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Items: 48

1.

Transcriptome analysis and identification of a transcriptional regulatory network in the response to H2O2.

Hieno A, Naznin HA, Inaba-Hasegawa K, Yokogawa T, Hayami N, Nomoto M, Tada Y, Yokogawa T, Higuchi-Takeuchi M, Hanada K, Matsui M, Ikeda Y, Hojo Y, Hirayama T, Kusunoki K, Koyama H, Mitsuda N, Yamamoto YY.

Plant Physiol. 2019 May 7. pii: pp.01426.2018. doi: 10.1104/pp.18.01426. [Epub ahead of print]

2.

STOP1 regulates the expression of HsfA2 and GDH genes critical for low-oxygen tolerance in Arabidopsis.

Enomoto T, Tokizawa M, Ito H, Iuchi S, Kobayashi M, Yamamoto YY, Kobayashi Y, Koyama H.

J Exp Bot. 2019 Mar 18. pii: erz124. doi: 10.1093/jxb/erz124. [Epub ahead of print]

PMID:
30882866
3.

Expression, Functional Characterization, and Preliminary Crystallization of the Cochaperone Prefoldin from the Thermophilic Fungus Chaetomium thermophilum.

Morita K, Yamamoto YY, Hori A, Obata T, Uno Y, Shinohara K, Noguchi K, Noi K, Ogura T, Ishii K, Kato K, Kikumoto M, Arranz R, Valpuesta JM, Yohda M.

Int J Mol Sci. 2018 Aug 19;19(8). pii: E2452. doi: 10.3390/ijms19082452.

4.

Time-Resolved Measurement of the ATP-Dependent Motion of the Group II Chaperonin by Diffracted Electron Tracking.

Ogawa N, Yamamoto YY, Abe K, Sekiguchi H, Sasaki YC, Ishikawa A, Frydman J, Yohda M.

Int J Mol Sci. 2018 Mar 22;19(4). pii: E950. doi: 10.3390/ijms19040950.

5.

Identifying the target genes of SUPPRESSOR OF GAMMA RESPONSE 1, a master transcription factor controlling DNA damage response in Arabidopsis.

Ogita N, Okushima Y, Tokizawa M, Yamamoto YY, Tanaka M, Seki M, Makita Y, Matsui M, Okamoto-Yoshiyama K, Sakamoto T, Kurata T, Hiruma K, Saijo Y, Takahashi N, Umeda M.

Plant J. 2018 May;94(3):439-453. doi: 10.1111/tpj.13866. Epub 2018 Mar 24.

6.

Light Controls Protein Localization through Phytochrome-Mediated Alternative Promoter Selection.

Ushijima T, Hanada K, Gotoh E, Yamori W, Kodama Y, Tanaka H, Kusano M, Fukushima A, Tokizawa M, Yamamoto YY, Tada Y, Suzuki Y, Matsushita T.

Cell. 2017 Nov 30;171(6):1316-1325.e12. doi: 10.1016/j.cell.2017.10.018. Epub 2017 Nov 9.

7.

Characterization of CcSTOP1; a C2H2-type transcription factor regulates Al tolerance gene in pigeonpea.

Daspute AA, Kobayashi Y, Panda SK, Fakrudin B, Kobayashi Y, Tokizawa M, Iuchi S, Choudhary AK, Yamamoto YY, Koyama H.

Planta. 2018 Jan;247(1):201-214. doi: 10.1007/s00425-017-2777-6. Epub 2017 Sep 18.

PMID:
28921050
8.

Asymmetry in the function and dynamics of the cytosolic group II chaperonin CCT/TRiC.

Yamamoto YY, Uno Y, Sha E, Ikegami K, Ishii N, Dohmae N, Sekiguchi H, Sasaki YC, Yohda M.

PLoS One. 2017 May 2;12(5):e0176054. doi: 10.1371/journal.pone.0176054. eCollection 2017.

9.

Identification of Arabidopsis genic and non-genic promoters by paired-end sequencing of TSS tags.

Tokizawa M, Kusunoki K, Koyama H, Kurotani A, Sakurai T, Suzuki Y, Sakamoto T, Kurata T, Yamamoto YY.

Plant J. 2017 May;90(3):587-605. doi: 10.1111/tpj.13511. Epub 2017 Apr 4.

10.

Prediction of bipartite transcriptional regulatory elements using transcriptome data of Arabidopsis.

Yamamoto YY, Ichida H, Hieno A, Obata D, Tokizawa M, Nomoto M, Tada Y, Kusunoki K, Koyama H, Hayami N.

DNA Res. 2017 Jun 1;24(3):271-278. doi: 10.1093/dnares/dsw065.

11.

Plant Promoter Database (PPDB).

Kusunoki K, Yamamoto YY.

Methods Mol Biol. 2017;1533:299-314.

PMID:
27987179
12.

Design of an optimal promoter involved in the heat-induced transcriptional pathway in Arabidopsis, soybean, rice and maize.

Maruyama K, Ogata T, Kanamori N, Yoshiwara K, Goto S, Yamamoto YY, Tokoro Y, Noda C, Takaki Y, Urawa H, Iuchi S, Urano K, Yoshida T, Sakurai T, Kojima M, Sakakibara H, Shinozaki K, Yamaguchi-Shinozaki K.

Plant J. 2017 Feb;89(4):671-680. doi: 10.1111/tpj.13420. Epub 2017 Feb 10.

13.

Characterization of group II chaperonins from an acidothermophilic archaeon Picrophilus torridus.

Yamamoto YY, Tsuchida K, Noguchi K, Ogawa N, Sekiguchi H, Sasaki YC, Yohda M.

FEBS Open Bio. 2016 Jun 14;6(7):751-64. doi: 10.1002/2211-5463.12090. eCollection 2016 Jul.

14.

Possible Involvement of MYB44-Mediated Stomatal Regulation in Systemic Resistance Induced by Penicillium simplicissimum GP17-2 in Arabidopsis.

Hieno A, Naznin HA, Hyakumachi M, Higuchi-Takeuchi M, Matsui M, Yamamoto YY.

Microbes Environ. 2016 Jun 25;31(2):154-9. doi: 10.1264/jsme2.ME16025. Epub 2016 Jun 10.

15.

Contribution of the C-Terminal Region of a Group II Chaperonin to its Interaction with Prefoldin and Substrate Transfer.

Zako T, Sahlan M, Fujii S, Yamamoto YY, Tai PT, Sakai K, Maeda M, Yohda M.

J Mol Biol. 2016 Jun 5;428(11):2405-2417. doi: 10.1016/j.jmb.2016.04.006. Epub 2016 Apr 11.

PMID:
27079363
16.

The Responses of Arabidopsis Early Light-Induced Protein2 to Ultraviolet B, High Light, and Cold Stress Are Regulated by a Transcriptional Regulatory Unit Composed of Two Elements.

Hayami N, Sakai Y, Kimura M, Saito T, Tokizawa M, Iuchi S, Kurihara Y, Matsui M, Nomoto M, Tada Y, Yamamoto YY.

Plant Physiol. 2015 Sep;169(1):840-55. doi: 10.1104/pp.15.00398. Epub 2015 Jul 14.

17.

High REDOX RESPONSIVE TRANSCRIPTION FACTOR1 Levels Result in Accumulation of Reactive Oxygen Species in Arabidopsis thaliana Shoots and Roots.

Matsuo M, Johnson JM, Hieno A, Tokizawa M, Nomoto M, Tada Y, Godfrey R, Obokata J, Sherameti I, Yamamoto YY, Böhmer FD, Oelmüller R.

Mol Plant. 2015 Aug;8(8):1253-73. doi: 10.1016/j.molp.2015.03.011. Epub 2015 Apr 13.

18.

SENSITIVE TO PROTON RHIZOTOXICITY1, CALMODULIN BINDING TRANSCRIPTION ACTIVATOR2, and other transcription factors are involved in ALUMINUM-ACTIVATED MALATE TRANSPORTER1 expression.

Tokizawa M, Kobayashi Y, Saito T, Kobayashi M, Iuchi S, Nomoto M, Tada Y, Yamamoto YY, Koyama H.

Plant Physiol. 2015 Mar;167(3):991-1003. doi: 10.1104/pp.114.256552. Epub 2015 Jan 27.

19.

Next-generation sequencing of genomic DNA fragments bound to a transcription factor in vitro reveals its regulatory potential.

Kurihara Y, Makita Y, Kawashima M, Hamasaki H, Yamamoto YY, Matsui M.

Genes (Basel). 2014 Dec 19;5(4):1115-31. doi: 10.3390/genes5041115.

20.

A stable and efficient nuclear transformation system for the diatom Chaetoceros gracilis.

Ifuku K, Yan D, Miyahara M, Inoue-Kashino N, Yamamoto YY, Kashino Y.

Photosynth Res. 2015 Feb;123(2):203-11. doi: 10.1007/s11120-014-0048-y. Epub 2014 Oct 9.

PMID:
25297896
21.

VuDREB2A, a novel DREB2-type transcription factor in the drought-tolerant legume cowpea, mediates DRE-dependent expression of stress-responsive genes and confers enhanced drought resistance in transgenic Arabidopsis.

Sadhukhan A, Kobayashi Y, Kobayashi Y, Tokizawa M, Yamamoto YY, Iuchi S, Koyama H, Panda SK, Sahoo L.

Planta. 2014 Sep;240(3):645-64. doi: 10.1007/s00425-014-2111-5. Epub 2014 Jul 17.

PMID:
25030652
22.

Inter-ring communication is dispensable in the reaction cycle of group II chaperonins.

Yamamoto YY, Abe Y, Moriya K, Arita M, Noguchi K, Ishii N, Sekiguchi H, Sasaki YC, Yohda M.

J Mol Biol. 2014 Jul 15;426(14):2667-78. doi: 10.1016/j.jmb.2014.05.013. Epub 2014 May 21.

PMID:
24859336
23.

ppdb: plant promoter database version 3.0.

Hieno A, Naznin HA, Hyakumachi M, Sakurai T, Tokizawa M, Koyama H, Sato N, Nishiyama T, Hasebe M, Zimmer AD, Lang D, Reski R, Rensing SA, Obokata J, Yamamoto YY.

Nucleic Acids Res. 2014 Jan;42(Database issue):D1188-92. doi: 10.1093/nar/gkt1027. Epub 2013 Nov 4.

24.

Analysis of environmental stress in plants with the aid of marker genes for H2O2 responses.

Hieno A, Naznin HA, Sawaki K, Koyama H, Sakai Y, Ishino H, Hyakumachi M, Yamamoto YY.

Methods Enzymol. 2013;527:221-37. doi: 10.1016/B978-0-12-405882-8.00012-X.

PMID:
23830634
25.

Identification of cis-acting promoter elements in cold- and dehydration-induced transcriptional pathways in Arabidopsis, rice, and soybean.

Maruyama K, Todaka D, Mizoi J, Yoshida T, Kidokoro S, Matsukura S, Takasaki H, Sakurai T, Yamamoto YY, Yoshiwara K, Kojima M, Sakakibara H, Shinozaki K, Yamaguchi-Shinozaki K.

DNA Res. 2012;19(1):37-49. doi: 10.1093/dnares/dsr040. Epub 2011 Dec 19.

26.

Characteristics of core promoter types with respect to gene structure and expression in Arabidopsis thaliana.

Yamamoto YY, Yoshioka Y, Hyakumachi M, Obokata J.

DNA Res. 2011 Oct;18(5):333-42. doi: 10.1093/dnares/dsr020. Epub 2011 Jul 10.

27.

Prediction of transcriptional regulatory elements for plant hormone responses based on microarray data.

Yamamoto YY, Yoshioka Y, Hyakumachi M, Maruyama K, Yamaguchi-Shinozaki K, Tokizawa M, Koyama H.

BMC Plant Biol. 2011 Feb 24;11:39. doi: 10.1186/1471-2229-11-39.

28.

A common sequence motif involved in selection of transcription start sites of Arabidopsis and budding yeast tRNA genes.

Yukawa Y, Dieci G, Alzapiedi M, Hiraga A, Hirai K, Yamamoto YY, Sugiura M.

Genomics. 2011 Mar;97(3):166-72. doi: 10.1016/j.ygeno.2010.12.001. Epub 2010 Dec 13.

29.

Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis.

Yamamoto YY, Yoshitsugu T, Sakurai T, Seki M, Shinozaki K, Obokata J.

Plant J. 2009 Oct;60(2):350-62. doi: 10.1111/j.1365-313X.2009.03958.x. Epub 2009 Jun 29.

30.

Live imaging of chloroplast FtsZ1 filaments, rings, spirals, and motile dot structures in the AtMinE1 mutant and overexpressor of Arabidopsis thaliana.

Fujiwara MT, Sekine K, Yamamoto YY, Abe T, Sato N, Itoh RD.

Plant Cell Physiol. 2009 Jun;50(6):1116-26. doi: 10.1093/pcp/pcp063. Epub 2009 Apr 28.

PMID:
19403522
31.

Widespread translational inhibition by plant miRNAs and siRNAs.

Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, Dunoyer P, Yamamoto YY, Sieburth L, Voinnet O.

Science. 2008 May 30;320(5880):1185-90. doi: 10.1126/science.1159151. Epub 2008 May 15.

32.

ppdb: a plant promoter database.

Yamamoto YY, Obokata J.

Nucleic Acids Res. 2008 Jan;36(Database issue):D977-81. Epub 2007 Oct 18.

33.

Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis.

Yamamoto YY, Ichida H, Abe T, Suzuki Y, Sugano S, Obokata J.

Nucleic Acids Res. 2007;35(18):6219-26. Epub 2007 Sep 12.

34.

Identification of plant promoter constituents by analysis of local distribution of short sequences.

Yamamoto YY, Ichida H, Matsui M, Obokata J, Sakurai T, Satou M, Seki M, Shinozaki K, Abe T.

BMC Genomics. 2007 Mar 8;8:67.

35.

Increased level of polyploidy1, a conserved repressor of CYCLINA2 transcription, controls endoreduplication in Arabidopsis.

Yoshizumi T, Tsumoto Y, Takiguchi T, Nagata N, Yamamoto YY, Kawashima M, Ichikawa T, Nakazawa M, Yamamoto N, Matsui M.

Plant Cell. 2006 Oct;18(10):2452-68. Epub 2006 Sep 29.

36.

Functional analysis of isoforms of NADPH: protochlorophyllide oxidoreductase (POR), PORB and PORC, in Arabidopsis thaliana.

Masuda T, Fusada N, Oosawa N, Takamatsu K, Yamamoto YY, Ohto M, Nakamura K, Goto K, Shibata D, Shirano Y, Hayashi H, Kato T, Tabata S, Shimada H, Ohta H, Takamiya K.

Plant Cell Physiol. 2003 Oct;44(10):963-74.

PMID:
14581621
37.

Analysis of hydrogen peroxide-independent expression of the high-light-inducible ELIP2 gene with the aid of the ELIP2 promoter-luciferase fusions.

Kimura M, Manabe K, Abe T, Yoshida S, Matsui M, Yamamoto YY.

Photochem Photobiol. 2003 Jun;77(6):668-74.

PMID:
12870854
38.

Gene trapping of the Arabidopsis genome with a firefly luciferase reporter.

Yamamoto YY, Tsuhara Y, Gohda K, Suzuki K, Matsui M.

Plant J. 2003 Jul;35(2):273-83.

39.

Identification of Arabidopsis genes regulated by high light-stress using cDNA microarray.

Kimura M, Yamamoto YY, Seki M, Sakurai T, Sato M, Abe T, Yoshida S, Manabe K, Shinozaki K, Matsui M.

Photochem Photobiol. 2003 Feb;77(2):226-33.

PMID:
12785063
40.

Polyribosome loading of spinach mRNAs for photosystem I subunits is controlled by photosynthetic electron transport.

Sherameti I, Nakamura M, Yamamoto YY, Pfannschmidt T, Obokata J, Oelmüller R.

Plant J. 2002 Dec;32(5):631-9.

41.

Arabidopsis transcriptional regulation by light stress via hydrogen peroxide-dependent and -independent pathways.

Kimura M, Yoshizumi T, Manabe K, Yamamoto YY, Matsui M.

Genes Cells. 2001 Jul;6(7):607-17.

42.
43.
44.

An Arabidopsis cotyledon-specific albino locus: a possible role in 16S rRNA maturation.

Yamamoto YY, Puente P, Deng XW.

Plant Cell Physiol. 2000 Jan;41(1):68-76.

PMID:
10750710
45.

Role of a COP1 interactive protein in mediating light-regulated gene expression in arabidopsis.

Yamamoto YY, Matsui M, Ang LH, Deng XW.

Plant Cell. 1998 Jul;10(7):1083-94.

46.

Light-responsive elements of the tobacco PSI-D gene are located both upstream and within the transcribed region.

Yamamoto YY, Kondo Y, Kato A, Tsuji H, Obokata J.

Plant J. 1997 Aug;12(2):255-65.

47.

Cloning of a nuclear-encoded photosystem I gene, psaEb, in Nicotiana sylvestris.

Kubota T, Yamamoto YY, Obokata J.

Plant Physiol. 1995 Jul;108(3):1297-8. No abstract available.

48.

5'-leader of a photosystem I gene in Nicotiana sylvestris, psaDb, contains a translational enhancer.

Yamamoto YY, Tsuji H, Obokata J.

J Biol Chem. 1995 May 26;270(21):12466-70.

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