Publications

2014

ORIGINAL ARTICLES

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 [in press]

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 [in press]

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 [in press]

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.

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

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.

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

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" (2014) Environmental Microbiology. doi: 10.1111/1462-2920.12515. [Epub ahead of print]

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

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.

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 [in press]

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

BOOKS

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.

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).

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.

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.

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.

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.

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.

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.

REVIEW ARTICLES

Nojiri H. "Impact of catabolic plasmids on host cell physiology." (2013) Curr Opin Biotechnol. 24(3):423-30.

Yamane H.:"Biosynthesis of Phytoalexins and Regulatory Mechanisms of It in Rice." (2013) Biosci Biotechnol Biochem Jun 7. (Award review)

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]

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.

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.

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.

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.

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.

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.

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.

REVIEW ARTICLES

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

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.

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.

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.

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.

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.

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.

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.

REVIEW ARTICLES

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

.

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.

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.

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.

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.

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.

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.

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.

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.

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)

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.

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.

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

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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 OsOPR7 gene 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.

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2007

ORIGINAL ARTICLES

Shintani, M., Urata, M., Inoue, K., Eto, K., Habe, H., Omori, T., Yamane, H., and Nojiri, H. : "The Sphingomonas 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 gene sfnA by a σ54-dependent activator of Pseudomonas 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.

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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 degrader Nocardioides 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 from Sphingomonas 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 Chloroflexi and 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.

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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 the Pseudomonas 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 in Terrabacter 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 fluorescens IP01 (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 from Pseudomonas 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.

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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- and syn-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 degrading Sphingomonas 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 resinovorans strain 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 resinovorans strain 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.

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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 in Pseudomonas 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 methylotroph Methylobacillus 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 degrader Pseudomonas 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-degrader Pseudomonas 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 recombinant Rhizobium 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 of Pseudomonas 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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