研究者詳細 - 花田　耕介

論文 - 花田　耕介

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A de novo gene originating from the mitochondria controls floral transition in Arabidopsis thaliana 査読有り国際誌

Tomoyuki Takeda, Kazumasa Shirai, You-wang Kim, Mieko Higuchi-Takeuchi, Minami Shimizu, Takayuki Kondo, Tomokazu Ushijima, Tomonao Matsushita, Kazuo Shinozaki, Kousuke Hanada

Plant Molecular Biology 2023年04月

Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants 査読有り国際誌

Kazumasa Shirai, Mitsuhiko P. Sato, Ranko Nishi, Masahide Seki, Yutaka Suzuki and Kousuke Hanada

Genome Research 31 1060 - 1068 2021年06月

Unearth of small open reading frames (sORFs) in drought stress transcriptome of Oryza sativa subsp. indica 査読有り

Sheue Ni Ong, Boon Chin Tan, Kousuke Hanada, Chee How Teo

Gene 2023年06月

An augmented attention-based lightweight CNN model for plant water stress detection 査読有り

Mohd Hider Kamarudin, Zool Hilmi Ismail, Noor Baity Saidi, Kousuke Hanada

Applied Intelligence 2023年04月

Enhanced growth rate under elevated CO2 conditions was observed for transgenic lines of genes identified by intraspecific variation analyses in Arabidopsis thaliana 査読有り

Riichi Oguchi, Kousuke Hanada, Minami Shimizu, Masako Mishio, Hiroshi Ozaki, Kouki Hikosaka

Plant Molecular Biology 1 - 13 2022年04月

Genome-Wide Association Study of Local Thai Indica Rice Seedlings Exposed to Excessive Iron 査読有り国際誌

Reunreudee Kaewcheenchai,Phanchita Vejchasarn, Kousuke Hanada,Kazumasa Shirai,Chatchawan Jantasuriyarat, Piyada Juntawong

Plants 10 ( 4 ) 798 2021年04月

Degree of functional divergence in duplicates is associated with distinct roles in plant evolution. 査読有り

Akihiro Ezoe, Kazumasa Shirai, Kousuke Hanada

Molecular Biology and Evolution 38 ( 4 ) 1447 - 1459 2021年04月

植物と共生菌の間でのシグナル伝達するペプチドの探索に向けて招待有り

伊東梓帆, 花田耕介

アグリバイオ 5 ( 5 ) 52 - 54 2021年03月

塩ストレス耐性を強化するペプチド性遺伝子招待有り

近藤隆之, 花田耕介

アグリバイオ 5 ( 5 ) 23 - 28 2021年03月

Effect of small coding genes on the circadian rhythms under elevated CO2 conditions in plants. 査読有り国際誌

Mieko Higuchi-Takeuchi, Takayuki Kondo, Minami Shimizu, You-Wang Kim, Kazuo Shinozaki, Kousuke Hanada

Plant Molecular Biology 104 ( 1-2 ) 55 - 65 2020年09月

豚で起きていたコロナウイルスに近縁なウイルスでのパンデミック感染の紹介招待有り査読有り

花田　耕介

生物の化学「遺伝」 75 ( 1 ) 16 - 19 2020年05月

Identification of endogenous small peptides involved in rice immunity through transcriptomics‐and proteomics‐based screening 査読有り

12. Wang P, Yao S, Kosami KI, Guo T, Li J, Zhang Y, Fukao Y, Kaneko‐Kawano Y, Zhang H, She YM, Wang P, Xing W, Hanada K, Liu R, Kawano

Plant Biotechnology Journal 18 ( 2 ) 415 - 428 2020年02月

Contribution of Functional Divergence Through Copy Number Variations to the Inter-Species and Intra-Species Diversity in Specialized Metabolites 招待有り査読有り

Shirai K., Hanada K.

Frontiers in Plant Science 10 2019年11月

担当区分：責任著者記述言語：英語掲載種別：研究論文（学術雑誌）

© Copyright © 2019 Shirai and Hanada. There is considerable diversity in the specialized metabolites within a single plant species (intra-species) and among different plant species (inter-species). The functional divergence associated with gene duplications largely contributes to the inter-species diversity in the specialized metabolites, whereas the intra-species diversity is due to gene dosage changes via gene duplications [i.e., copy number variants (CNVs)] at the intra-species level of evolution. This is because CNVs are thought to undergo associated with less functional divergence at the intra-species level of evolution. However, functional divergence caused by CNVs may induce specialized metabolite diversity at the intra-species and inter-species levels of evolution. We herein discuss the functional divergence of CNVs in metabolic quantitative trait genes (mQTGs). We focused on 5,654 previously identified mQTGs in 270 Arabidopsis thaliana accessions. The ratio of nonsynonymous to synonymous variations tends to be higher for mQTGs with CNVs than for mQTGs without CNVs within A. thaliana accessions, suggesting that CNVs are responsible for the functional divergence among mQTGs at the intra-species level of evolution. To evaluate the contribution of CNVs to inter-species diversity, we calculated the ratio of nonsynonymous to synonymous substitutions in the Arabidopsis lineage. The ratio tends to be higher for the mQTGs with CNVs than for the mQTGs without CNVs. Additionally, we determined that mQTGs with CNVs are subject to positive selection in the Arabidopsis lineage. Our data suggest that CNVs are closely related to functional divergence contributing to adaptations via the production of diverse specialized metabolites at the intra-species and inter-species levels of evolution.

DOI： 10.3389/fpls.2019.01567

Scopus

その他リンク： https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85076708024&origin=inward

Tyr82 amino acid mutation in pb1 polymerase induces an influenza virus mutator phenotype 査読有り

Naito T., Shirai K., Mori K., Muratsu H., Ushirogawa H., Ohniwa R., Hanada K., Saito M.

Journal of Virology 93 ( 22 ) 2019年11月

記述言語：英語掲載種別：研究論文（学術雑誌）

© 2019 American Society for Microbiology. In various positive-sense single-stranded RNA viruses, a low-fidelity viral RNA-dependent RNA polymerase (RdRp) confers attenuated phenotypes by increasing the mutation frequency. We report a negative-sense single-stranded RNA virus RdRp mutant strain with a mutator phenotype. Based on structural data of RdRp, rational targeting of key residues, and screening of fidelity variants, we isolated a novel low-fidelity mutator strain of influenza virus that harbors a Tyr82-to-Cys (Y82C) singleamino- acid substitution in the PB1 polymerase subunit. The purified PB1-Y82C polymerase indeed showed an increased frequency of misincorporation compared with the wild-type PB1 in an in vitro biochemical assay. To further investigate the effects of position 82 on PB1 polymerase fidelity, we substituted various amino acids at this position. As a result, we isolated various novel mutators other than PB1-Y82C with higher mutation frequencies. The structural model of influenza virus polymerase complex suggested that the Tyr82 residue, which is located at the nucleoside triphosphate entrance tunnel, may influence a fidelity checkpoint. Interestingly, although the PB1- Y82C variant replicated with wild-type PB1-like kinetics in tissue culture, the 50% lethal dose of the PB1-Y82C mutant was 10 times lower than that of wild-type PB1 in embryonated chicken eggs. In conclusion, our data indicate that the Tyr82 residue of PB1 has a crucial role in regulating polymerase fidelity of influenza virus and is closely related to attenuated pathogenic phenotypes in vivo. IMPORTANCE Influenza A virus rapidly acquires antigenic changes and antiviral drug resistance, which limit the effectiveness of vaccines and drug treatments, primarily owing to its high rate of evolution. Virus populations formed by quasispecies can contain resistance mutations even before a selective pressure is applied. To study the effects of the viral mutation spectrum and quasispecies, high- and low-fidelity variants have been isolated for several RNA viruses. Here, we report the discovery of a low-fidelity RdRp variant of influenza A virus that contains a substitution at Tyr82 in PB1. Viruses containing the PB1-Y82C substitution showed growth kinetics and viral RNA synthesis levels similar to those of the wild-type virus in cell culture; however, they had significantly attenuated phenotypes in a chicken egg infection experiment. These data demonstrated that decreased RdRp fidelity attenuates influenza A virus in vivo, which is a desirable feature for the development of safer live attenuated vaccine candidates.

DOI： 10.1128/JVI.00834-19

Scopus

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Dephosphorylation of clustered phosphoserine residues in human Grb14 by protein phosphatase 1 and its effect on insulin receptor complex formation 査読有り

Taira J., Yoshida K., Takemoto M., Hanada K., Sakamoto H.

Journal of Peptide Science 25 ( 10 ) 2019年10月

記述言語：英語掲載種別：研究論文（学術雑誌）

© 2019 European Peptide Society and John Wiley & Sons, Ltd. The physical interaction of the human growth factor receptor-bound protein 14 (hGrb14) and the insulin receptor (IR) represses insulin signaling. With respect to the recruiting mechanism of hGrb14 to IR respond to insulin stimulus, our previous reports have suggested that phosphorylation of Ser358, Ser362, and Ser366 in hGrb14 by glycogen synthase kinase-3 repressed hGrb14–IR complex formation. In this study, we investigated phosphatase-mediated dephosphorylation of the hGrb14 phosphoserine residues. An in vitro phosphatase assay with hGrb14-derived synthetic phosphopeptides suggested that protein phosphatase 1 (PP1) is involved in the dephosphorylation of Ser358 and Ser362. Furthermore, coimmunoprecipitation experiments suggested that insulin-induced hGrb14–IR complex formation was repressed by the substitution of Ser358 or Ser362 with glutamic acid. These findings suggested that phosphate groups on Ser358 and Ser362 in hGrb14 are dephosphorylated by PP1, and the dephosphorylation facilitates hGrb14–IR complex formation.

DOI： 10.1002/psc.3207

Scopus

その他リンク： https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85074742761&origin=inward

Hormone-like peptides and small coding genes in plant stress signaling and development 招待有り査読有り

Takahashi F., Hanada K., Kondo T., Shinozaki K.

Current Opinion in Plant Biology 51 88 - 95 2019年10月

担当区分：筆頭著者記述言語：英語掲載種別：記事・総説・解説・論説等（学術雑誌）

© 2019 Elsevier Ltd Recent works have shed light on the long-distance interorgan signaling by which hormone-like peptides precisely regulate physiological effects in a manner similar to phytohormones. Many such peptides have already been identified in the primary model plant, Arabidopsis thaliana. In addition, Arabidopsis genome reanalysis revealed over 7000 novel candidate small coding genes, some of which are likely to be associated with hormone-like peptides. Hormone-like peptides have also been reported to play critical roles in interorgan communications during morphogenesis and stress responses. In this review, we focus on the functional roles of hormone-like peptides and small coding genes in cell-to-cell and/or long-distance communications during plant stress signaling and development and discuss the evolutionary conservation of these peptides among plants.

DOI： 10.1016/j.pbi.2019.05.011

Scopus

その他リンク： https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85068048113&origin=inward

Transcriptome analysis and identification of a transcriptional regulatory network in the response to H<inf>2</inf>O<inf>2</inf> 査読有り

Hieno A., Naznin H., 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 Y.

Plant Physiology 180 ( 3 ) 1629 - 1646 2019年07月

記述言語：英語掲載種別：研究論文（学術雑誌）

© 2019 American Society of Plant Biologists. Hydrogen peroxide (H2O2) is a common signal molecule initiating transcriptional responses to all the known biotic and abiotic stresses of land plants. However, the degree of involvement of H2O2 in these stress responses has not yet been well studied. Here we identify time-dependent transcriptome profiles stimulated by H2O2 application in Arabidopsis (Arabidopsis thaliana) seedlings. Promoter prediction based on transcriptome data suggests strong crosstalk among high light, heat, and wounding stress responses in terms of environmental stresses and between the abscisic acid (ABA) and salicylic acid (SA) responses in terms of phytohormone signaling. Quantitative analysis revealed that ABA accumulation is induced by H2O2 but SA is not, suggesting that the implied crosstalk with ABA is achieved through ABA accumulation while the crosstalk with SA is different. We identified potential direct regulatory pairs between regulator transcription factor (TF) proteins and their regulated TF genes based on the time-course transcriptome analysis for the H2O2 response, in vivo regulation of the regulated TF by the regulator TF identified by expression analysis of mutants and overexpressors, and in vitro binding of the regulator TF protein to the target TF promoter. These analyses enabled the establishment of part of the transcriptional regulatory network for the H2O2 response composed of 15 regulatory pairs of TFs, including five pairs previously reported. This regulatory network is suggested to be involved in a wide range of biotic and abiotic stress responses in Arabidopsis.

DOI： 10.1104/pp.18.01426

Scopus

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シロイヌナズナの短いコーディング遺伝子に特化した発現データベースと過剰発現体ライブラリーの構築招待有り

武田智之, 花田耕介

植物の生長調節 ( 一般社団法人植物化学調節学会 ) 54 ( 1 ) 60 - 65 2019年01月

担当区分：責任著者記述言語：日本語掲載種別：研究論文（学術雑誌）

<p>Functional roles of small coding genes tend to be ignored in 20 years because small coding genes have not been identified in even highly accurate genomes of model organisms.　In plants, it is recognized that small coding genes play essential roles within a single cell as well as intercellular signal transductions like hormone-like peptides.　However, many of small coding genes are not annotated in plant genomes even if novel hormone-like peptides encoded by small coding genes tend to be hidden in plant genomes.　Here, we introduce transcriptome database （HanaDB-AT） and transgenic library of overexpression with focusing on Arabidopsis novel and annotated small coding genes.　The database and transgenic library should be useful tools to discover novel hormone-like peptides as well as other functional peptides in small coding genes.</p>

DOI： 10.18978/jscrp.54.1_60

CiNii Article

その他リンク： https://ci.nii.ac.jp/naid/130007668423

A highly specific genome-wide association study integrated with transcriptome data reveals the contribution of copy number variations to specialized metabolites in Arabidopsis thaliana accessions 査読有り

Kazumasa Shirai, Fumio Matsuda, Ryo Nakabayashi, Masanori Okamoto, Maho Tanaka, Akihiro Fujimoto, Minami Shimizu, Kazuo Shinozaki, Motoaki Seki, Kazuki Saito, Kousuke Hanada

Molecular Biology and Evolution 2017年09月

Mutant selection in the self-incompatible plant radish (Raphanus sativus L. var. sativus) using two-step TILLING. 査読有り

Kohzuma K, Chiba M, Nagano S, Anai T, Ueda MU, Oguchi R, Shirai K, Hanada K, Hikosaka K, Fujii N.

Breed Science 67 ( 3 ) 268 - 276 2017年06月

Molecular Evolution and Functional Characterization of a Bifunctional Decarboxylase Involved in Lycopodium Alkaloid Biosynthesis. 査読有り

Bunsupa S, Hanada K, Maruyama A, Aoyagi K, Komatsu K, Ueno H, Yamashita M, Sasaki R, Oikawa A, Saito K, Yamazaki M.

Plant Physiolgy 171 ( 4 ) 2432 - 2444 2016年06月

What plant trait explains the variations in relative growth rate and in its response to the elevated CO2 concentration among Arabidopsis thaliana ecotypes derived from a variety of habitats? 査読有り

Oguchi R, Ozaki H, Hanada K, Hikosaka K.

Oecologia 2016年05月

Phytochrome controls alternative splicing to mediate light responses in Arabidopsis. 査読有り

Shikata H, Hanada K, Ushijima T, Nakashima M, Suzuki Y, Matsushita T

Proc Natl Acad Sci U S A. 2014年12月

Transcriptomic analysis of rice in response to iron deficiency and excess. 査読有り

2. Bashir K, Hanada K, Shimizu M, Seki M, Nakanishi H and Nishizawa NK

Rice 2014年09月

Substantial expression of novel small open reading frames in Oryza sativa.

3. Okamoto M, Higuchi-Takeuchi M, Shimizu M, Shinozaki K, Hanada K

Plant Signaling & Behavior 2014年02月

25. ゲノム解析によるコムギABA受容体の同定および生化学的解析(口頭発表,植物化学調節学会第49回大会) 招待有り

妻鹿良亮, 花田耕介, 岡本昌憲

植物化学調節学会研究発表記録集 ( 一般社団法人植物化学調節学会 ) 49 ( 0 ) 2014年01月

Small open reading frames associated with morphogenesis are hidden in plant genomes. 査読有り

Hanada K, Higuchi-Takeuchi M, Okamoto M, Yoshizumi T, Shimizu M, Nakaminami K, Nishi R, Ohashi C, Iida K, Tanaka M, Horii Y, Kawashima M, Matsui K, Toyoda T, Shinozaki K, Seki M, Matsui M.

Proc Natl Acad Sci U S A. 110 2395 - 2400 2013年02月

Positional correlation analysis improves reconstruction of full-length transcripts and alternative isoforms from noisy array signals or short reads. 査読有り

Kawaguchi S, Iida K, Harada E, Hanada K, Matsui A, Okamoto M, Shinozaki K, Seki M, and ToyodaT

Bioinformatics ( 28 ) 929 - 937 2012年04月

Two glycosyltransferases involved in anthocyanin modification delineated by transcriptome independent component analysis in Arabidopsis thaliana. 査読有り

8. Yonekura-Sakakibara K, Fukushima A, Nakabayashi R, Hanada K, Matsuda F, Sugawara S, Inoue E, Kuromori T, Ito T, Shinozaki K, Wangwattana B, Yamazaki M, Saito K

The Plant Journal 69 ( 1 ) 154 - 167 2012年01月

Tissue-specific Transcriptome Analysis Reveals Cell Wall Metabolism, Flavonol Biosynthesis, and Defense Responses are Activated in the Endosperm of Germinating Arabidopsis thaliana Seeds. 査読有り

Endo A[e], Tatematsu K[e], Hanada K[e], Duermeyer L, Okamoto M, Yonekura-Sakakibara K, Saito K, Toyoda T, Kawakami N, Kamiya Y, Seki M, Nambara E*

Plant and Cell Physiology 2012年01月

Origin and evolution of genes related to ABA metabolism and its signaling pathways. 査読有り

Hanada K*, Hase T, Toyoda T, Shinozaki K and Okamoto M

Journal of Plant Research 124 ( 4 ) 455 - 465 2011年07月

An evolutionary view of functional diversity in family 1 glycosyltransferases. 査読有り

Yonekura-Sakakibara K* and Hanada K.

The Plant Journal 66 ( 1 ) 182 - 193 2011年04月

ARTADE2DB: Improved Statistical Inferences for Arabidopsis Gene Functions and Structure Predictions by Dynamic-Structure-Based Dynamic Expression (DSDE) Analyses. 査読有り

10. Iida K, Kawaguchi S, Kobayashi N, Yoshida Y, Ishii M, Harada E, Hanada K, Matsui A, Okamoto M, Ishida J, Tanaka M, Morosawa T, Seki M, Toyoda T*

Cell Physiology 52 ( 2 ) 254 - 264 2011年02月

Toward genome-wide metabolotyping and elucidation of metabolic system: metabolic profiling of large-scale bioresources.

Hirai MY*, Sawada Y, Kanaya S, Kuromori T, Kobayashi M, Klausnitzer R, Hanada K, Akiyama K, Sakurai T, Saito K, Shinozaki K.

Journal of Plant Research 123 ( 3 ) 291 - 298 2010年05月

sORF finder: a program package to identify small open reading frames(sORFs) with high coding potential. 査読有り

Hanada K*, Akiyama K, Sakurai T, Toyoda T, Shinozaki K, Shiu SH.

Bioinformatics 26 ( 3 ) 399 - 400 2010年02月

Evolutionary Persistence of Functional Compensation by Duplicate Genes in Arabidopsis. 査読有り

Hanada K*, Kuromori T, Myouga F, Toyoda T, Li WH and Shinozaki K.

Genome Biology and Evolution 29 ( 1 ) 409 - 414 2009年10月

PosMed-plus: an intelligent search engine that inferentially integrates cross-species information resources for molecular breeding of plants. 査読有り

17. Makita Y, Kobayashi N, Mochizuki Y, Yoshida Y, Asano S, Heida N, Deshpande M, Bhatia R, Matsushima A, Ishii M, Kawaguchi S, Iida K, Hanada K, Kuromori T, Seki M, Shinozaki K, Toyoda T*

Plant and Cell Physiology 50 ( 7 ) 1249 - 1259 2009年07月

Evolutionary history and stress regulation of plant receptor-like kinase/pelle genes. 査読有り

Lehti-Shiu MD, Zou C, Hanada K, Shiu SH*.

Plant Physiology 150 ( 1 ) 12 - 26 2009年05月

Increased expression and protein divergence inIncreased expression and protein divergence in duplicate genes is associated with morphological diversification. 査読有り

Hanada K*, Kuromori T, Myouga F, Toyoda T, Shinozaki K.

PLOS Genetics 5 ( 12 ) 2009年05月

Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis. 査読有り

19. Kurihara Y, Matsui A, Hanada K, Kawashima M, Ishida J, Morosawa T, Tanaka M, Kaminuma E, Mochizuki Y, Matsushima A, Toyoda T, Shinozaki K, Seki M*

National Academy of Sciences of the United States of America 106 ( 7 ) 2453 - 2458 2009年02月

Functional role of Pack-MULEs in rice inferred from purifying selection and expression profile. 査読有り

Hanada K, Vallejo V, Nobuta, K, Slotkin K, Lisch D, Meyers BC, Shiu SH, Jiang N*

The Plant Cell 21 ( 1 ) 25 - 38 2009年01月

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