植物分子生理学研究室
Lab for Plant Molecular Physiology, Fac Appl Biol Sci, Gifu University
PUBLICATION: PMP Lab
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>Personal data: Yamamoto YY
( ! favorite, $ F1000 BIOLOGY selected, # >100 citations)
64.
Combinatorial effects of cis-regulatory elements and functions in plants.
Ezeh OS, Yamamoto YY (2024) Reviews Agri Sci (in press)
63.
Cytosolic heme catabolism by alternative localization of heme oxygenase 1 in plant cells.
Chen Y, Nishimura K, Tokizawa M, Yamamoto YY, Oka Y, Matsushita T, Hanada K, Shirai K, Mano S, Shimizu T, Masuda T (2024) Plant Physiol (in press)
62.
Conservation and diversification of the cold stress response in higher plants.
Debbarma A, Chaturvedi R, Maruyama K, Yamamoto YY (2024) In “Plant in challenging environments” eds Panda SK, Khan MA, Springer Nature Switzerland AG (in press)
61.
STOP1-regulated SMALL AUXIN UP RNA55 (SAUR55) is involved in proton/malate co-secretion for Al tolerance in Arabidopsis.
Agrahari RK, Kobayashi Y, Enomoto T, Miyachi T, Fujita M, Iuchi S, Kobayashi M, Yamamoto YY, Koyama H (2024) Plant Direct 8: e557.
https://doi.org/10.1002/pld3.557
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60.
The transcription factors, STOP1 and TCP20, are required for root system architecture alterations in response to nitrate deficiency.
Tokizawa M, Enomoto T, Chandnani R, Mora-Macías J, Burbridge C, Armenta-Medina A, Kobayashi Y, Yamamoto YY, Koyama H, Kochian LV (2023) Proc Natl Acad Sci USA 120: e2300446120.
https://doi.org/10.1073/pnas.2300446120
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59. !
Sequence-based evaluation of promoter context for prediction of transcriptional start sites in Arabidopsis and rice.
Hiratsuka T, Makita Y, Yamamoto YY. (2022) Sci Rep 12: 6976.
https://doi.org/10.1038/s41598-022-11169-w
tools at Github
58.
Mechanosensory trichome cells evoke a mechanical stimuli-induced immune response in Arabidopsis thaliana.
Matsumura M, Nomoto M, Itaya T, Aratani Y, Iwamoto M, Matsuura T, Hayashi Y, Mori T, Skelly M, Yamamoto YY, Kinoshita T, Mori I, Suzuki T, Betsuyaku S, Spoel S, Toyota M, Tada Y. (2022) Nat Commun 13:1216.
https://doi.org/10.1038/s41467-022-28813-8
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57.
Suppression of MYC transcription activators by the immune cofactor NPR1 fine tunes plant immune responses.
Nomoto M, Skelly MJ, Itaya T, Suzuki T, Matsushita T, Tokizawa M, Kuwata K, Mori H, Yamamoto YY, Higashiyama T, Tsukagoshi H, Shoel SH, Tada Y. (2021) Cell Rep 37: 110125.
https://doi.org/10.1016/j.celrep.2021.110125
56.
Expression GWAS of PGIP1 identifies STOP1-dependent and -independent regulation of PGIP1 in aluminum stress signaling in Arabidopsis.
Agrahari RK, Enomoto T, Ito H, Nakano Y, Yanase E, Watanabe T, Sadhukhan A, Iuchi S, Kobayashi M, Panda SK, Yamamoto YY, Koyama H, Kobayashi H. (2021) Front Plant Sci 12: 774687.
https://doi.org/10.3389/fpls.2021.774687
55. !
Cryptic promoter activation occurs by at least two different mechanisms in the Arabidopsis genome.
Kudo H, Matsuo M, Satoh S, Hata T, Hachisu R, Nakamura M, Yamamoto YY, Kimura H, Matsui M, Obokata J. (2021) Plant J 108: 29-39.
54.
Efficient Agrobacterium tumefaciens-mediated stable genetic transformation of green microalgae, Chlorella sorokiniana.
Sharma PK, Gould VV, Yamamoto Y, Sahoo L. (2021) 3 Biotech 11: 196.
https://doi.org/10.1007/s13205-021-02750-7
53.
Primary metabolism and transcriptional regulation in higher plants.
Hayami N, Yamamoto YY. (2021) Reviews Agri Sci 9: 117-127.
https://dx.doi.org/10.7831/ras.9.0_117
52.
High affinity promoter binding of STOP1 is essential for the early aluminum-inducible expression of novel Al resistance genes GDH1 and GDH2 in Arabidopsis.
Tokizawa M, Enomoto T, Ito H, Wu L, Kobayashi Y, Mora-Macias J, Armenta-Medina D, Iuchi S, Kobayashi M, Nomoto M, Tada Y, Fujita M, Shinozaki K, Yamamoto YY, Kochian LV, Koyama H. (2021) J Exp Bot 72: 2769-2789.
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51.
Genome-wide association study and genomic prediction elucidate the distinct genetic architecture of aluminum and proton tolerance in Arabidopsis thaliana.
Nakano Y, Kusunoki K, Hoekenga OA, Tanaka K, Iuchi S, Sakata Y, Kobayashi M, Yamamoto YY, Koyama H, Kobayashi Y. (2020) Front Plant Sci 11:405.
50.
Cytosolic GLUTAMINE SYNTHETASE 1;1 modulates metabolism and chloroplast development in roots. Kusano M, Fukushima A, Tabuchi-Kobayashi M, Funayama K, Kojima S, Maruyama K, Yamamoto YY, Nishizawa T, Kobayashi M, Wakazaki M, Sato M, Toyooka K, Osanai-Kondo K, Utsumi Y, Seki M, Fukai C, Saito K, Yamaya T. (2020) Plant Physiol 182: 1894-1909.
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49.
Sensitive To Proton Rhizotoxicity1 regulates salt and drought tolerance of Arabidopsis thaliana through transcriptional regulation of CIPK23.
Sadhukhan A, Enomoto T, Kobayashi Y, Watanabe T, Iuchi S, Kobayashi M, Sahoo L, Yamamoto YY, Koyama, H. (2019) Plant Cell Physiol 60: 2113-2126.
48. !
Transcriptome analysis of the H2O2 response in Arabidopsis and partial identification of the transcriptional regulatory network.
Hieno A, Naznin HA, Hasegawa-Inaba K, Yokogawa T, Hayami N, Nomoto M, Tada Y, Yokogawa T, Higuchi M, Hanada K, Matui M, Hirayama T, Kusunoki K, Koyama H, Mitsuda N, Yamamoto YY. (2019) Plant Physiol 180: 1629-1646.
47.
SnRK1 kinase and the NAC transcription factor SOG1 are components of a novel signaling pathway mediating the low energy response triggered by depleted amounts of ATP.
Hamasaki H, Kurihara Y, Kuromori T, Kusano H, Nagata N, Yamamoto YY, Shimada H, Matsui M. (2019) Front Plant Sci 10: Article 503.
46.
Characterization of NtSTOP1-regulating genes in tobacco under aluminum stress.
Ito H, Kobayashi Y, Yamamoto YY, Koyama H. (2019) Soil Sci Plant Nutr 65: 251-258.
doi: 10.1080/00380768.2019.1603064
45.
STOP1 regulates expression of HSFA2 and GDHs critical for low-oxygen tolerance in Arabidopsis.
Enomoto T, Tokizawa M, Ito H, Iuchi S, Kobayashi M, Yamamoto YY, Kobayashi Y, Koyama H. (2019) J Exp Bot 70: 3297-3311.
44.
REDOX homeostasis in plants.
Panda SK, Yamamoto YY (eds) (2019), Springer Nature, ISBN 978-3-319-95314-4.
doi: 10.1007/978-3-319-95315-1
43.
H2O2-mediated biotic and abiotic stress responses in plants.
Hieno A, Naznin HA, Yamamoto YY. (2019) In “REDOX homeostasis in plants”, Panda SK and Yamamoto YY (eds), pp19-42, Springer Nature, ISBN 978-3-319-95314-4.
doi: 10.1007/978-3-319-95315-1_2
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42.
2.予測される作物栽培問題: 2-2干ばつ、洪水環境下での作物の生産性
小山博之、榎本拓也、山本義治(2018) 日本土壌肥料科学雑誌 89: 475-482.
41. # <OUTSTANDING PAPER AWARD by TPJ in 2018>
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, Yoshiyama OK, Sakamoto T, Kurata T, Takahashi N, Umeda M. (2018) Plant J 94: 439-453.
40.
Characterization of CcSTOP1, a C2H2 type transcription factor regulates Al tolerance genes in pigeonpea.
Daspute AA, Kobayashi Y, Panda SK, Fakrudin B, Kobayashi Y, Tokizawa M, Iuchi S, Choudhary A, Yamamoto YY, Koyama H. (2018) Planta 247: 201-214.
doi: 10.1007/s00425-017-2777-6
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39.
Nobel prizes for research in plant science: past, present and future.
Hayami N, Sri Kanta S (2017) Reviews Agri Sci 5: 83-99.
38. ! $ # F1000 BIOLOGY
Light control of 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. (2017) Cell 171: 1316-1325.
doi: 10.1016/j.cell.2017.10.018
37.
Biocontrol potential of an endophytic Streptomyces sp. strain MBCN152-1 against Alternaria brassiclcola on cabbage plug seedlings.
Hassan N, Nakasuji S, Elsharkawy MM, Naznin HA, Kubota M, Jetta H, Shimizu M. (2017) Microbes Environ 32: 133-141.
36.
Prediction of direct targets of Arabidopsis RRTF1, a H2O2 responsive AP2/ERF transcription factor which mediates multiple stress signals.
HienoA, Matsuo M, Oelmüller R, Yamamoto YY. (2017) Endocytobiosis Cell Res 28: 9-13.
35. !
Identification of Arabidopsis genic and non-genic promoters by pair-end sequencing of TSS tags.
Tokizawa M, Kusunoki K, Koyama H, Kurotani A, Sakurai T, Suzuki Y, Kurata T, Yamamoto YY.(2017) Plant J 90: 587-605.
tools at Github
34. !
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. (2017) DNA Res 24: 271-278.
33. !
Design of a synthetic 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, TokoroY, Noda C, Takaki Y, Urawa N, Iuchi S, Urano K, Sakurai T, Kojima M, Sakakibara H, Shinozaki K, Yamaguchi-Shinozaki K. (2017) Plant J 89: 671-681.
32.
ppdb, Plant Promoter Database.
Kusunoki K, Yamamoto YY. (2017) van Dijik, Aalt-Jan (ed) “Plant Genomics Databases”, in Methods in Molecular Biology 1533: 299-314, Springer, Dordrecht,
PISBN:978-1-4939-6656-1,
doi: 10.1007/978-1-4939-6658-5
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31.
Environmental stresses and transcriptional responses for safe chloroplast operation.
Hayami N, Yamamoto YY (2016) Endocytobiosis Cell Res 27 (3): 16-20.
30.
Possible involvement of MYB44-mediated stomatal regulation in induced systemic resistance by Penicillium simplicissimum GP17-2 in Arabidopsis.
Hieno A, Naznin HA, Hyakumachi M, Higuchi M, Matsui M, Yamamoto YY. (2016) Microbes Environ 31: 154-159.
29.
Specific detection of Type 1 and Type 2 isolates of Pyrenochaeta lycopersici by loop-mediated isothermal amplification reaction.
Hieno A, Naznin HA, Suga H, Yamamoto YY, Hyakumachi M. (2016) Acta Agri Scand, Sect B 66: 353-358.
doi: 10.1080/09064710.2015.1120341
Journal Site PubMed
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28.
Adaptive strategies of Arabidopsis thaliana to acid soil environment.
Nakano, Y, Kusunoki K, Iuchi S, Tokizawa M, Yamamoto YY, Kobayashi M, Kobayashi Y, Koyama H (2015) Proceedings of the 4th UGSAS-GU International Symposium 2015. pp42-43.
27.
Prediction-oriented promoter analysis of Arabidopsis ELIP2 revealed novel transcriptional regulatory elements that unite UV-B, high light and cold stress response.
Hayami N, Sakai Y, Saito T, Kimura M, Tokizawa M, Nomoto M, Tada Y, Iuchi S, Yamamoto YY (2015) Proceedings of the 4th UGSAS-GU International Symposium 2015. pp40-41.
26.
光防御関連遺伝子ELIP2プロモーターから同定された強光、低温、UV-Bストレス応答を統合する転写制御配列
速水菜月、坂井優作、時澤睦朋、井内聖、野元美佳、多田安臣、山本義治 （2015）光合成研究 25: 84-91. Journal Site pdf
25. !
The Response of Arabidopsis ELIP2 to UV-B, high light, and cold stress are regulated by a transcriptional regulatory unit composed of two elements.
Hayami N#, Sakai Y#, Saito T, Kimura M, Tokizawa M, Nomoto M, Tada Y, Iuchi S, Yamamoto YY (2015) Plant Physiol 169: 840-855.
24. #
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 (2015) Mol Plant 8: 1253-1273.
doi: 10.1016/j.molp.2015.03.011
23. #
STOP1, CAMTA2 and other transcription factors are involved in aluminum-inducible AtALMT1 expression.
Tokizawa M, Kobayashi Y, Saito T, Kobayashi M, Iuchi S, Nomoto M, Tada Y, Yamamoto YY*, Koyama H* (2015) Plant Physiol 167: 991-1003.
22.
A stable and efficient nuclear transformation system for the diatom Chaetoceros gracillis.
Ifuku K, Yan D, Miyahara M, Inoue-Kashino N, Yamamoto YY, Kashino Y (2015) Photosynth Res 123: 203-211.
doi: 10.1007/s11120-014-0048-y
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21. !
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 (2014) Genes 5: 1115-1131.
20.
Enhanced resistance of plants to disease using Trichoderma spp.
Saldajeno MGB, Naznin HA, Elsharkawy MM, Shimizu M, Hyakumachi M (2014) in “Biotechnology and Biology of Trichoderma (1st Ed)”, Eds: Gupta V, Schmoll M, Herrera-Estrella A, Upadhyay R, Druzhinina I, Tuohy M, pp 477-493, Elsevier, Amsterdam.
ISBN: 9780444595768
19.
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 risistance in transgenic Arabidopsis
Sadhukhan A, Kobayashi Y, Kobayashi Y, Tokizawa M, Yamamoto YY, Iuchi S, Koyama H, Panda SK, Sahoo L (2014) Planta 240: 645-664.
doi: 10.1007/s00425-014-2111-5
18.
Systemic resistance induced by volatile organic compounds emitted by plant growth-promoting fungi in Arabidopsis thaliana
Naznin HA, Kiyohara D, Kimura M, Miyazawa M, Shimizu M, Hyakumachi M (2014) PLoS One 9: E86882.
doi: 10.1371/journal.pone.0086882
17. !
ppdb: Plant Promoter Database ver 3.0
Hieno A, Naznin HA, Hyakumachi M, Sakurai T, Tokizawa M, Koyama H, Sato N, Nishiyama T, Hasebe M, Zimmer AD, Dang D, Reski R, Rensing S, Obokata J, Yamamoto YY (2014) Nucleic Acids Res 42: D1188-1192.
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16.
Analysis of volatile organic compaounds emitted by plant growth-promoting fungus Phoma sp GS8-3 for growth promotion effects on tobacco
Naznin HA, Kimura M, Miyazawa M, Hyakumachi M (2013) Microbes Environ 28, 42-49.
15.
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 (2013) Methods Enzymol 527 , 221-237.
doi: 10.1016/B978-0-12-405882-8.00012-X
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14.
Systemic resistance induced in Arabidopsis thaliana by Trichoderma asperellum SKT-1, a microbial pesticide of seedborne diseases of rice
Yoshioka Y, Ichikawa H, Naznin HA, Kogure A, Hyakucachi M (2012) Pest Manag Sci 68, 60-66.
13. ! ###
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, Yoshikawa K, Kojima M, Sakakibara H, Shinozaki K, Yamaguchi-Shinozaki K (2012) DNA Res 19, 37-49.
12.
植物プロモーターデータベースppdbの紹介
山本義治、日恵野綾香 新学術領域研究「植物の環境感覚：刺激受容から細胞応答まで」ニュースレター 4.2012 (2012)
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11. !
Characteristics of core promoter types with respect to gene structure and expression in Arabidopsis thaliana
Yamamoto YY*, Yoshioka Y, Hyakumachi M, and Obokata J (2011) DNA Res (*corresponding author), 18, 333-342.
Supplemental file (RARf tables used in the article)
10. !
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 (2011) BMC Plant Biol 11, 39, (*corresponding author)
Journal Site pdf <Most viewed article of the journal>
9.
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. (2011) Genomics 97, 166-172.
doi: 10.1016/j.ygeno.2010.12.001
8.
Rhizotoxic ions: ‘-Omics’ approaches for studying abiotic stress tolerance in plants
Zhao C-R, Yamamoto YY, Koyama H (2011) In “Omics and Plant Abiotic Stress Tolerance” (Oak Park, USA, Bentham Science Publishers) pp128-132.
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7.
高等植物におけるpol-II依存性プロモーター
山本義治 横浜市立大学論叢（60 (2): 133-141, 2010 ）
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6. ! COVER ARTICLE
Identification of photosynthetic sacoglossans from Japan
Yamamoto YY, Yusa Y, Yamamoto S, Hirano Y, Hirano Y, Motomura T, Tanemura T, Obokata J. (2009) Endocytobiosis Cell Res 19, 112-119.
5. ! $ # F1000 BIOLOGY
Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis
Yamamoto YY, Yoshitsugu T, Sakurai T, Seki M, Shinozaki K, Obokata J.(2009) Plant J 60: 350-362.
doi: 10.1111/j.1365-313X.2009.03958.x
4.
Live imaging of chloroplast FtsZ1 filaments, rings, spirals, and motile dot structures in the AtMinE1 mutant and overexpressor of Arabidopsis thaliana
Fujiwara M, Sekine K, Yamamoto YY, Abe T, Sato N, Itoh R. (2009) Plant Cell Physiol 50, 1116-1126.
3.
Extraction of position-sensitive promoter constituents
Yamamoto YY, Obokata J. (2009) In “Computational biology: new research”, Russe AS (ed), (Hauppauge, NY, Nova Science Publishers), pp361-373.
2.
植物・藻類・細菌の材料の入手と栽培・培養：タバコ
山本義治、小保方潤一 低温科学「光合成研究法」67: 39-42 (2009).
1.
タバコ形質転換法：核ゲノム
長尾一生、山本義治、小保方潤一 低温科学「光合成研究法」67: 617-622 (2009).
Highly Cited Researchers of Gifu University
