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Plant Genetic Engineering Research Unit

2010

  1. Fukuda A, Nakamura A, Hara N, Toki S, Tanaka Y (2010) Molecular and functional analyses of rice NHX-type Na+/H+ antiporter genes Planta (Online First) 10.1007/s00425-010-1289-4
  2. Habu Y, Yoshikawa M (2010) Locus-specific dependency of endogenous silent loci on MOM1 and non-CG methylation in Arabidopsis thaliana Plant Signaling & Behavior 5(6):724-726 10.4161/psb.5.6.11663
  3. Nakagawa M, Takahashi S, Tanaka A, Narumi I, Sakamoto A.N (2010) Role of AtPolζ, AtRev1 and AtPolη in UV-induced mutagenesis in Arabidopsis Plant Physiology (Preview) 10.1104/pp.110.166082
  4. Osakabe K, Osakabe Y, Toki S (2010) Site-directed mutagenesis in Arabidopsis using custom-designed zinc finger nucleases Proceedings of the National Academy of Sciences of the United States of America 107(26):12034-12039 10.1073/pnas.1000234107
  5. Saika H, Toki S (2010) Mature seed-derived callus of the model indica rice variety Kasalath is highly competent in Agrobacterium-mediated transformation Plant Cell Reports (Online First) 10.1007/s00299-010-0921-x
  6. She K-C, Kusano H, Koizumi K, Yamakawa H, Hakata M, Imamura T, Fukuda M, Naito N, Tsurumaki Y, Yaeshima M, Tsuge T, Matsumoto K, Kudoh M, Itoh E, Kikuchi S, Kishimoto N, Yazaki J, Ando T, Yano M, Aoyama T, Sasaki T, Satoh H, Shimada H (2010) A novel factor FLOURY ENDOSPERM2 is involved in regulation of rice grain size and starch quality The Plant Cell (Advance Online) 10.1105/tpc.109.070821
  7. Tanabata T, Taguchi-Shiobara F, Kishimoto N, Chechetka S, Shinomura T, Habu Y (2010) A phenomics approach detected differential epigenetic growth regulation between inbreds and their hybrid in Oryza sativa Molecular Breeding 26(4):729-734 10.1007/s11032-010-9484-3
  8. Yun M-S, Kawagoe Y (2010) Septum formation in amyloplasts produces compound granules in the rice endosperm and is regulated by plastid division proteins Plant and Cell Physiology 51(9):1469-1479 10.1093/pcp/pcq116
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2009

  1. Abe K, Osakabe K, Ishikawa Y, Tagiri A, Yamanouchi H, Takyuu T, Yoshioka T, Ito T, Kobayashi M, Shinozaki K, Ichikawa H, Toki S (2009) Inefficient double-strand DNA break repair is associated with increased fasciation in Arabidopsis BRCA2 mutants Journal of Experimental Botany 60(9):2751-2761 10.1093/jxb/erp135
  2. Kitajima A, Asatsuma S, Okada H, Hamada Y, Kaneko K, Nanjo Y, Kawagoe Y, Toyooka K, Matsuoka K, Takeuchi M, Nakano A, Mitsui T (2009) The rice α-amylase glycoprotein is targeted from the Golgi apparatus through the secretory pathway to the plastids The Plant Cell 21(9):2844-2858 10.1105/tpc.109.068288
  3. Numa H, Kim J-M, Matsui A, Kurihara Y, Morosawa T, Ishida J, Mochizuki Y, Kimura H, Shinozaki K, Toyoda T, Seki M, Yoshikawa M, Habu Y (2009) Transduction of RNA-directed DNA methylation signals to repressive histone marks in Arabidopsis thaliana The EMBO Journal 29(2):352-362 10.1038/emboj.2009.374
  4. Onda Y, Kumamaru T, Kawagoe Y (2009) ER membrane-localized oxidoreductase Ero1 is required for disulfide bond formation in the rice endosperm Proceedings of the National Academy of Sciences of the United States of America 106(33):14156–14161 10.1073/pnas.0904429106
  5. Osakabe Y, Mizuno S, Tanaka H, Maruyama K, Osakabe K, Todaka D, Fujita Y, Kobayashi M, Shinozaki K, Yamaguchi-Shinozaki K (2010) Overproduction of the membrane-bound receptor-like protein kinase1, RPK1, enhances abiotic stress tolerance in Arabidopsis Journal of Biological Chemistry 285(12):9190-9201 10.1074/jbc.M109.051938
  6. Osakabe Y, Osakabe K, Chiang V.L (2009) Characterization of the tissue-specific expression of phenylalanine ammonia-lyase gene promoter from loblolly pine (Pinus taeda) in Nicotiana tabacum Plant Cell Reports 28(9):1309-1317 10.1007/s00299-009-0707-1
  7. Takahara K, Kasajima I, Takahashi H, Hashida S, Itami T, Onodera H, Toki S, Yanagisawa S, Kawai-Yamada M, Uchimiya H (2010) Metabolome and photochemical analysis of rice plants over-expressing Arabidopsis NAD kinase gene Plant Physiology 152(4):1863-1873 10.1104/pp.110.153098
  8. Tsujimoto-Inui Y, Naito Y, Sakurai N, Suzuki H, Sasaki R, Takahashi H, Ohtsuki N, Nakano T, Yanagisawa S, Shibata D, Uchimiya H, Shinshi H, Suzuki K (2009) Functional genomics of the Dof transcription factor family genes in suspension-cultured cells of Arabidopsis thaliana Plant Biotechnology 26(1):15-28 
  9. Yun M-S, Kawagoe Y (2009) Amyloplast division progresses simultaneously at multiple sites in the endosperm of rice Plant and Cell Physiology 50(9):1617-1626 10.1093/pcp/pcp104
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2008

  1. Ando S, Tsushima S, Kamachi S, Konagaya K, Tabei Y (2008) Alternative transcription initiation of the nitrilase gene (BrNIT2) caused by infection with Plasmodiophora brassicae Woron. in Chinese cabbage (Brassica rapa L.) Plant Molecular Biology 68(6):557-569 10.1007/s11103-008-9390-9
  2. Čaikovski M, Yokthongwattana C, Habu Y, Nishimura T, Mathieu O, Paszkowski J (2008) Divergent evolution of CHD3 proteins resulted in MOM1 refining epigenetic control in vascular plants PLoS Genetics 4(8):e1000165 10.1371/journal.pgen.1000165
  3. Konagaya K, Ando S, Kamachi S, Tsuda M, Tabei Y (2008) Efficient production of genetically engineered, male-sterile Arabidopsis thaliana using anther-specific promoters and genes derived from Brassica oleracea and B. rapa Plant Cell Reports 27(11):1741-1754 10.1007/s00299-008-0598-6
  4. Ogawa T, Kawahigashi H, Toki S, Handa H (2008) Efficient transformation of wheat by using a mutated rice acetolactate synthase gene as a selectable marker Plant Cell Reports 27(8):1325-1331 10.1007/s00299-008-0553-6
  5. Saika H, Toki S (2009) Visual selection allows immediate identification of transgenic rice calli efficiently accumulating transgene products Plant Cell Reports 28(4):619-626 10.1007/s00299-009-0671-9
  6. Sakane I, Kamataki C, Takizawa Y, Nakashima M, Toki S, Ichikawa H, Ikawa S, Shibata T, Kurumizaka H (2008) Filament formation and robust strand exchange activities of the rice DMC1A and DMC1B proteins Nucleic Acids Research 36(13):4266-4276 10.1093/nar/gkn405
  7. Takamiya T, Hosobuchi S, Noguchi T, Asai K, Nakamura E, Habu Y, Paterson A.H, Iijima H, Murakami Y, Okuizumi H (2008) Inheritance and alteration of genome methylation in F1 hybrid rice Electrophoresis 29(19):4088-4095 10.1002/elps.200700784
  8. Yamada-Akiyama H, Akiyama Y, Ebina M, Xu Q, Tsuruta S, Yazaki J, Kishimoto N, Kikuchi S, Takahara M, Takamizo T, Sugita S, Nakagawa H (2009) Analysis of expressed sequence tags in apomictic guineagrass (Panicum maximum) Journal of Plant Physiology 166(7):750-761 10.1016/j.jplph.2008.10.001
  9. Yun M-S, Chen W, Deng F, Yogo Y (2009) Selective growth suppression of five annual plant species by chalcone and naringenin correlates with the total amount of 4-coumarate: coenzyme A ligase Weed Biology and Management 9(1):27-37 10.1111/j.1445-6664.2008.00315.x
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2007

  1. Endo M, Osakabe K, Ono K, Handa H, Shimizu T, Toki S (2007) Molecular breeding of a novel herbicide-tolerant rice by gene targeting The Plant Journal 52(1):157-166 10.1111/j.1365-313X.2007.03230.x
  2. Gao J-S, Sasaki N, Kanegae H, Konagaya K, Takizawa K, Hayashi N, Okano Y, Kasahara M, Matsushita Y, Nyunoya H (2007) The TIR-NBS but not LRR domains of two novel N-like proteins are functionally competent to induce the elicitor p50-dependent hypersensitive response Physiological and Molecular Plant Pathology 71(1-3):78-87 10.1016/j.pmpp.2007.11.002
  3. Kamachi S, Mochizuki A, Nishiguchi M, Tabei Y (2007) Transgenic Nicotiana benthamiana plants resistant to cucumber green mottle mosaic virus based on RNA silencing Plant Cell Reports 26(8):1283-1288 10.1007/s00299-007-0358-z
  4. Komatsu S, Yang G, Khan M, Onodera H, Toki S, Yamaguchi M (2007) Over-expression of calcium-dependent protein kinase 13 and calreticulin interacting protein 1 confers cold tolerance on rice plants Molecular Genetics and Genomics 277(6):713-723 10.1007/s00438-007-0220-6
  5. Mimida N, Kitamoto H, Osakabe K, Nakashima M, Ito Y, Heyer W-D, Toki S, Ichikawa H (2007) Two alternatively spliced transcripts generated from OsMUS81, a rice homolog of yeast MUS81, are up-regulated by DNA-damaging treatments Plant and Cell Physiology 48(4):648-654 10.1093/pcp/pcm029
  6. Mizuno S, Osakabe Y, Maruyama K, Ito T, Osakabe K, Sato T, Shinozaki K, Yamaguchi-Shinozaki K (2007) Receptor-like protein kinase 2 (RPK 2) is a novel factor controlling anther development in Arabidopsis thaliana The Plant Journal 50(5):751-766 10.1111/j.1365-313X.2007.03083.x
  7. Nakamura H, Hakata M, Amano K, Miyao A, Toki N, Kajikawa M, Pang J, Higashi N, Ando S, Toki S, Fujita M, Enju A, Seki M, Nakazawa M, Ichikawa T, Shinozaki K, Matsui M, Nagamura Y, Hirochika H, Ichikawa H (2007) A genome-wide gain-of-function analysis of rice genes using the FOX-hunting system Plant Molecular Biology 65(4):357-371 10.1007/s11103-007-9243-y
  8. Nakayama S, Uga Y, Oo T.M, Kawase M (2008) Chromosomes and 5S rDNA-repeats of wild taro Colocasia esculenta from Myanmar Tropical Agriculture and Development 52(1):32-35 
  9. Ogo Y, Kobayashi T, Nakanishi Itai R, Nakanishi H, Kakei Y, Takahashi M, Toki S, Mori S, Nishizawa N.K (2008) A novel NAC transcription factor, IDEF2, that recognizes the iron deficiency-responsive element 2 regulates the genes involved in iron homeostasis in plants Journal of Biological Chemistry 283(19):13407-13417 10.1074/jbc.M708732200
  10. Satoh K, Doi K, Nagata T, Kishimoto N, Suzuki K, Otomo Y, Kawai J, Nakamura M, Hirozane-Kishikawa T, Kanagawa S, Arakawa T, Takahashi-Iida J, Murata M, Ninomiya N, Sasaki D, Fukuda S, Tagami M, Yamagata H, Kurita K, Kamiya K, Yamamoto M, Kikuta A, Bito T, Fujitsuka N, Ito K, Kanamori H, Choi I-R, Nagamura Y, Matsumoto T, Murakami K, Matsubara K, Carninci P, Hayashizaki Y, Kikuchi S (2007) Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray PLoS ONE 2(11):e1235 10.1371/journal.pone.0001235
  11. Shimono M, Sugano S, Nakayama A, Jiang C-J, Ono K, Toki S, Takatsuji H (2007) Rice WRKY45 plays a crucial role in benzothiadiazole-inducible blast resistance The Plant Cell 19(6):2064-2076 10.1105/tpc.106.046250

  12. Yan H, Saika H, Maekawa M, Takamure I, Tsutsumi N, Kyozuka J, Nakazono M (2007) Rice tillering dwarf mutant dwarf3 has increased leaf longevity during darkness-induced senescence or hydrogen peroxide-induced cell death Genes & Genetic Systems 82(4):361-366 10.1266/ggs.82.361
  13. Yun M-S, Chen W, Deng F, Yogo Y (2007) Propanil and swep inhibit 4-coumarate:CoA ligase activity in vitro Pest Management Science 63(8):815-820 10.1002/ps.1404
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2006

  1. Ando S, Tsushima S, Tagiri A, Kamachi S, Konagaya K, Hagio T, Tabei Y (2006) Increase in BrAO1 gene expression and aldehyde oxidase activity during clubroot development in Chinese cabbage (Brassica rapa L.) Molecular Plant Pathology 7(4):223-234 10.1111/j.1364-3703.2006.00333.x
  2. Endo M, Ishikawa Y, Osakabe K, Nakayama S, Kaya H, Araki T, Shibahara K, Abe K, Ichikawa H, Valentine L, Hohn B, Toki S (2006) Increased frequency of homologous recombination and T-DNA integration in Arabidopsis CAF-1 mutants The EMBO Journal 25(23):5579-5590 10.1038/sj.emboj.7601434
  3. Endo M, Osakabe K, Ichikawa H, Toki S (2006) Molecular Characterization of True and Ectopic Gene Targeting Events at the Acetolactate Synthase Gene in Arabidopsis Plant and Cell Physiology 47(3):372-379 10.1093/pcp/pcj003
  4. Habu Y, Mathieu O, Tariq M, Probst A V, Smathajitt C, Zhu T, Paszkowski J (2006) Epigenetic regulation of transcription in intermediate heterochromatin EMBO Reports 7(12):1279-1284 10.1038/sj.embor.7400835
  5. Kitanaga Y, Jian C, Hasegawa M, Yazaki J, Kishimoto N, Kikuchi S, Nakamura H, Ichikawa H, Asami T, Yoshida S, Yamaguchi I, Suzuki Y (2006) Sequential regulation of gibberellin, brassinosteroid, and jasmonic acid biosynthesis occurs in rice coleoptiles to control the transcript levels of anti-microbial Thionin Genes Bioscience, Biotechnology and Biochemistry 70(10):2410-2419 10.1271/bbb.60145
  6. Osakabe K, Abe K, Yoshioka T, Osakabe Y, Todoriki S, Ichikawa H, Hohn B, Toki S (2006) Isolation and characterization of the RAD54 gene from Arabidopsis thaliana The Plant Journal 48(6):827-842 10.1111/j.1365-313X.2006.02927.x
  7. Saika H, Matsumura H, Takano T, Tsutsumi N, Nakazono M (2006) A point mutation of Adh1 gene is involved in the repression of coleoptile elongation under submergence in rice Breeding Science 56(1):69-74 10.1270/jsbbs.56.69
  8. Saika H, Okamoto M, Miyoshi K, Kushiro T, Shinoda S, Jikumaru Y, Fujimoto M, Arikawa T, Takahashi H, Ando M, Arimura S, Miyao A, Hirochika H, Kamiya Y, Tsutsumi N, Nambara E, Nakazono M (2007) Ethylene promotes submergence-induced expression of OsABA8ox1, a gene that encodes ABA 8'-hydroxylase in rice Plant and Cell Physiology 48(2):287-298 10.1093/pcp/pcm003
  9. Suzuki M, Takahashi M, Tsukamoto T, Watanabe S, Matsuhashi S, Yazaki J, Kishimoto N, Kikuchi S, Nakanishi H, Mori S, Nishizawa K.N (2006) Biosynthesis and secretion of mugineic acid family phytosiderophores in zinc-deficient barley The Plant Journal 48(1):85-97 10.1111/j.1365-313X.2006.02853.x
  10. Taguchi-Shiobara F, Yazaki J, Ishikawa M, Fujii F, Shimbo K, Shimatani Z, Nagata Y, Hashimoto A, Ohta T, Sato Y, Honda S, Yamamoto K, Sakata K, Sasaki T, Kishimoto N, Kikuchi S (2006) A microarray analysis of rice near-isogenic lines that cover QTLs associated with callus proliferation Japan Agricultural Research Quarterly 40(3):243-249 
  11. Toki S, Hara N, Ono K, Onodera H, Tagiri A, Oka S, Tanaka H (2006) Early infection of scutellum tissue with Agrobacterium allows high-speed transformation of rice The Plant Journal 47(6):969-976 10.1111/j.1365-313X.2006.02836.x
  12. Tsuji H, Saika H, Tsutsumi N, Hirai A, Nakazono M (2006) Dynamic and reversible changes in histone H3-Lys4 methylation and H3 acetylation occurring at submergence-inducible genes in rice Plant and Cell Physiology 47(7):995-1003 10.1093/pcp/pcj072
  13. Wasaki J , Shinano T, Onishi K, Yonetani R, Yazaki J, Fujii F, Shimbo K, Ishikawa M, Shimatani Z, Nagata Y, Hashimoto A, Ohta T, Sato Y, Miyamoto C, Honda S, Kojima K, Sasaki T, Kishimoto N, Kikuchi S, Osaki M (2006) Transcriptomic analysis indicates putative metabolic changes caused by manipulation of phosphorus availability in rice leaves Journal of Experimental Botany 57(9):2049-2059 10.1093/jxb/erj158
  14. Yamato K.T, Ishizaki K, Fujisawa M, Okada S, Nakayama S, Fujishita M, Bando H, Yodoya K, Hayashi K, Bando T, Hasumi A, Nishio T, Sakata R, Yamamoto M, Yamaki A, Kajikawa M, Yamano T, Nishide T, Choi S, Shimizu-Ueda Y, Hanajiri T, Sakaida M, Kono K, Takenaka M, Yamaoka S, Kuriyama C, Kohzu Y, Nishida H, Brennicke A, Shin-i T, Kohara Y, Kohchi T, Fukuzawa H, Ohyama K (2007) Gene organization of the liverwort Y chromosome reveals distinct sex chromosome evolution in a haploid system Proceedings of the National Academy of Sciences of the United States of America 104(15):6472-6477 10.1073/pnas.0609054104
  15. Yoshida K, Imaizumi N, Kaneko S, Kawagoe Y, Tagiri A, Tanaka H, Nishitani K, Komae K (2006) Carbohydrate-binding module of a rice endo-β-1,4-glycanase, OsCel9A, expressed in auxin-induced lateral root primordia, is post-translationally truncated Plant and Cell Physiology 47(11):1555-1571 10.1093/pcp/pcl021
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