Jun 3;9(6):e98737[PubMed]
• Inoue K, Usami Y, Ashikawa Y, Noguchi H, Umeda T, Yamagami-Ashikawa A, Horisaki T, Uchimura H, Terada T, Nakamura S, Shimizu K, Habe H, Yamane H, Fujimoto Z, Nojiri H. "Structural Basis of the Divergent Oxygenation Reactions Catalyzed by the Rieske Non-heme Iron Oxygenase, Carbazole 1,9a-Dioxygenase" (2014) Appl Environ Microbiol. 80(9):2821-32[PubMed]
• Shintani M, Matsui K, Inoue J, Hosoyama A, Ohji S, Yamazoe A, Nojiri H, Kimbara K, Ohkuma M. "Single-cell analyses revealed transfer ranges of IncP-1, IncP-7, and IncP-9 plasmids in a soil bacterial community" (2014) Appl Environ Microbiol. 80(1):138-45.[PubMed]

REVIEW ARTICLES

• Miyamoto K, Shimizu T, Okada K. "Transcriptional regulation of the biosynthesis of phytoalexin: a lesson from specialized metabolites in rice" (2014) Plant Biotechnology 31,377-388 (2014)
• Schmelz EA, Huffaker A, Sims JW, Christensen SA, Lu X, Okada K, Peters RJ."Biosynthesis, elicitation and roles of monocot terpenoid phytoalexins." (2014) Plant J 79(4):659-678[PubMed]

AWARDS

• 松澤 淳 (D2)（ポスター賞）第14回日本蛋白質科学会年会
• 吉田悠里 (D1) が第24回イソプレノイド研究会で奨励賞を受賞しました。

2013

ORIGINAL ARTICLES

• Matsuzawa J, Umeda T, Aikawa H, Suzuki C, Fujimoto Z, Okada K, Yamane H, Nojiri H. "Crystallization and preliminary X-ray diffraction studies of the reduced form of the terminal oxygenase component of the Rieske nonhaem iron oxygenase system carbazole 1,9a-dioxygenase" (2013) Acta Crystallogr Sect F Struct Biol Cryst Commun. 69(Pt 11):1284-7.[PubMed]
• Shintani M, Hosoyama A, Ohji S, Tsuchikane K, Takarada H, Yamazoe A, Fujita N, Nojiri H. "Complete Genome Sequence of the Carbazole Degrader Pseudomonas resinovorans Strain CA10 (NBRC 106553)" (2013) Genome Announc. 1(4).[PubMed]
• Yokotani N, Sato Y, Tanabe S, Chujo T, Shimizu T, Okada K, Yamane H, Masaki Shimono M, Sugano S, Takatsuji H, Kaku H, Minami E, Nishizawa Y. "OsWRKY76 is a rice transcriptional repressor playing opposite roles in blast disease resistance and cold stress tolerance" (2013) J. Exp. Botany. 64(16):5085-5097.[PubMed]
• Shimizu T, Miyamoto K, Miyamoto K, Minami E, Nishizawa Y,Iino M, Nojiri H, Yamane H, Okada K.: "OsJAR1 Contributes Mainly to Biosynthesis of the Stress-Induced Jasmonoyl-Isoleucine Involved in Defense Responses in Rice" (2013) Biosci Biotechnol Biochem.77(7):1556-1564.[PubMed]
• Toyomasu T, Usui M, Sugawara C, Otomo K, Hirose Y, Miyao A, Hirochika H, Okada K, Shimizu T, Koga J, Hasegawa M, Chuba M, Kawana Y, Kuroda M, Minami E, Mitsuhashi W, Yamane H.: "Reverse-genetic approach to verify physiological roles of rice phytoalexins: characterization of a knockdown mutant of OsCPS4 phytoalexin biosynthetic gene in rice." (2013) Physiol Plant. 150: 55–62.[PubMed]
• Li W, Shao M, Yang J, Zhong W, Okada K, Yamane H, Qian G, Liu F.: "Oscyp71Z2 involves diterpenoid phytoalexin biosynthesis that contributes to bacterial blight resistance in rice." (2013) Plant Sci.207:98-107.[PubMed]
• Chujo T, Miyamoto K, Shimogawa T, Shimizu T, Otake Y, Yokotani N, Nishizawa Y, Shibuya N, Nojiri H, Yamane H, Minami E, Okada K: "OsWRKY28, a PAMP-responsive transrepressor, negatively regulates innate immune responses in rice against rice blast fungus" (2013) Plant Molecular Biology, 82(1-2):23-37.[PubMed]
• Riemann M, Haga K, Shimizu T, Okada K, Ando S, Mochizuki S, Nishizawa Y, Yamanouchi U, Nick P, Yano M, Minami E, Takano M, Yamane H, Iino M. "Identification of rice ALLENE OXIDE CYCLASE mutants and the function of jasmonate for defence against Magnaporthe oryzae" (2013) Plant J. 74(2):226-238.[PubMed]

REVIEW ARTICLES

• Nojiri H. "Impact of catabolic plasmids on host cell physiology." (2013) Curr Opin Biotechnol. 24(3):423-30.[PubMed]
• Yamane H.:"Biosynthesis of Phytoalexins and Regulatory Mechanisms of It in Rice." (2013) Biosci Biotechnol Biochem Jun 7. (Award review)[PubMed]
• Miyamoto K, Okada K : Operon-like Gene Cluster in Plant: The Regulatory Mechanism of the Phytoalexin Production in Rice; Kagaku to Seibutsu, 51, 310-317 (2013). In Japanese.

BOOKS

• Nojiri H, Tsuda M, Fukuda M, Kamagata Y : Biodegradative Bacteria:How Bacteria Degrade, Survive, Adapt, and Evolve In (Eds.) VIII, 358 p. 79 illus., 22 illus. in color.(2014).

2012

ORIGINAL ARTICLES

• Ashikawa Y, Fujimoto Z, Usami Y, Inoue K, Noguchi H, Yamane H, Nojiri H. "Structural insight into the substrate- and dioxygen-binding manner in the catalytic cycle of rieske nonheme iron oxygenase system, carbazole 1,9a-dioxygenase." (2012) BMC Struct Biol. [in press][PubMed]
• Ayabe-Chujo Y, Usami Y, Yoshida T, Omori T, Nojiri H. "Membrane topology and functional analysis of Methylobacillus sp. 12S genes epsF and epsG, encoding polysaccharide chain-length determining proteins. (2012) Biosci Biotechnol Biochem. 76(3):608-12.[PubMed]
• Shimizu T, Lin F, Hasegawa M, Nojiri H, Yamane H, Okada K. "The potential bioproduction of the pharmaceutical agent sakuranetin, a flavonoid phytoakexin in rice" (2012) Bioengineered Bugs 3(6):352-7.[PubMed]
• Shimizu T, Lin F, Hasegawa M, Okada K, Nojiri H, Yamane H. "Purification and identification of naringenin 7-O-methyltransferase, a key enzyme in the biosynthesis of the flavonoid phytoalexin sakuranetin in rice "(2012) J Biol Chem., 287(23):19315-19325.[PubMed]
• Miyamoto K, Shimizu T, Mochizuki S, Nishizawa Y, Minami E, Nojiri H, Yamane H, Okada K. "Stress-induced expression of the transcription factor RERJ1 is tightly regulated in response to jasmonic acid accumulation in rice"(2012) Protoplasma 250(1):241-9.[PubMed]
• Miyamoto K, Shimizu T, Lin F, Sainsbury F, Thuenemann E, Lomonossoff G, Nojiri H, Yamane H, Okada K. "Identification of an E-box motif responsible for the expression of jasmonic acid-induced chitinase gene OsChia4a in rice"(2012) J Plant Physiol., 169:621-627.[PubMed]
• Hamada H, Kurusu T, Okuma E, Nokajima H, Kiyoduka M, Koyano T, Sugiyama Y, Okada K, Koga J, Saji H, Miyao A, Hirochika H, Yamane H, Murata Y, Kuchitsu K. "Regulation of a proteinaceous elicitor-induced Ca2+ influx and production of phytoalexins by a putative voltage-gated cation channel, OsTPC1, in cultured rice cells." (2012) J Biol Chem., 287(13):9931-9939.[PubMed]
• Wang Q, Hillwig ML, Okada K, Yamazaki K, Wu Y, Swaminathan S, Yamane H, Peters RJ."Characterization of CYP76M5-8 indicates metabolic plasticity within a plant biosynthetic gene cluster." (2012) J Biol Chem., 287(9):6159-6168.[PubMed]

REVIEW ARTICLES

• Nojiri H. "Structural and molecular genetic analyses of the bacterial carbazole degradation system." (2012) Biosci Biotechnol Biochem., 76(1):1-18.[PubMed]

2011

ORIGINAL ARTICLES

• Horisaki T, Yoshida E, Sumiya K, Takemura T, Yamane H, and Nojiri H "Isolation and characterization of monochloroacetic acid-degrading bacteria" (2011) J. Gen. Appl. Microbiol., 57, 277-284.[PubMed]
• Takeda T, Yun CS, Shintani M, Yamane H, Nojiri H. "Distribution of genes encoding nucleoid-associated protein homologs in plasmids."(2011) Int J Evol Biol. :685015.[PubMed]
• Suzuki C, Yun CS, Umeda T, Terabayashi T, Watanabe K, Yamane H, Nojiri H. "Oligomerization and DNA-binding capacity of Pmr, a histone-like protein H1 (H-NS) family protein encoded on IncP-7 carbazole-degradative plasmid pCAR1." (2011) Biosci Biotechnol Biochem. 75:711-7.[PubMed]
• Shintani M, Horisaki T, Yamane H, Ohkuma M, Nojiri H. "Evolution of the IncP-7 carbazole-degradative plasmid pCAR1 improves survival of its host Pseudomonas fluorescens Pf0-1 in artificial water microcosms." (2011) Microbiology. 157:2276-86.[PubMed]
• Shintani M, Tokumaru H, Takahashi Y, Miyakoshi M, Yamane H, Nishida H, Nojiri H. "Alterations of RNA maps of IncP-7 plasmid pCAR1 in various Pseudomonas bacteria." (2011) Plasmid. 66:85-92.[PubMed]
• Shintani M, Matsumoto T, Yoshikawa H, Yamane H, Ohkuma M, Nojiri H. (2011) DNA rearrangement occurred in the carbazole degradative plasmid pCAR1 and the chromosome of its unsuitable host Pseudomonas fluorescens Pf0-1. Microbiology. in press.[PubMed]
• Ando S, Sato Y, Shigemori H, Shimizu T, Okada K, Yamane H, Jikumaru Y, Kamiya Y, Yamada K, Akimoto-Tomiyama C, Tanabe S, Nishizawa Y, Minami E. "Identification and characterization of 2'-deoxyuridine from the supernatant of conidial suspensions of rice blast fungus as an infection-promoting factor in rice plants." (2011) Mol Plant Microbe Interact. May;24(5):519-32.[PubMed]

REVIEW ARTICLES

• Okada K. "The biosynthesis of isoprenoids and the mechanisms regulating it in plants." (2011) Biosci Biotechnol Biochem. 75:1219-25.(Award review)[PubMed]

2010

ORIGINAL ARTICLES

• Umeda T, Katsuki J, Ashikawa Y, Usami Y, Inoue K, Noguchi H, Fujimoto Z, Yamane H, Nojiri H. "Crystallization and preliminary X-ray diffraction studies of a terminal oxygenase of carbazole 1,9a-dioxygenase from Novosphingobium sp. KA1." (2010) Acta Crystallogr Sect F Struct Biol Cryst Commun. 66:1480-3.[PubMed]
• Yun CS, Suzuki C, Naito K, Takeda T, Takahashi Y, Sai F, Terabayashi T, Miyakoshi M, Shintani M, Nishida H, Yamane H, Nojiri H. "Pmr, a histone-like protein H1 (H-NS) family protein encoded by the IncP-7 plasmid pCAR1, is a key global regulator that alters host function." (2010) J Bacteriol. 192:4720-31.[PubMed]
• Shintani M, Yamane H, Nojiri H. "Behavior of various hosts of the IncP-7 carbazole-degradative plasmid pCAR1 in artificial microcosms." (2010.)Biosci Biotechnol Biochem. 74:343-9.[PubMed]
• Shintani M, Takahashi Y, Tokumaru H, Kadota K, Hara H, Miyakoshi M, Naito K, Yamane H, Nishida H, Nojiri H. 2010. Response of the Pseudomonas host chromosomal transcriptome to carriage of the IncP-7 plasmid pCAR1. Environ Microbiol. 12:1413-26.[PubMed]
• Shimizu T, Nakano T, Takamizawa D, Desaki Y, Ishii-Minami N, Nishizawa Y, Minami E, Okada K, Yamane H, Kaku H, Shibuya N. "Two LysM receptor molecules, CEBiP and OsCERK1, cooperatively regulate chitin elicitor signaling in rice." (2010) Plant J. Oct;64(2):204-14.[PubMed]
• Hasegawa M, Mitsuhara I, Seo S, Imai T, Koga J, Okada K, Yamane H, Ohashi Y. "Phytoalexin accumulation in the interaction between rice and the blast fungus." (2010) Mol Plant Microbe Interact. Aug;23(8):1000-11.[PubMed]
• Kishi-Kaboshi M, Okada K, Kurimoto L, Murakami S, Umezawa T, Shibuya N, Yamane H, Miyao A, Takatsuji H, Takahashi A, Hirochika H. "A rice fungal MAMP-responsive MAPK cascade regulates metabolic flow to antimicrobial metabolite synthesis." (2010) Plant J. Aug;63(4):599-612.[PubMed]
• Kurusu T, Hamada J, Nokajima H, Kitagawa Y, Kiyoduka M, Takahashi A, Hanamata S, Ohno R, Hayashi T, Okada K, Koga J, Hirochika H, Yamane H, Kuchitsu K. "Regulation of microbe-associated molecular pattern-induced hypersensitive cell death, phytoalexin production, and defense gene expression by calcineurin B-like protein-interacting protein kinases, OsCIPK14/15, in rice cultured cells." (2010) Plant Physiol. Jun;153(2):678-92.[PubMed]

REVIEW ARTICLES

• Shintani M, Takahashi Y, Yamane H, Nojiri H. "The behavior and significance of degradative plasmids belonging to Inc groups in Pseudomonas within natural environments and microcosms." (2010) Microbes Environ. 25:253-65. (Review)[PubMed]

2009

ORIGINAL ARTICLES

• Shintani, M., H. Yamane, and H. Nojiri. Behavior of different hosts of the IncP-7 carbazole-degradative plasmid pCAR1 in the artificial microcosms. Biosci. Biotechnol. Biochem., in press.[PubMed]
• Shintani, M., Y. Takahashi, H. Tokumaru, K. Kadota, H. Hara, M. Miyakoshi, K. Naito, H. Yamane, H. Nishida, and H. Nojiri. Response of the Pseudomonas host chromosomal transcriptome to carriage of the IncP-7 plasmid pCAR1. Environ. Microbiol., in press.[PubMed]
• Habe, H., Kobuna, A. Hosoda, T. Kosaka, T. Endoh, H. Tamura, H. Yamane, H. Nojiri, T. Omori, and K. Watanabe. Identification of the electron transfer flavoprotein as an upregulated enzyme in the benzoate utilization of Desulfotignum balticum. Biosci. Biotechnol. Biochem. (2009) 73, 1647-1652.[PubMed]
• Inoue, K., Y. Ashikawa, T. Umeda, M. Abo, J. Katsuki, Y. Usami, H.Noguchi, Z. Fujimoto, T. Terada, H. Yamane, and H. Nojiri. "Specific interactions between the ferredoxin and terminal oxygenase components of a class IIB Rieske nonheme iron oxygenase, carbazole 1,9a-dioxygenase." J. Mol. Biol., (2009) 392: 436-451.[PubMed]
• Okada A, Okada K, Miyamoto K, Koga J, Shibuya N, Nojiri H, Yamane H. "OsTGAP1, a bZIP transcription factor, coordinately regulates the inductive production of diterpenoid phytoalexins in rice." J Biol Chem. (2009) Sep 25;284(39):26510-2651.[PubMed]
• Chujo T, Sugioka N, Masuda Y, Shibuya N, Takemura T, Okada K, Nojiri H, Yamane H. "Promoter analysis of the elicitor-induced WRKY gene OsWRKY53, which is involved in defense responses in rice." Biosci Biotechnol Biochem. (2009)Aug;73(8):1901-1904.[PubMed]
• Kato T, Tanabe S, Nishimura M, Ohtake Y, Nishizawa Y, Shimizu T, Jikumaru Y, Koga J, Okada K, Yamane H, Minami E. "Differential responses of rice to inoculation with wild-type and non-pathogenic mutants of Magnaporthe oryzae." Plant Mol Biol. (2009) Aug;70(6):617-625.[PubMed]
• Toyomasu T, Kagahara T, Hirose Y, Usui M, Abe S, Okada K, Koga J, Mitsuhashi W, Yamane H. "Cloning and characterization of cDNAs encoding ent-copalyl diphosphate synthases in wheat: insight into the evolution of rice phytoalexin biosynthetic genes." Biosci Biotechnol Biochem. (2009) Mar 23;73(3):772-725.[PubMed]
• Takahashi Y, Shintani M, Li L, Yamane H, Nojiri H. "Carbazole-degradative IncP-7 plasmid pCAR1.2 is structurally unstable in Pseudomonas fluorescens Pf0-1, which accumulates catechol, the intermediate of the carbazole degradation pathway." Appl Environ Microbiol. (2009) 75(12):3920-3929.[PubMed]
• Takahashi Y, Shintani M, Yamane H, Nojiri H. "The complete nucleotide sequence of pCAR2: pCAR2 and pCAR1 were structurally identical IncP-7 carbazole degradative plasmids." Biosci Biotechnol Biochem. (2009)Mar 23;73(3):744-746.[PubMed]
• Miyakoshi, M., Nishida, H., Shintani, M., Yamane, H., Nojiri, H. "High-resolution mapping of plasmid transcriptomes in different host bacteria." BMC Genomics,2009 Jan 9;10:12.[PubMed]

REVIEW ARTICLES

• Kazunori Okada : Biosynthetic Gene Clusters for Phytoalexin in Rice., Kagaku to Seibutsu 47, 43-50 (2009).
• Hideaki Nojiri, Yurika Takahashi, and Masaki Shintani: "Significance of horizontal gene transfer via plasmid conjugation to use bacteria in the natural environment" was published in Bioscience & industry 67(2) pp.59`64 2009/2

2008

ORIGINAL ARTICLES

• Uchimura, H., Horisaki, T., Umeda, T., Noguchi, H., Usami, Y., Li, L., Terada, T., Nakamura, S., Shimizu, K., Takemura, T., Habe, H., Furihata, K., Omori, T., Yamane, H., Nojiri, H."Alteration of the substrate specificity of the angular dioxygenase carbazole 1,9a-dioxygenase" Biosci Biotechnol Biochem, 72(12):3237-3248 (2008)[PubMed]
• Ko KW, Lin F, Katsumata T, Sugai Y, Miyazaki S, Kawaide H, Okada K, Nojiri H, Yamane H.hFunctional identification of a rice ent-kaurene oxidase, OsKO2, using the Pichia pastoris expression systemh Biosci Biotechnol Biochem. 72(12):3285-3288 (2008)[PubMed]
• Umeda T, Katsuki J, Usami Y, Inoue K, Noguchi H, Fujimoto Z, Ashikawa Y, Yamane H, Nojiri H. gCrystallization and preliminary X-ray diffraction studies of a novel ferredoxin involved in the dioxygenation of carbazole by Novosphingobium sp. KA1h Acta Crystallogr Sect F Struct Biol Cryst Commun (2008) 64(Pt 7):632-635. [PubMed]
• Hayashi Y, Toyomasu T, Hirose Y, Onodera Y, Mitsuhashi W, Yamane H, Sassa T, Dairi T gComparison of the enzymatic properties of ent-copalyl diphosphate synthases in the biosynthesis of phytoalexins and gibberellins in riceh Biosci Biotechnol Biochem. 72(2):523-530 (2008)[PubMed]
• Toyomasu T, Kagahara T, Okada K, Koga J, Hasegawa M, Mitsuhashi W, Sassa T, Yamane H gDiterpene phytoalexins are biosynthesized in and exuded from the roots of rice seedlingsh Biosci Biotechnol Biochem. 72(2):562-567 (2008) 8)[PubMed]
• Shintani M, Matsui K, Takemura T, Yamane H, Nojiri H gBehavior of the IncP-7 carbazole-degradative plasmid pCAR1 in artificial environmental samplesh Appl Microbiol Biotechnol. (2008) 80(3):485-497[PubMed]
• Chujo, T., Kato, T., Yamada, K., Takai, R., Akimoto-Tomiyama, C., Minami, E., Nagamura, Y., Shibuya, N., Yasuda, M., Nakashita, H., Nojiri, H., and Yamane, H. : "Characterization of an elicitor-induced rice WRKY gene, OsWRKY71" Bioscience, Biotechnology, and Biochemistry, 72, 240-245 (2008). [PubMed]
• Shintani, M., Fukushima, N., Tezuka, M., Yamane, H., and Nojiri, H. : "Conjugative transfer of the IncP-7 carbazole degradative plasmid, pCAR1, in river water samples" Biotechnology Letters, 30, 117-122 (2008). [PubMed]
• Shimizu, T., Jikumaru, Y., Okada, A., Okada, K., Koga, J., Umemura, K., Minami, E., Shibuya, N., Hasegawa, M., Kodama, O, Nojiri, H., and Yamane, H. : "Effects of a bile acid elicitor, cholic acid, on the biosynthesis of diterpenoid phytoalexins in suspension-cultured rice cells" Phytochemistry, 69, 973-981 (2008). [PubMed]
• Tani, T., Sobajima, H., Okada, K., Chujo, T., Arimura, S., Tsutsumi, N., Nishimura, M., Seto, H., Nojiri, H., and Yamane, H. : "Identification of the OsOPR7gene encoding 12-oxophytodienoate reductase involved in the biosynthesis of jasmonic acid in rice" Planta, 227, 517-526 (2008). [PubMed]
• Okada, K., Kashihara, H., Yamaguchi, S., Kawaide, H., Kamiya, Y., Nojiri, H., and Yamane, H. : "Genetic evidence for the role of isopentenyl diphosphate isomerases in the mevalonate pathway and plant development in Arabidopsis" Plant and Cell Physiology, 49, 604-616 (2008). [PubMed]
• Habe, H., Kobuna, A., Hosoda, A., Kouzuma, A., Yamane, H., Nojiri, H., Omori, T., and Watanabe, K. : "Subtractive hybridization and random arbitrarily primed PCR analyses of a benzoate-assimilating bacterium, Desulfotignum balticum" Applied Microbiology and Biotechnology, 79, 87-95 (2008). [PubMed]
• Kouzuma, A., Endoh, T., Omori, T., Nojiri, H., Yamane, H., and Habe, H. : "Transcription factors CysB and SfnR constitute the hierarchical regulatory system for the sulfate starvation response in Pseudomonas putida" Journal of Bacteriology, in press. [PubMed]

BOOKS

• Nojiri, H., Sota, M., and Shintani, M. : "Catabolic plasmids involved in the degradation of polycyclic aromatic hydrocarbons and heteroaromatic compounds" In "Microbiology Monographs: Microbial Megaplasmids", ed. Schwartz E., Springer, Heidelberg, Germany, in press.
• Konno, K., Sabelis, M., Takabayashi, J., Yamane, H., Sassa, T., and Oikawa, H. : "Chemical defense and toxins of plants" In "Comprehensive Natural Products Chemistry II Voi. 8", ed. Mori, K., Elsevier, Oxford, UK, in press.

REVIEW ARTICLES

• Nojiri, H., Takahashi, Y., Naito, K., Matsumoto, T., and Shintani, M. : "Plasmid biology for innovative utilization of xenobiotic degrading bacteria" BIOINDUSTRY, in press. In Japanese.

2007

ORIGINAL ARTICLES

• Shintani, M., Urata, M., Inoue, K., Eto, K., Habe, H., Omori, T., Yamane, H., and Nojiri, H. : "TheSphingomonas plasmid pCAR3 is involved in complete mineralization of carbazole" Journal of Bacteriology, 189, 2007-2020 (2007). [PubMed]
• Ashikawa, Y., Uchimura, H. Fujimoto, Z., Inoue, K., Noguchi, H., Yamane, H., and Nojiri, H. : "Crystallization and preliminary X-ray diffraction studies of the ferredoxin reductase component in the Rieske nonheme iron oxygenase system carbazole 1,9a-dioxygenase" Acta Crystallographica, F63, 499-502 (2007).[PubMed]
• Chujo, T., Takai, R., Akimoto-Tomiyama, C., Ando, S., Minami, E., Nagamura, Y., Kaku, H., Shibuya, N., Yasuda, M., Nakashita, H., Umemura, K., Okada, A., Okada, K., Nojiri, H., and Yamane, H. : "Involvement of the elicitor-induced gene OsWRKY53 in the expression of defense-related genes in rice" Biochimica et Biophysica Acta, 1769, 497-505 (2007). [PubMed]
• Okada, A., Shimizu, T., Okada, K., Kuzuyama, T., Koga, J., Shibuya, N., Nojiri, H., and Yamane, H. : "Elicitor induced activation of the methylerythritol phosphate pathway toward phytoalexins biosynthesis in rice" Plant Molecular Biology, 65, 177-187 (2007). [PubMed]
• Habe, H., Kouzuma, A., Endoh, T., Omori, T., Yamane, H., and Nojiri, H. : "Transcriptional regulation of the sulfate-starvation-induced genesfnA by a σ54-dependent activator ofPseudomonas putida" Microbiology, 153, 3091-3098 (2007). [PubMed]
• Inoue, K., Ashikawa, Y., Usami, Y., Noguchi, H., Fujimoto, Z., Yamane, H., and Nojiri, H. : "Crystallization and preliminary crystallographic analysis of the ferredoxin component of carbazole 1,9a-dioxygenase from Nocardioides aromaticivorans IC177" Acta Crystallographica, F63, 855-857 (2007). [PubMed]
• Kouzuma, A., Endoh, T., Omori, T., Nojiri, H., Yamane, H., Habe, H. : "The ptsP gene encoding the PTS family protein EINtr is essential for dimethyl sulfone utilization by Pseudomonas putida" FEMS Microbiology Letters, 275, 175-181 (2007). [PubMed]
• Miyakoshi, M., Shintani, M., Terabayashi, T., Kai, S., Yamane, H., and Nojiri, H. : "Transcriptome analysis of Pseudomonas putida KT2440 harboring the completely sequenced IncP-7 plasmid pCAR1" Journal of Bacteriology, 189, 6849-6860 (2007).[PubMed]
• Nemoto, T., Okada, A., Okada, K., Shibuya, N., Toyomasu, T., Nojiri, H., and Yamane, H. : "Promoter analysis of the rice stemar-13-ene synthase gene OsDTC2, which is involved in the biosynthesis of the phytoalexin oryzalexin S” Biochimica et Biophysica Acta, 1769, 678-683 (2007). [PubMed]
• Shimura, K., Okada, A., Okada, K., Jikumaru, Y., Ko, K.W., Toyomasu, T., Sassa, T., Hasegawa, M., Kodama, O., Shibuya, N., Koga, J., Nojiri, H., and Yamane, H. : “Identification of a biosynthetic gene cluster in rice for momilactones" Journal of Biological Chemistry, 282, 34013-34018 (2007).[PubMed]
• Sobajima, H., Tani, T., Chujo, T., Okada, K., Suzuki, K., Mori, S., Minami, E., Nishiyama, M., Nojiri, H., and Yamane, H. : "Identification of a jasmonic acid-responsive region in the promoter of the rice 12-oxophytodienoic acid reductase 1 gene OsOPR1" Bioscience, Biotechnology, and Biochemistry, 71, 3110-3115 (2007). [PubMed]

BOOKS

• Nojiri, H., and Omori, T. : "Carbazole metabolism by pseudomonads" In "Pseudomonas volume 5", eds. Ramos, J.L., and Filloux, A., Springer, New York, New York, USA, 107-145 (2007).

REVIEW ARTICLES

• Inoue, K., and Nojiri, H. : "Electron transport in multi-component aromatic hydroxylating dioxygenases" Kagaku to Seibutsu, 45，468-475 (2007). In Japanese.
• Kouzuma, A., Yamane, H., and Habe, H. : "Application of sulfate starvation response of bacteria to production of useful compounds" Kagaku to Seibutsu, 45, 609-610 (2007). In Japanese.
• Nojiri, H., Miyakoshi, M., Shintani, M., Nishida, H. : "Plasmid function in natural environment" Kagaku to Seibutsu, 45, 635-643 (2007). In Japanese.
• Yamane, H., Toyomasu, T., and Sassa, T. : "Phytoalexin biosynthesis and its regulatory mechanisms" Proteins, Nucleic acid and Enzyme, 52, 648-653 (2007). In Japanese.

2006

ORIGINAL ARTICLES

• Tanabe, S., Okada, M., Jikumaru, Y., Yamane, H., Kaku, H., Shibuya, N., and Minami, E. : “Induction of resistance against rice blast fungus in rice plants treated with a potent elicitor, N-acetylchitooligosaccharide” Bioscience, Biotechnology, and Biochemistry, 70, 1599-1605 (2006). [PubMed]
• Desaki, Y., Miya, Y., Venkatesh, B., Tsuyumu, S., Yamane, H., Kaku, H., Minami, E., and Shibuya, N. : “Bacterial lipopolysaccharides induce defense responses associated with programmed cell death in rice cells” Plant and Cell Physiology, 47, 1530-1540 (2006). [PubMed]
• Kanno, Y., Otomo, K., Kenmoku, H., Mitsuhashi, W., Yamane, H., Oikawa, H., Toshima, H., Matsuoka, M., Sassa, T., and Toyomasu, T. : “Characterization of a rice gene family encoding type-A diterpene cyclases” Bioscience, Biotechnology, and Biochemistry, 70, 1702-1710 (2006). [PubMed]
• Miyakoshi, M., Urata, M., Habe, H., Omori, T., Yamane, H., and Nojiri, H. : “Differentiation of carbazole catabolic operons by replacement of the regulated promoter via transposition of an insertion sequence” Journal of Biological Chemistry, 281, 8450-8457 (2006). [PubMed]
• Ashikawa, Y., Fujimoto, Z., Noguchi, H., Habe, H., Omori, T., Yamane, H., and Nojiri, H. : “Electron transfer complex formation between oxygenase and ferredoxin components in Rieske nonheme iron oxygenase system” Structure, 14, 1779-1789 (2006). [PubMed]
• Urata, M., Uchimura, H., Noguchi, H., Sakaguchi, T., Takemura, T., Eto, K., Habe, H., Omori, T., Yamane, H., and Nojiri, H. : “Plasmid pCAR3 contains multiple gene sets involved in the conversion of carbazole to anthranilate” Applied and Environmental Microbiology, 72, 3198-3205 (2006). [PubMed]
• Shintani, M., Yano, H., Habe, H., Omori, T., Yamane, H., Tsuda, M., Nojiri, H. : “Characterization of the replication, maintenance, and transfer features of the IncP-7 plasmid pCAR1, which carries genes involved in carbazole and dioxin degradation” Applied and Environmental Microbiology, 72, 3206-3216 (2006). [PubMed]
• Inoue, K., Habe, H., Yamane, H., and Nojiri, H. : “Characterization of novel carbazole catabolism genes from Gram-positive carbazole degraderNocardioides aromaticivorans IC177” Applied and Environmental Microbiology, 72, 3321-3329 (2006). [PubMed]
• Jun, S.-Y., Fushinobu, S., Nojiri, H., Omori, T., Shoun, H., and Wakagi, T. : “Improving the catalytic efficiency of a meta-cleavage product hydrolase (CumD) from Pseudomonas fluorescens IP01” Biochimica et Biophysica Acta, 1764, 1159-1166 (2006). [PubMed]
• Kouzuma, A., Pinyakong, O., Nojiri, H., Omori, T., Yamane, H., and Habe, H. : “Functional and transcriptional analyses of the initial oxygenase genes for acenaphthene degradation fromSphingomonas sp. strain A4” Microbiology, 152, 2455-2467 (2006). [PubMed]
• Santoh, K., Kouzuma, A., Ishizeki, R., Iwata, K., Shimura, M., Hayakawa, T., Hoaki, T., Nojiri, H., Omori, T., Yamane, H., and Habe, H. : “Detection of a bacterial group within the phylum Chloroflexiand reductive-dehalogenase-homologous genes in the pentachlorobenzene-dechlorinating estuarine sediment from the Arakawa river, Japan” Microbes and Environment, 21, 154-162 (2006).
• Inoue, K., Ashikawa, Y., Usami, Y., Noguchi, H., Fujimoto, Z., Yamane, H., and Nojiri, H. : “Crystallization and preliminary X-ray diffraction studies of the terminal oxygenase component of carbazole 1,9a-dioxygenase from Nocardioides aromaticivorans IC177” Acta Crystallographica, F62, 1212-1214 (2006). [PubMed]

REVIEW ARTICLES

• Uchida, E. and Nojiri, H. : "Phytoremediation" Kagaku to Seibutsu, 44, 578-580 (2006). In Japanese.
• Ashikawa, Y., Inoue, K., Katsuki, J., Usami, Y., Noguchi, H., Nojiri, H. : "Structure and function in substrate recognition and electron transport of aromatic hydroxylating dioxygenases systems" J. Environ. Biotechnol., 6, 69-78 (2006). In Japanese.

2005

ORIGINAL ARTICLES

• Sakakibara, H., Kasahara, H., Ueda, N., Kojima, M., Takei, K., Hishiyama, S., Asami, T., Okada, K., Kamiya, Y., Yamaya, T., and Yamaguchi, S. : “Agrobacterium tumefaciens increases cytokinin production in plastids by modifying the biosynthetic pathway in the host plant” Proceeding of National Academy of Science U.S.A., 102, 9972-9977 (2005). [PubMed]
• Shimada, A., Yamane, H., and Kimura, Y. : “Interaction between aspterric acid and indole-3-acetic acid on reproductive growth in Arabidopsis thaliana" Zeitschrift fur Naturforschung, 60c, 572-576 (2005). [PubMed]
• Kiribuchi, K., Jikumaru, Y., Kaku, H., Minami, E., Hasegawa, M., Kodama, O., Seto, H., Okada, K., Nojiri, H., and Yamane, H. : “Involvement of the basic helix-loop-helix transcription factor RERJ1 in wounding and drought stress responses in rice plants” Bioscience, Biotechnology and Biochemistry, 69, 1042-1044 (2005). [PubMed]
• Nojiri, H., Ashikawa, Y., Noguchi, H., Nam, J.-W., Urata, M., Fujimoto, Z., Uchimura, H., Terada, T., Nakamura, S., Shimizu, K., Yoshida, T., Habe, H., and Omori, T. : “Structure of the terminal oxygenase component of angular dioxygenase, carbazole 1,9a-dioxygenase” Journal of Molecular Biology, 351, 355-370 (2005). [PubMed]
• Endo, T., Habe, H., Nojiri, H., Yamane, H., and Omori, T. : “The σ54-dependent transcriptional activator SfnR regulates the expression of thePseudomonas putida sfnFG operon responsible for dimethyl sulphone utilization” Molecular Microbiology, 55, 897-911 (2005). [PubMed]
• Dong, X., Fushinobu, S., Fukuda, E., Terada, T., Nakamura, S., Shimizu, K., Nojiri, H., Omori, T., Shoun, H., and Wakagi, T. : “Crystal structure of the terminal oxygenase component of cumene dioxygenase from Pseudomonas fluorescens IP01” Journal of Bacteriology, 187, 2483-2490 (2005).[PubMed]
• Nam, J.-W., Noguchi, H., Fujimoto, Z., Mizuno, H., Ashikawa, Y., Abo, M., Fushinobu, S., Kobashi, N., Wakagi, T., Iwata, K., Yoshida, T., Habe, H., Yamane, H., Omori, T., and Nojiri, H. : “Crystal structure of the ferredoxin component of carbazole 1,9a-dioxygenase of Pseudomonas resinovorans strain CA10, a novel Rieske non-heme iron oxygenase system” Proteins, 58, 779-789 (2005). [PubMed]
• Uchida, E., Ouchi, T., Suzuki, Y., Yoshida, T., Habe, H., Yamaguchi, I., Omori, T., and Nojiri, H. : “Secretion of bacterial xenobiotic-degrading enzymes from transgenic plants by an apoplastic expressional system: an applicability for phytoremediation” Environmental Science Technology, 39, 7671-7677 (2005). [PubMed]
• Habe, H., Chung, J.-S., Ishida, A., Kasuga, K., Ide, K., Takemura, T., Nojiri, H., Yamane, H., and Omori, T. : “The fluorene catabolic linear plasmid inTerrabacter sp. strain DBF63 carries the β-ketoadipate pathway genes, pcaRHGBDCFIJ, also found in proteobacteria” Microbiology, 151, 3713-3722 (2005). [PubMed]
• Shintani, M., Yoshida, T., Habe, H., Omori, T., and Nojiri, H. : “Large plasmid pCAR2 and class II transposon Tn4676 are functional mobile genetic elements to distribute the carbazole/dioxin-degradative car gene cluster in different bacteria” Applied Microbiology and Biotechnology, 67, 370-382 (2005). [PubMed]
• Takagi, T., Habe, H., Yoshida, T., Yamane, H., Omori, T., and Nojiri, H. : “Characterization of [3Fe-4S] ferredoxin DbfA3, which functions in the angular dioxygenase system of Terrabacter sp. strain DBF63” Applied Microbiology and Biotechnology, 68, 336-345 (2005). [PubMed]
• Fushinobu, S., Jun, S.-Y., Hidaka, M., Nojiri, H., Yamane, H., Shoun, H., Omori, T., and Wakagi, T. : “A series of crystal structures of a meta-cleavage product hydrolase from Pseudomonas fluorescensIP01 (CumD) complexed with various cleavage products” Bioscience, Biotechnology, and Biochemistry, 69, 491-498 (2005). [PubMed]
• Inoue, K., Habe, H., Yamane, H., Omori, T., and Nojiri, H. : “Diversity of carbazole-degrading bacteria having the car gene cluster: isolation of a novel Gram-positive carbazole-degrading bacterium” FEMS Microbiology Letters, 245, 145-153 (2005). [PubMed]
• Shintani, M., Habe, H., Tsuda, M., Omori, T., Yamane, H., and Nojiri, H. : “Recipient range of IncP-7 conjugative plasmid pCAR2 fromPseudomonas putida HS01 is broader than from other Pseudomonas strains” Biotechnology Letters, 27, 1847-1853 (2005). [PubMed]
• Ashikawa, Y., Fujimoto, Z., Noguchi, H., Habe, H., Omori, T., Yamane, H., and Nojiri, H. : “Crystallization and preliminary X-ray diffraction analysis of the electron-transfer complex between the terminal oxygenase component and ferredoxin in the Rieske non-haem iron oxygenase system carbazole 1,9a-dioxygenase” Acta Crystallographica, F61, 577-580 (2005).[PubMed]

BOOKS

• Inoue, K., Widada, J., Omori, T., and Nojiri, H. : "Molecular techniques of xenobiotic-degrading bacteria and their catabolic genes in bioremediation" In "Bioremediation of aquatic and terrestrial ecosystems", eds. Fingerman, M., and Nagabhushanam, R., Science Publishers, Inc., New Hampshire, USA, 1-30 (2005).

REVIEW ARTICLES

• Nojiri, H., Uchida, E., and Omori, T. : "Rhizosecretion: Application of xenobiotic-secreting plants in bioremediation" BRAIN Techno News, 107, 10-15 (2005). In Japanese.
• Nojiri, H., and Tsuda, M. : "Preface for functional evolution of xenobiotic-degrading bacteria" Protein, Nucleic acid, and Enzyme, 50, 1505-1510 (2005). In Japanese.
• Nojiri, H., Ashikawa, Y., Noguchi, H., and Uchimura, H. : "Diversity in structure, interaction among components, and electron transport system of bacterial aromatic hydroxylating dioxygenases" Protein, Nucleic acid, and Enzyme, 50, 1519-1526 (2005). In Japanese.

2004

ORIGINAL ARTICLES

• Cho, EM., Okada, A., Kenmoku, H., Otomo, K., Toyomasu, T., Mitsuhashi, W., Sassa, T., Yajima, A., Yabuta, G., Mori, K., Oikawa, H., Toshima, H., Shibuya, H., Nojiri, H., Omori, T., Nishiyama, M., and Yamane, H. : “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 Journal, 37, 1-8 (2004). [PubMed]
• Nemoto, T., Cho, EM., Okada, A., Okada, K., Otomo, K., Kanno, Y., Toyomasu, T., Mitsuhashi, W., Sassa, T., Minami, E., Shibuya, N., Nishiyama, M., Nojiri, H., Yamane, H. : “Stemar-13-ene synthase, a diterpene cyclase involved in the biosynthesis of the phytoalexin oryzalexin S in rice.” FEBS Lett., 571, 182-186 (2004). [PubMed]
• Kiribuchi, K., Sugimori, M., Takeda, M., Otani, T., Okada, K., Onodera, H., Ugaki, M., Tanaka, Y., Tomiyama-Akimoto, C., Yamaguchi, T., Minami, E., Shibuya, N., Omori, T., Nishiyama, M., Nojiri, H., Yamane, H. : “RERJ1, a jasmonic acid-responsive gene from rice, encodes a basic helix-loop-helix protein.” Biochemical and Biophysical Research Communications, 325, 857-863 (2004). [PubMed]
• Okada, K., Ohara, K., Yazaki, K., Nozaki, K., Uchida, N., Kawamukai, M., Nojiri, H., Yamane,H. : “The AtPPT1 gene encoding 4-hydroxybenzoate polyprenyl diphosphate transferase in ubiquinone biosynthesis is required for embryo development in Arabidopsis thaliana" Plant Molecular Biology, 55, 567-577 (2004). [PubMed]
• Otsuka, M., Kenmoku, H., Ogawa, M., Okada, K., Mitsuhashi, W., Sassa, T., Kamiya, Y., Toyomasu, T., Yamaguchi, S. : “Emission of ent-kaurene, a diterpenoid hydrocarbon precursor for gibberellins, into the headspace from plants.” Plant Cell Physiology, 45, 1129-1138 (2004). [PubMed]
• Jikumaru, Y., Asami, T., Seto, H., Yoshida, S., Yokoyama, T., Obara, N., Hasegawa, M., Kodama, O., Nishiyama, M., Okada, K., Nojiri, H., Yamane, H. : “Preparation and biological activity of molecular probes to identify and analyze jasmonic acid-binding proteins” Bioscience, Biotechnology, and Biochemistry, 68, 1461-1466 (2004). [PubMed]
• Konishi, H., Yamane, H., Maeshima, M., and Komatsu, S. : “Characterization of fructose-bisphosphate aldolase regulated by gibberellin in roots of rice seedling” Plant Molecular Biology, 56, 839-848 (2004). [PubMed]
• Otomo, K., Kenmoku, H., Oikawa, H., Konig, WA., Toshima, H., Mitsuhashi, W., Yamane, H., Sassa, T., Toyomasu, T. : “Biological functions of ent- andsyn-copalyl diphosphate synthases in rice: key enzymes for the branch point of gibberellin and phytoalexin biosynthesis” Plant Journal, 39, 886-893 (2004). [PubMed]
• Otomo, K., Kanno, Y., Motegi, A., Kenmoku, H., Yamane, H., Mitsuhashi, W., Oikawa, H., Toshima, H., Itoh, H., Matsuoka, M., Sassa, T., Toyomasu, T. : “Diterpene cyclases responsible for the biosynthesis of phytoalexins, momilactones A, B, and oryzalexins A-F in rice” Bioscience, Biotechnology, and Biochemistry, 68, 2001-2006 (2004). [PubMed]
• Habe, H., Chung, J.-S., Kato, H., Ayabe, Y., Kasuga, K., Yoshida, T., Nojiri, H., Yamane, H., and Omori, T. : “Characterization of the upper pathway genes for fluorene metabolism in Terrabacter sp. strain DBF63” Journal of Bacteriology, 186, 5938-5944 (2004). [PubMed]
• Inoue, K., Widada, J., Nakai, S., Endoh, T., Urata, M., Ashikawa, Y., Shintani, M., Saiki, Y., Yoshida, T., Habe, H., Omori, T., and Nojiri, H. : “Divergent structures of carbazole degradative car operons isolated from Gram-negative bacteria” Bioscience, Biotechnology, and Biochemistry, 68, 1467-1480 (2004). [PubMed]
• Pinyakong, O., Habe, H., Kouzuma, H., Nojiri, H., Yamane, H., and Omori, T. : “Isolation and characterization of genes encoding polycyclic aromatic hydrocarbon dioxygenase from acenaphthene and acenaphthylene degradingSphingomonas sp. strain A4” FEMS Microbiology Letters, 238, 297-305 (2004). [PubMed]
• Noumura, T., Habe, H., Widada, J., Chung, J.-S., Yoshida, T., Nojiri, H., and Omori, T. : “Genetic characterization of the dibenzofuran-degrading Actinobacteria carrying the dbfA1A2 gene homologues isolated from activated sludge” FEMS Microbiology Letters, 239, 147-155 (2004).[PubMed]
• Habe, H., Kanemitsu, M., Nomura, M., Takemura, T., Iwata, K., Nojiri, H., Yamane, H., and Omori, T. : “Isolation and characterization of an alkaliphilic bacterium utilizing pyrene as a carbon source” Journal of Bioscience and Bioengineering, 98, 306-308 (2004). [PubMed]
• Urata, M., Miyakoshi, M., Kai, S., Maeda, K., Habe, H., Omori, T., Yamane, H., and Nojiri, H. : “Transcriptional regulation of the ant operon, encoding two-component anthranilate 1,2-dioxygenase, on the carbazole-degradative plasmid pCAR1 of Pseudomonas resinovoransstrain CA10” Journal of Bacteriology, 186, 6815-6823 (2004). [PubMed]
• Iwata, K., Noguchi, H., Usami, Y., Nam, J.-W., Fujimoto, Z., Mizuno, H., Habe, H., Yamane, H., Omori, T., and Nojiri, H. : “Crystallization and preliminary crystallographic analysis of the 2’-aminobiphenyl-2,3-diol 1,2-dioxygenase from the carbazole-degrader Pseudomonas resinovoransstrain CA10” Acta Crystallographica, D60, 2340-2342 (2004). [PubMed]
• Urata, M., Uchida, E., Nojiri, H., Omori, T., Obo, R., Miyaura, N., and Ouchiyama, N. : “Genes involved in aniline degradation by Delftia acidovorans strain 7N and its distribution in the natural environment” Bioscience, Biotechnology, and Biochemistry, 68, 2457-2465 (2004). [PubMed]

REVIEW ARTICLE

• Nojiri, H., Shintani, M., and Omori, T. : “Divergence of mobile genetic elements involved in the distribution of xenobiotic-catabolic capacity” Applied Microbiology and Biotechnology, 64, 154-174 (2004). [PubMed]
• Toyomasu, T., Yamane, H., and Sassa, T. : “Diterpene cyclases” Regulation of Plant Growth & Development, 39, 225-231 (2004). In Japanese.

2003

ORIGINAL ARTICLES

• Sobajima, H., Takeda, M., Sugimori, M., Kobashi, N., Kiribuchi, K., Cho, EM., Akimoto, C., Yamaguchi, T., Minami, E., Shibuya, N., Schaller, F., Weiler, EW., Yoshihara, T., Nishida, H., Nojiri, H., Omori, T., Nishiyama, M., and Yamane, H. : “Cloning and characterization of a jasmonic acid-responsive gene encoding 12-oxophytodienoic acid reductase in suspension-cultured rice cells.” Planta, 216, 692-698 (2003). [PubMed]
• Maeda, K., Nojiri, H., Shintani, M., Yoshida, T., Habe, H., and Omori, T. : “Complete nucleotide sequence of carbazole/dioxin-degrading plasmid pCAR1 in Pseudomonas resinovorans strain CA10 indicates its mosaicity and the presence of large catabolic transposon Tn4676" Journal of Molecular Biology, 326, 21-33 (2003). [PubMed]
• Hirano, H., Yoshida, T., Fuse, H., Endo, T., Habe, H., Nojiri, H., and Omori, T. : “Marinobacterium sp. strain DMS-S1 uses dimethyl sulphide as a sulphur source after light-dependent transformation by excreted flavins” Environmental Microbiology, 5, 503-509 (2003). [PubMed]
• Pinyakong, O., Habe, H., Yoshida, T., Nojiri, H., and Omori, T. : “Identification of three novel salicylate 1-hydroxylases involved in the phenanthrene degradation of Sphingobium sp. strain P2” Biochemical and Biophysical Research Communications, 301, 350-357 (2003). [PubMed]
• Habe, H., Morii, K., Fushinobu, S., Nam, JW., Ayabe, Y., Yoshida, T., Wakagi, T., Yamane, H., Nojiri, H., and Omori, T. : “Crystal structure of a histidine-tagged serine hydrolase involved in the carbazole degradation (CarC enzyme) ” Biochemical and Biophysical Research Communications, 303, 631-639 (2003). [PubMed]
• Habe, H., Miyakoshi, M., Chung, J.-S., Kasuga, K., Yoshida, T., Nojiri, H., and Omori, T. : “Phthalate catabolic gene cluster is linked to the angular dioxygenase gene in Terrabacter sp. strain DBF63” Applied Microbiology and Biotechnology, 61, 44-54 (2003). [PubMed]
• Endoh, T., Kasuga, K., Horinouchi, M., Yoshida, T., Habe, H., Nojiri, H., and Omori, T. : “Characterization and identification of genes essential for dimethyl sulfide utilization inPseudomonas putida strain DS1” Applied Microbiology and Biotechnology, 62, 83-91 (2003). [PubMed]
• Yoshida, T., Ayabe, Y., Yasunaga, M., Usami, Y., Habe, H., Nojiri, H., and Omori, T. : “Genes involved in the synthesis of the exopolysaccharide methanolan by the obligate methylotrophMethylobacillus sp. strain 12S” Microbiology, 149, 431-444 (2003).
• Endoh, T., Habe, H., Yoshida, T., Nojiri, H., and Omori, T. : “A CysB-regulated and σ54-dependent regulator, SfnR, is essential for dimethyl sulfone metabolism of Pseudomonas putida strain DS1” Microbiology, 149, 991-1000 (2003). [PubMed]
• Nojiri, H., Taira, H., Iwata, K., Morii, K., Nam, J.-W., Yoshida, T., Habe, H., Nakamura, S., Shimizu, K., Yamane, H., and Omori, T. : “Purification and characterization of meta-cleavage compound hydrolase from a carbazole degraderPseudomonas resinovorans strain CA10” Bioscience, Biotechnology, and Biochemistry, 67, 36-45 (2003). [PubMed]
• Iwata, K., Nojiri, H., Shimizu, K., Yoshida, T., Habe, H., and Omori, T. : “Expression, purification, and characterization of 2’-aminobiphenyl-2,3-diol 1,2-dioxygenase from carbazole-degraderPseudomonas resinovorans strain CA10” Bioscience, Biotechnology, and Biochemistry, 67, 300-307 (2003). [PubMed]
• Saiki, Y., Habe, H., Yuuki, T., Ikeda, M., Toshida, T., Nojiri, H., and Omori, T. : “Rhizoremediation of dioxin-like compounds by a recombinantRhizobium tropici strain expressing carbazole 1,9a-dioxygenase constitutively” Bioscience, Biotechnology, and Biochemistry, 67, 1144-1148 (2003). [PubMed]
• Shintani, M., Nojiri, H., Yoshida, T., Habe, H., and Omori, T. : “Carbazole/dioxin-degrading car gene cluster is located on the chromosome ofPseudomonas stutzeri strain OM1 in a form different from the simple transposition of Tn4676” Biotechnology Letters, 25, 1255-1261 (2003). [PubMed]

REVIEW ARTICLE

• Pinyakong, O., Habe, H., and Omori, T. : “The unique aromatic catabolic genes in sphingomonads degrading polycyclic aromatic hydrocarbons (PAHs)” Journal of General and Applied Microbiology, 49, 1-19 (2003). [PubMed]

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