94 results on '"Tetsuya Kurata"'
Search Results
2. DNA methylation is reconfigured at the onset of reproduction in rice shoot apical meristem
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Asuka Higo, Noriko Saihara, Fumihito Miura, Yoko Higashi, Megumi Yamada, Shojiro Tamaki, Tasuku Ito, Yoshiaki Tarutani, Tomoaki Sakamoto, Masayuki Fujiwara, Tetsuya Kurata, Yoichiro Fukao, Satoru Moritoh, Rie Terada, Toshinori Kinoshita, Takashi Ito, Tetsuji Kakutani, Ko Shimamoto, and Hiroyuki Tsuji
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Science - Abstract
The shoot apical meristem of flowering plants transitions from forming leaves to floral organs. Here Higo et al. show that DNA methylation of many transposons that are hypermethylated in gametes is established in the SAM before flowering, suggesting it protects against harmful transposition long before germ cell differentiation.
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- 2020
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3. Root-Knot and Cyst Nematodes Activate Procambium-Associated Genes in Arabidopsis Roots
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Yasuka L. Yamaguchi, Reira Suzuki, Javier Cabrera, Satoru Nakagami, Tomomi Sagara, Chika Ejima, Ryosuke Sano, Yuichi Aoki, Rocio Olmo, Tetsuya Kurata, Takeshi Obayashi, Taku Demura, Takashi Ishida, Carolina Escobar, and Shinichiro Sawa
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plant-parasitic nematodes ,RNA-sequencing ,procambial cells ,root-knot nematode ,cyst nematode ,M. incognita ,Plant culture ,SB1-1110 - Abstract
Developmental plasticity is one of the most striking features of plant morphogenesis, as plants are able to vary their shapes in response to environmental cues. Biotic or abiotic stimuli often promote organogenesis events in plants not observed under normal growth conditions. Root-knot nematodes (RKNs) are known to parasitize multiple species of rooting plants and to induce characteristic tissue expansion called galls or root-knots on the roots of their hosts by perturbing the plant cellular machinery. Galls contain giant cells (GCs) and neighboring cells, and the GCs are a source of nutrients for the parasitizing nematode. Highly active cell proliferation was observed in galls. However, the underlying mechanisms that regulate the symptoms triggered by the plant-nematode interaction have not yet been elucidated. In this study, we deciphered the molecular mechanism of gall formation with an in vitro infection assay system using RKN Meloidogyne incognita, and the model plant Arabidopsis thaliana. By taking advantages of this system, we performed next-generation sequencing-based transcriptome profiling, and found that the expression of procambium identity-associated genes were enriched during gall formation. Clustering analyses with artificial xylogenic systems, together with the results of expression analyses of the candidate genes, showed a significant correlation between the induction of gall cells and procambium-associated cells. Furthermore, the promoters of several procambial marker genes such as ATHB8, TDR and WOX4 were activated not only in M. incognita-induced galls, but similarly in M. javanica induced-galls and Heterodera schachtii-induced syncytia. Our findings suggest that phytoparasitic nematodes modulate the host’s developmental regulation of the vascular stem cells during gall formation.
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- 2017
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4. Isolation of new gravitropic mutants under hypergravity conditions
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Akiko Mori, Masatsugu Toyota, Masayoshi Shimada, Mika Mekata, Tetsuya Kurata, Masao Tasaka, and Miyo Terao Morita
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Gravitropism ,Hypergravity ,Arabidopsis thaliana ,whole genome sequencing ,Enhancer mutant ,Plant culture ,SB1-1110 - Abstract
Forward genetics is a powerful approach used to link genotypes and phenotypes, and mutant screening/analysis has provided deep insights into many aspects of plant physiology. Gravitropism is a tropistic response in plants, in which hypocotyls and stems sense the direction of gravity and grow upwards. Previous studies of gravitropic mutants have suggested that shoot endodermal cells in Arabidopsis stems and hypocotyls are capable of sensing gravity (i.e., statocytes). In the present study, we report a new screening system using hypergravity conditions to isolate enhancers of gravitropism mutants, and we also describe a rapid and efficient genome mapping method, using Next-Generation Sequencing (NGS) and Single Nucleotide Polymorphism (SNP)-based markers. Using the endodermal-amyloplast less 1 (eal1) mutant, which exhibits defective development of endodermal cells and gravitropism, we found that hypergravity (10 g) restored the reduced gravity responsiveness in eal1 hypocotyls and could, therefore, be used to obtain mutants with further reduction in gravitropism in the eal1 background. Using the new screening system, we successfully isolated six ene (enhancer of eal1) mutants that exhibited little or no gravitropism under hypergravity conditions, and using NGS and map-based cloning with SNP markers, we narrowed down the potential causative genes, which revealed a new genetic network for shoot gravitropism in Arabidopsis.
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- 2016
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5. Correction: The Tinkerbell (Tink) Mutation Identifies the Dual-Specificity MAPK Phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) as a Novel Regulator of Organ Size in Arabidopsis.
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Kim L Johnson, Sascha Ramm, Christian Kappel, Sally Ward, Ottoline Leyser, Tomoaki Sakamoto, Tetsuya Kurata, Michael W Bevan, and Michael Lenhard
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Medicine ,Science - Published
- 2015
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6. Two different rickettsial bacteria invading Volvox carteri.
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Kaoru Kawafune, Yuichi Hongoh, Takashi Hamaji, Tomoaki Sakamoto, Tetsuya Kurata, Shunsuke Hirooka, Shin-ya Miyagishima, and Hisayoshi Nozaki
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Medicine ,Science - Abstract
BACKGROUND:Bacteria of the family Rickettsiaceae are principally associated with arthropods. Recently, endosymbionts of the Rickettsiaceae have been found in non-phagotrophic cells of the volvocalean green algae Carteria cerasiformis, Pleodorina japonica, and Volvox carteri. Such endosymbionts were present in only C. cerasiformis strain NIES-425 and V. carteri strain UTEX 2180, of various strains of Carteria and V. carteri examined, suggesting that rickettsial endosymbionts may have been transmitted to only a few algal strains very recently. However, in preliminary work, we detected a sequence similar to that of a rickettsial gene in the nuclear genome of V. carteri strain EVE. METHODOLOGY/PRINCIPAL FINDINGS:Here we explored the origin of the rickettsial gene-like sequences in the endosymbiont-lacking V. carteri strain EVE, by performing comparative analyses on 13 strains of V. carteri. By reference to our ongoing genomic sequence of rickettsial endosymbionts in C. cerasiformis strain NIES-425 cells, we confirmed that an approximately 9-kbp DNA sequence encompassing a region similar to that of four rickettsial genes was present in the nuclear genome of V. carteri strain EVE. Phylogenetic analyses, and comparisons of the synteny of rickettsial gene-like sequences from various strains of V. carteri, indicated that the rickettsial gene-like sequences in the nuclear genome of V. carteri strain EVE were closely related to rickettsial gene sequences of P. japonica, rather than those of V. carteri strain UTEX 2180. CONCLUSION/SIGNIFICANCE:At least two different rickettsial organisms may have invaded the V. carteri lineage, one of which may be the direct ancestor of the endosymbiont of V. carteri strain UTEX 2180, whereas the other may be closely related to the endosymbiont of P. japonica. Endosymbiotic gene transfer from the latter rickettsial organism may have occurred in an ancestor of V. carteri. Thus, the rickettsiae may be widely associated with V. carteri, and likely have often been lost during host evolution.
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- 2015
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7. The Tinkerbell (Tink) Mutation Identifies the Dual-Specificity MAPK Phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) as a Novel Regulator of Organ Size in Arabidopsis.
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Kim L Johnson, Sascha Ramm, Christian Kappel, Sally Ward, Ottoline Leyser, Tomoaki Sakamoto, Tetsuya Kurata, Michael W Bevan, and Michael Lenhard
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Medicine ,Science - Abstract
Mitogen-activated dual-specificity MAPK phosphatases are important negative regulators in the MAPK signalling pathways responsible for many essential processes in plants. In a screen for mutants with reduced organ size we have identified a mutation in the active site of the dual-specificity MAPK phosphatase indole-3-butyric acid-response5 (IBR5) that we named tinkerbell (tink) due to its small size. Analysis of the tink mutant indicates that IBR5 acts as a novel regulator of organ size that changes the rate of growth in petals and leaves. Organ size and shape regulation by IBR5 acts independently of the KLU growth-regulatory pathway. Microarray analysis of tink/ibr5-6 mutants identified a likely role for this phosphatase in male gametophyte development. We show that IBR5 may influence the size and shape of petals through auxin and TCP growth regulatory pathways.
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- 2015
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8. System for stable β-estradiol-inducible gene expression in the moss Physcomitrella patens.
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Minoru Kubo, Akihiro Imai, Tomoaki Nishiyama, Masaki Ishikawa, Yoshikatsu Sato, Tetsuya Kurata, Yuji Hiwatashi, Ralf Reski, and Mitsuyasu Hasebe
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Medicine ,Science - Abstract
Inducible transgene expression provides a useful tool to analyze gene function. The moss Physcomitrellapatens is a model basal land plant with well-developed research tools, including a high efficiency of gene targeting and substantial genomics resources. However, current systems for controlled transgene expression remain limited. Here we report the development of an estrogen receptor mediated inducible gene expression system, based on the system used in flowering plants. After identifying the appropriate promoters to drive the chimeric transducer, we succeeded in inducing transcription over 1,000-fold after 24 h incubation with β-estradiol. The P. patens system was also effective for high-level long-term induction of gene expression; transcript levels of the activated gene were maintained for at least seven days on medium containing β-estradiol. We also established two potentially neutral targeting sites and a set of vectors for reproducible expression of two transgenes. This β-estradiol-dependent system will be useful to test genes individually or in combination, allowing stable, inducible transgenic expression in P. patens.
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- 2013
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9. Digital gene expression profiling by 5'-end sequencing of cDNAs during reprogramming in the moss Physcomitrella patens.
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Tomoaki Nishiyama, Kaori Miyawaki, Masumi Ohshima, Kari Thompson, Akitomo Nagashima, Mitsuyasu Hasebe, and Tetsuya Kurata
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Medicine ,Science - Abstract
Stem cells self-renew and repeatedly produce differentiated cells during development and growth. The differentiated cells can be converted into stem cells in some metazoans and land plants with appropriate treatments. After leaves of the moss Physcomitrella patens are excised, leaf cells reenter the cell cycle and commence tip growth, which is characteristic of stem cells called chloronema apical cells. To understand the underlying molecular mechanisms, a digital gene expression profiling method using mRNA 5'-end tags (5'-DGE) was established. The 5'-DGE method produced reproducible data with a dynamic range of four orders that correlated well with qRT-PCR measurements. After the excision of leaves, the expression levels of 11% of the transcripts changed significantly within 6 h. Genes involved in stress responses and proteolysis were induced and those involved in metabolism, including photosynthesis, were reduced. The later processes of reprogramming involved photosynthesis recovery and higher macromolecule biosynthesis, including of RNA and proteins. Auxin and cytokinin signaling pathways, which are activated during stem cell formation via callus in flowering plants, are also activated during reprogramming in P. patens, although no exogenous phytohormone is applied in the moss system, suggesting that an intrinsic phytohormone regulatory system may be used in the moss.
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- 2012
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10. Subtilase activity in intrusive cells mediates haustorium maturation in parasitic plants
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Andreas Schaller, Takanori Wakatake, Satoko Yoshida, Tetsuya Kurata, Juliane K. Ishida, Ken Shirasu, Ryosuke Sano, Satoshi Ogawa, Yasunori Ichihashi, Taku Demura, and Thomas Spallek
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0106 biological sciences ,Facultative parasite ,Proteases ,Physiology ,Cell ,Plant Science ,Biology ,Genes, Plant ,Plant Roots ,01 natural sciences ,Subtilase ,Host-Parasite Interactions ,03 medical and health sciences ,Focus Issue on Parasitic Plants ,Orobanchaceae ,Gene Expression Regulation, Plant ,Haustorium ,Gene expression ,Genetics ,medicine ,Subtilisins ,Gene ,030304 developmental biology ,0303 health sciences ,Host (biology) ,Cell biology ,medicine.anatomical_structure ,010606 plant biology & botany - Abstract
Parasitic plants that infect crops are devastating to agriculture throughout the world. These parasites develop a unique inducible organ called the haustorium that connects the vascular systems of the parasite and host to establish a flow of water and nutrients. Upon contact with the host, the haustorial epidermal cells at the interface with the host differentiate into specific cells called intrusive cells that grow endophytically toward the host vasculature. Following this, some of the intrusive cells re-differentiate to form a xylem bridge (XB) that connects the vasculatures of the parasite and host. Despite the prominent role of intrusive cells in host infection, the molecular mechanisms mediating parasitism in the intrusive cells remain poorly understood. In this study, we investigated differential gene expression in the intrusive cells of the facultative parasite Phtheirospermum japonicum in the family Orobanchaceae by RNA-sequencing of laser-microdissected haustoria. We then used promoter analyses to identify genes that are specifically induced in intrusive cells, and promoter fusions with genes encoding fluorescent proteins to develop intrusive cell-specific markers. Four of the identified intrusive cell-specific genes encode subtilisin-like serine proteases (SBTs), whose biological functions in parasitic plants are unknown. Expression of SBT inhibitors in intrusive cells inhibited both intrusive cell and XB development and reduced auxin response levels adjacent to the area of XB development. Therefore, we propose that subtilase activity plays an important role in haustorium development in P. japonicum.
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- 2020
11. Physcomitrella STEMIN transcription factor induces stem cell formation with epigenetic reprogramming
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Minoru Kubo, Yukiko Kabeya, Shuji Shigenobu, Tetsuya Kurata, Tomoaki Nishiyama, Mio Morishita, Yoshikatsu Sato, Yosuke Tamada, Mitsuyasu Hasebe, Yohei Higuchi, Shunsuke Ichikawa, Takaaki Ishikawa, Masaki Ishikawa, and Yuji Hiwatashi
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0106 biological sciences ,0301 basic medicine ,Physcomitrella ,Cellular differentiation ,Plant Science ,Physcomitrella patens ,Methylation ,01 natural sciences ,Epigenesis, Genetic ,Histones ,03 medical and health sciences ,Histone H3 ,Gene Expression Regulation, Plant ,Epigenetics ,Plant Proteins ,biology ,Stem Cells ,food and beverages ,Cellular Reprogramming ,biology.organism_classification ,Bryopsida ,Chromatin ,Cell biology ,Plant Leaves ,030104 developmental biology ,Stem cell ,Reprogramming ,Transcription Factors ,010606 plant biology & botany - Abstract
Epigenetic modifications, including histone modifications, stabilize cell-specific gene expression programmes to maintain cell identities in both metazoans and land plants1-3. Notwithstanding the existence of these stable cell states, in land plants, stem cells are formed from differentiated cells during post-embryonic development and regeneration4-6, indicating that land plants have an intrinsic ability to regulate epigenetic memory to initiate a new gene regulatory network. However, it is less well understood how epigenetic modifications are locally regulated to influence the specific genes necessary for cellular changes without affecting other genes in a genome. In this study, we found that ectopic induction of the AP2/ERF transcription factor STEMIN1 in leaf cells of the moss Physcomitrella patens decreases a repressive chromatin mark, histone H3 lysine 27 trimethylation (H3K27me3), on its direct target genes before cell division, resulting in the conversion of leaf cells to chloronema apical stem cells. STEMIN1 and its homologues positively regulate the formation of secondary chloronema apical stem cells from chloronema cells during development. Our results suggest that STEMIN1 functions within an intrinsic mechanism underlying local H3K27me3 reprogramming to initiate stem cell formation.
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- 2019
12. Parallel evolution of UbiA superfamily proteins into aromatic
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Ryosuke, Munakata, Alexandre, Olry, Tomoya, Takemura, Kanade, Tatsumi, Takuji, Ichino, Cloé, Villard, Joji, Kageyama, Tetsuya, Kurata, Masaru, Nakayasu, Florence, Jacob, Takao, Koeduka, Hirobumi, Yamamoto, Eiko, Moriyoshi, Tetsuya, Matsukawa, Jérémy, Grosjean, Célia, Krieger, Akifumi, Sugiyama, Masaharu, Mizutani, Frédéric, Bourgaud, Alain, Hehn, and Kazufumi, Yazaki
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Evolution, Molecular ,Prenylation ,Furocoumarins ,food and beverages ,Biological Sciences ,Phylogeny ,Angelica ,Citrus paradisi ,Plant Proteins - Abstract
Plants produce ∼300 aromatic compounds enzymatically linked to prenyl side chains via C–O bonds. These O-prenylated aromatic compounds have been found in taxonomically distant plant taxa, with some of them being beneficial or detrimental to human health. Although their O-prenyl moieties often play crucial roles in the biological activities of these compounds, no plant gene encoding an aromatic O-prenyltransferase (O-PT) has been isolated to date. This study describes the isolation of an aromatic O-PT gene, CpPT1, belonging to the UbiA superfamily, from grapefruit (Citrus × paradisi, Rutaceae). This gene was shown responsible for the biosynthesis of O-prenylated coumarin derivatives that alter drug pharmacokinetics in the human body. Another coumarin O-PT gene encoding a protein of the same family was identified in Angelica keiskei, an apiaceous medicinal plant containing pharmaceutically active O-prenylated coumarins. Phylogenetic analysis of these O-PTs suggested that aromatic O-prenylation activity evolved independently from the same ancestral gene in these distant plant taxa. These findings shed light on understanding the evolution of plant secondary (specialized) metabolites via the UbiA superfamily.
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- 2021
13. Parallel evolution of UbiA superfamily proteins into aromatic O -prenyltransferases in plants
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Eiko Moriyoshi, Kanade Tatsumi, Tetsuya Kurata, Kazufumi Yazaki, Frédéric Bourgaud, Masaharu Mizutani, Célia Krieger, Hirobumi Yamamoto, Takao Koeduka, Florence Jacob, Akifumi Sugiyama, Ryosuke Munakata, Joji Kageyama, Masaru Nakayasu, Takuji Ichino, Cloé Villard, Jérémy Grosjean, Alexandre Olry, Tetsuya Matsukawa, Tomoya Takemura, Alain Hehn, Research Institute for Sustainable Humanosphere (RISH), Kyoto University [Kyoto], Laboratoire Agronomie et Environnement (LAE), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Japan Science and Technology Agency (JST), PalmElit, Yamaguchi University [Yamaguchi], Toyo University, Kindai University, Graduate School of Bioagricultural Sciences, Nagoya University, Kobe University, Plant Advanced Technologies S.A., IMPACT Biomolécules, and ANR-15-IDEX-0004,LUE,Isite LUE(2015)
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0106 biological sciences ,0303 health sciences ,Multidisciplinary ,biology ,Phylogenetic tree ,Chemistry ,[SDV]Life Sciences [q-bio] ,food and beverages ,SUPERFAMILY ,biology.organism_classification ,Coumarin ,01 natural sciences ,03 medical and health sciences ,chemistry.chemical_compound ,Rutaceae ,Biosynthesis ,Prenylation ,Biochemistry ,Parallel evolution ,Gene ,030304 developmental biology ,010606 plant biology & botany - Abstract
Significance Plants produce approximately 300 O -prenylated aromatics, with their O -prenyl moieties often being crucial to their bioactivities. This study identified a gene from grapefruit encoding an aromatic O -prenyltransferase ( O- PT) belonging to the UbiA superfamily. The O -PT was shown responsible for the biosynthesis of pharmaceutically active O -prenylated coumarins that cause grapefruit–drug interactions, an adverse effect disturbing the pharmacokinetics of more than 85 medications. Another UbiA O -PT for coumarins was isolated from Angelica keiskei , an apiaceous medicinal plant. Phylogenetic analysis of the rutaceous and apiaceous O -PTs suggested that aromatic O -prenylation activity emerged in parallel in these distant plant taxa. The molecular evolution of aromatic O -PTs from plant UbiA proteins may aid citrus breeding and a synthetic biology approach to bioactive O -prenylated coumarins.
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- 2021
14. Parallel evolution of UbiA superfamily proteins into aromatic O-prenyltransferases in plants
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Tetsuya Kurata, Takuji Ichino, Jérémy Grosjean, Kanade Tatsumi, Alexandre Olry, Akifumi Sugiyama, Masaharu Mizutani, Alain Hehn, Hirobumi Yamamoto, Kazufumi Yazaki, Célia Krieger, Eiko Moriyoshi, Ryosuke Munakata, Joji Kageyama, Frédéric Bourgaud, Masaru Nakayasu, Tomoya Takemura, Tetsuya Matsukawa, Takao Koeduka, Florence Jacob, and Cloé Villard
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chemistry.chemical_compound ,Rutaceae ,Biosynthesis ,chemistry ,Protein family ,Phylogenetic tree ,biology ,Prenylation ,Biochemistry ,Parallel evolution ,Coumarin ,biology.organism_classification ,Gene - Abstract
Plants produce approximately 300 aromatic molecules enzymatically linked to prenyl side chains via C-O bonds. These O-prenylated aromatics have been found in taxonomically distant plant taxa as compounds beneficial or detrimental to human health, with O-prenyl moieties often playing crucial roles in their biological activities. To date, however, no plant gene encoding an aromatic O-prenyltransferase (O-PT) has been described. This study describes the isolation of an aromatic O-PT gene, CpPT1, belonging to the UbiA superfamily, from grapefruit (Citrus × paradisi, Rutaceae). This gene is responsible for the biosynthesis of O-prenylated coumarin derivatives that alter drug pharmacokinetics in the human body. Another coumarin O-PT gene of the same protein family was identified in Angelica keiskei, an apiaceous medicinal plant containing pharmaceutically active O-prenylated coumarins. Phylogenetic analysis of these O-PTs suggested that aromatic O-prenylation activity evolved independently from the same ancestral gene in these distant plant taxa. These findings shed light on understanding the evolution of plant secondary metabolites via the UbiA superfamily.
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- 2020
15. Subtilase activity in the intrusive cells mediates haustorium maturation in parasitic plants
- Author
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Juliane K. Ishida, Ryosuke Sano, Andreas Schaller, Takanori Wakatake, Satoko Yoshida, Tetsuya Kurata, Ken Shirasu, Thomas Spallek, Yasunori Ichihashi, Satoshi Ogawa, and Taku Demura
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Facultative parasite ,biology ,Orobanchaceae ,Parasitic plant ,Host (biology) ,Haustorium ,fungi ,food and beverages ,Xylem ,biology.organism_classification ,Gene ,Subtilase ,Cell biology - Abstract
Parasitic plants that infect crops are devastating to agriculture throughout the world. They develop a unique inducible organ called the haustorium, which connects the vascular systems of the parasite and host to establish a flow of water and nutrients. Upon contact with the host, the haustorial epidermal cells at the interface with the host differentiate into specific cells called intrusive cells that grow endophytically towards the host vasculature. Then, some of the intrusive cells re-differentiate to form a xylem bridge that connects the vasculatures of the parasite and host. Despite the prominent role of intrusive cells in host infection, the molecular mechanisms mediating parasitism in the intrusive cells are unknown. In this study, we investigated differential gene expression in the intrusive cells of the facultative parasitePhtheirospermum japonicumin the family Orobanchaceae by RNA-Sequencing of laser-microdissected haustoria. We then used promoter analyses to identify genes that are specifically induced in intrusive cells, and used promoter fusions with genes encoding fluorescent proteins to develop intrusive cell-specific markers. Four of the intrusive cell-specific genes encode subtilisin-like serine proteases (SBTs), whose biological functions in parasitic plants are unknown. Expression of an SBT inhibitor in the intrusive cells inhibited their development, inhibited the development of the xylem bridge, and reduced auxin response levels near the site where the xylem bridge normally develops. Therefore, we propose that subtilase activity plays an important role in haustorium development in this parasitic plant.One sentence summaryTissue-specific analysis showed that the subtilases specifically expressed in intrusive cells regulate auxin-mediated host-parasite connections in the parasitic plantPhtheirospermum japonicum.
- Published
- 2020
16. A Missense Mutation in the NSF Gene Causes Abnormal Golgi Morphology in Arabidopsis thaliana
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Tomoaki Sakamoto, Akihiko Nakano, Chieko Saito, Tomohiro Uemura, Sayuri Tanabashi, Keiko Shoda, and Tetsuya Kurata
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0106 biological sciences ,0301 basic medicine ,Glycosylation ,biology ,Physiology ,Mutant ,Wild type ,Cell Biology ,General Medicine ,Golgi apparatus ,biology.organism_classification ,01 natural sciences ,Phenotype ,Cell biology ,03 medical and health sciences ,chemistry.chemical_compound ,symbols.namesake ,030104 developmental biology ,chemistry ,Cytoplasm ,symbols ,Arabidopsis thaliana ,Molecular Biology ,Gene ,010606 plant biology & botany - Abstract
The Golgi apparatus is a key station of glycosylation and membrane traffic. It consists of stacked cisternae in most eukaryotes. However, the mechanisms how the Golgi stacks are formed and maintained are still obscure. The model plant Arabidopsis thaliana provides a nice system to observe Golgi structures by light microscopy, because the Golgi in A. thaliana is in the form of mini-stacks that are distributed throughout the cytoplasm. To obtain a clue to understand the molecular basis of Golgi morphology, we took a forward-genetic approach to isolate A. thaliana mutants that show abnormal structures of the Golgi under a confocal microscope. In the present report, we describe characterization of one of such mutants, named #46-3. The #46-3 mutant showed pleiotropic Golgi phenotypes. The Golgi size was in majority smaller than the wild type, but varied from very small ones, sometimes without clear association of cis and trans cisternae, to abnormally large ones under a confocal microscope. At the ultrastructual level by electron microscopy, queer-shaped large Golgi stacks were occasionally observed. By positional mapping, genome sequencing, and complementation and allelism tests, we linked the mutant phenotype to the missense mutation D374N in the NSF gene, encoding the N-ethylmaleimide-sensitive factor (NSF), a key component of membrane fusion. This residue is near the ATP-binding site of NSF, which is very well conserved in eukaryotes, suggesting that the biochemical function of NSF is important for maintaining the normal morphology of the Golgi.Key words: Golgi morphology, N-ethylmaleimide-sensitive factor (NSF), Arabidopsis thaliana.
- Published
- 2018
17. Transcription Factors VND1-VND3 Contribute to Cotyledon Xylem Vessel Formation
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Tetsuya Kurata, Hitoshi Endo, Ryosuke Sano, Masatoshi Yamaguchi, Tian Tian Tan, Taku Demura, and Misato Ohtani
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0301 basic medicine ,chemistry.chemical_classification ,Physiology ,Cellular differentiation ,fungi ,Lateral root ,food and beverages ,Xylem ,Plant Science ,Biology ,biology.organism_classification ,Cell biology ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,chemistry ,Auxin ,Arabidopsis ,Cytokinin ,Botany ,Genetics ,Vessel element ,Transcription factor - Abstract
Arabidopsis (Arabidopsis thaliana) VASCULAR-RELATED NAC-DOMAIN1 (VND1) to VND7 encode a group of NAC domain transcription factors that function as master regulators of xylem vessel element differentiation. These transcription factors activate the transcription of genes required for secondary cell wall formation and programmed cell death, key events in xylem vessel element differentiation. Because constitutive overexpression of VND6 and VND7 induces ectopic xylem vessel element differentiation, functional studies of VND proteins have largely focused on these two proteins. Here, we report the roles of VND1, VND2, and VND3 in xylem vessel formation in cotyledons. Using our newly established in vitro system in which excised Arabidopsis cotyledons are stimulated to undergo xylem cell differentiation by cytokinin, auxin, and brassinosteroid treatment, we found that ectopic xylem vessel element differentiation required VND1, VND2, and VND3 but not VND6 or VND7. The importance of VND1, VND2, and VND3 also was indicated in vivo; in the vnd1 vnd2 vnd3 seedlings, xylem vessel element differentiation of secondary veins in cotyledons was inhibited under dark conditions. Furthermore, the light responsiveness of VND gene expression was disturbed in the vnd1 vnd2 vnd3 mutant, and vnd1 vnd2 vnd3 failed to recover lateral root development in response to the change of light conditions. These findings suggest that VND1 to VND3 have specific molecular functions, possibly linking light conditions to xylem vessel formation, during seedling development.
- Published
- 2017
18. Localization of ENHANCER OF TRY AND CPC1 protein in Arabidopsis root epidermis
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Tetsuya Kurata, Takuji Wada, and Rumi Tominaga-Wada
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0301 basic medicine ,Physiology ,Cellular differentiation ,Arabidopsis ,macromolecular substances ,Plant Science ,Plant Roots ,Plant Epidermis ,Green fluorescent protein ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Arabidopsis thaliana ,MYB ,Enhancer ,integumentary system ,biology ,Epidermis (botany) ,Arabidopsis Proteins ,fungi ,technology, industry, and agriculture ,Plants, Genetically Modified ,biology.organism_classification ,Molecular biology ,Hairless ,DNA-Binding Proteins ,030104 developmental biology ,Agronomy and Crop Science - Abstract
CAPRICE (CPC) is a R3-type MYB transcription factor, which induces root-hair cell differentiation in Arabidopsis thaliana. The CPC homologous gene ENHANCER TRY AND CPC1 (ETC1) has a similar function to CPC, and acts in concert with CPC. The CPC protein moves between root epidermal cells, from hairless cells to the neighboring cells, and promotes root-hair differentiation. Therefore, ETC1 is predicted to have movement ability similar to that of CPC. In this study, we generated ETC1:ETC1:GFP and CPC:ETC1:GFP transgenic plants to clarify whether ETC1 exhibits cell-to-cell movement. Transgenic plants showed many-root-haired and trichome-less phenotypes, similar to those observed in CPC:CPC:GFP plants, suggesting a similar function of ETC1 and CPC. However, the ETC1:GFP fusion protein located exclusively to the hairless cells in both ETC1:ETC1:GFP and CPC:ETC1:GFP transgenic plants. These results indicate that, unexpectedly, the ETC1 protein cannot move in the root epidermis from hairless cells to the neighboring cells.
- Published
- 2017
19. Chloroplastic <scp>ATP</scp> synthase builds up a proton motive force preventing production of reactive oxygen species in photosystem I
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Tetsuya Kurata, Tatsuaki Goh, Yoichiro Fukao, Masaki Hashiguchi, Ryosuke Sano, Katsumi Amako, Kimitsune Ishizaki, Hidehiro Fukaki, Taku Demura, Daisuke Takagi, Chikahiro Miyake, and Shinichiro Sawa
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0106 biological sciences ,0301 basic medicine ,Photosynthetic reaction centre ,Photoinhibition ,Light ,Arabidopsis ,Plant Science ,Photosystem I ,Thylakoids ,01 natural sciences ,Electron Transport ,03 medical and health sciences ,Genetics ,Chloroplast Proton-Translocating ATPases ,Photosynthesis ,Photosystem I Protein Complex ,ATP synthase ,biology ,Arabidopsis Proteins ,Chemiosmosis ,Proton-Motive Force ,food and beverages ,Cell Biology ,Electron transport chain ,Chloroplast ,030104 developmental biology ,Biochemistry ,Thylakoid ,Mutation ,biology.protein ,Reactive Oxygen Species ,010606 plant biology & botany - Abstract
Over-reduction of the photosynthetic electron transport (PET) chain should be avoided, because the accumulation of reducing electron carriers produces reactive oxygen species (ROS) within photosystem I (PSI) in thylakoid membranes and causes oxidative damage to chloroplasts. To prevent production of ROS in thylakoid membranes the H+ gradient (ΔpH) needs to be built up across the thylakoid membranes to suppress the over-reduction state of the PET chain. In this study, we aimed to identify the critical component that stimulates ΔpH formation under illumination in higher plants. To do this, we screened ethyl methane sulfonate (EMS)-treated Arabidopsis thaliana, in which the formation of ΔpH is impaired and the PET chain caused over-reduction under illumination. Subsequently, we isolated an allelic mutant that carries a missense mutation in the γ-subunit of chloroplastic CF0 CF1 -ATP synthase, named hope2. We found that hope2 suppressed the formation of ΔpH during photosynthesis because of the high H+ efflux activity from the lumenal to stromal side of the thylakoid membranes via CF0 CF1 -ATP synthase. Furthermore, PSI was in a more reduced state in hope2 than in wild-type (WT) plants, and hope2 was more vulnerable to PSI photoinhibition than WT under illumination. These results suggested that chloroplastic CF0 CF1 -ATP synthase adjusts the redox state of the PET chain, especially for PSI, by modulating H+ efflux activity across the thylakoid membranes. Our findings suggest the importance of the buildup of ΔpH depending on CF0 CF1 -ATP synthase to adjust the redox state of the reaction center chlorophyll P700 in PSI and to suppress the production of ROS in PSI during photosynthesis.
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- 2017
20. Identification of Arabidopsis genic and non‐genic promoters by paired‐end sequencing of <scp>TSS</scp> tags
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Hiroyuki Koyama, Atsushi Kurotani, Yoshiharu Y. Yamamoto, Tetsuya Kurata, Yutaka Suzuki, Tetsuya Sakurai, Tomoaki Sakamoto, Kazutaka Kusunoki, and Mutsutomo Tokizawa
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0301 basic medicine ,Genetics ,Arabidopsis Proteins ,Arabidopsis ,Promoter ,Cell Biology ,Plant Science ,Biology ,biology.organism_classification ,Deep sequencing ,03 medical and health sciences ,030104 developmental biology ,Gene Expression Regulation, Plant ,Transcription (biology) ,Transcriptional regulation ,Transcription Initiation Site ,Promoter Regions, Genetic ,Gene ,Paired-end tag ,GC-content - Abstract
Information about transcription start sites (TSSs) provides baseline data for the analysis of promoter architecture. In this paper we used paired- and single-end deep sequencing to analyze Arabidopsis TSS tags from several libraries prepared from roots, shoots, flowers and etiolated seedlings. The clustering of approximately 33 million mapped TSS tags led to the identification of 324 461 promoters that covered 79.7% (21 672/27 206) of protein-coding genes in the Arabidopsis genome. In addition we identified intragenic, antisense and orphan promoters that were not associated with any gene models. Of these, intragenic promoters exhibited unique characteristics regarding dinucleotide sequences at TSSs and core promoter element composition, suggesting that these promoters use different mechanisms of transcriptional initiation. An analysis of base composition with regard to promoter position revealed a low GC content throughout the promoter region and several local strand biases that were evident for TATA-type promoters, but not for Coreless-type promoters. Most observed strand biases coincided with strand biases of single nucleotide polymorphism rate. Our analysis also revealed that transcription of a gene is supported by an average of 2.7 genic promoters, among which one specific promoter, designated as a top promoter, substantially determines the expression level of the gene.
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- 2017
21. Genetic Enhancer Analysis Reveals that FLORAL ORGAN NUMBER2 and OsMADS3 Co-operatively Regulate Maintenance and Determinacy of the Flower Meristem in Rice
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Tetsuya Kurata, Hiro-Yuki Hirano, Tomoaki Sakamoto, Wakana Tanaka, and Yukiko Yasui
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0106 biological sciences ,0301 basic medicine ,Gynoecium ,Physiology ,Meristem ,Mutant ,Stamen ,MADS Domain Proteins ,Flowers ,Plant Science ,Biology ,medicine.disease_cause ,01 natural sciences ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Arabidopsis ,medicine ,Enhancer ,Plant Proteins ,Genetics ,Mutation ,fungi ,food and beverages ,Oryza ,Cell Biology ,General Medicine ,Meristem maintenance ,Plants, Genetically Modified ,biology.organism_classification ,030104 developmental biology ,010606 plant biology & botany - Abstract
Meristems such as the shoot apical meristem and flower meristem (FM) act as a reservoir of stem cells, which reproduce themselves and supply daughter cells for the differentiation of lateral organs. In Oryza sativa (rice), the FLORAL ORGAN NUMBER2 (FON2) gene, which is similar to Arabidopsis CLAVATA3, is involved in meristem maintenance. In fon2 mutants, the numbers of floral organs are increased due to an enlargement of the FM. To identify new factors regulating meristem maintenance in rice, we performed a genetic screening of mutants that enhanced the fon2 mutation, and found a mutant line (2B-424) in which pistil number was dramatically increased. By using a map-based approach and next-generation sequencing, we found that the line 2B-424 had a complete loss-of-function mutation (a large deletion) in OsMADS3, a class C MADS-box gene that is known to be involved in stamen specification. Disruption of OsMADS3 in the fon2 mutant by CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9) technology caused a flower phenotype similar to that of 2B-424, confirming that the gene responsible for enhancement of fon2 was OsMADS3. Morphological analysis showed that the fon2 and osmads3 mutations synergistically affected pistil development and FM determinacy. We also found that whorl 3 was duplicated in mature flowers and the FM was enlarged at an early developmental stage in severe osmads3 single mutants. These findings suggest that OsMADS3 is involved not only in FM determinacy in late flower development but also in FM activity in early flower development.
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- 2017
22. WIND1 Promotes Shoot Regeneration through Transcriptional Activation of ENHANCER OF SHOOT REGENERATION1 in Arabidopsis
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Tetsuya Kurata, Kengo Morohashi, Masaru Nakata, Mariko Ohnuma, Shinichiro Komaki, Momoko Ikeuchi, Bart Rymen, Hirofumi Harashima, Erich Grotewold, Keiko Sugimoto, Masaru Ohme-Takagi, and Akira Iwase
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0301 basic medicine ,Genetics ,Regulation of gene expression ,biology ,Callus formation ,Regeneration (biology) ,fungi ,food and beverages ,Cell Biology ,Plant Science ,biology.organism_classification ,Cell biology ,body regions ,03 medical and health sciences ,030104 developmental biology ,Arabidopsis ,Shoot ,Arabidopsis thaliana ,Enhancer ,Transcription factor - Abstract
Many plant species display remarkable developmental plasticity and regenerate new organs after injury. Local signals produced by wounding are thought to trigger organ regeneration but molecular mechanisms underlying this control remain largely unknown. We previously identified an AP2/ERF transcription factor WOUND INDUCED DEDIFFERENTIATION1 (WIND1) as a central regulator of wound-induced cellular reprogramming in plants. In this study, we demonstrate that WIND1 promotes callus formation and shoot regeneration by upregulating the expression of the ENHANCER OF SHOOT REGENERATION1 (ESR1) gene, which encodes another AP2/ERF transcription factor in Arabidopsis thaliana The esr1 mutants are defective in callus formation and shoot regeneration; conversely, its overexpression promotes both of these processes, indicating that ESR1 functions as a critical driver of cellular reprogramming. Our data show that WIND1 directly binds the vascular system-specific and wound-responsive cis-element-like motifs within the ESR1 promoter and activates its expression. The expression of ESR1 is strongly reduced in WIND1-SRDX dominant repressors, and ectopic overexpression of ESR1 bypasses defects in callus formation and shoot regeneration in WIND1-SRDX plants, supporting the notion that ESR1 acts downstream of WIND1. Together, our findings uncover a key molecular pathway that links wound signaling to shoot regeneration in plants.
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- 2016
23. TheSAC51Family Plays a Central Role in Thermospermine Responses in Arabidopsis
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Taku Takahashi, Tomoaki Sakamoto, Tetsuya Kurata, Mai Yamamoto, Hiroko Fukushima, Qingqing Cai, Nami Ishii, and Hiroyasu Motose
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0301 basic medicine ,Translation ,Physiology ,Mutant ,Arabidopsis ,Plant Science ,medicine.disease_cause ,Models, Biological ,Open Reading Frames ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Genes, Reporter ,Xylem ,Upstream open reading frame ,Basic Helix-Loop-Helix Transcription Factors ,medicine ,Arabidopsis thaliana ,Amino Acid Sequence ,Gene ,Genetics ,Mutation ,biology ,Arabidopsis Proteins ,food and beverages ,Cell Biology ,General Medicine ,biology.organism_classification ,Null allele ,Phenotype ,Thermospermine ,Mutagenesis, Insertional ,Xylem differentiation ,030104 developmental biology ,Seedlings ,Spermine ,Sequence Alignment ,uORF - Abstract
The acaulis5 (acl5) mutant of Arabidopsis thaliana is defective in the biosynthesis of thermospermine and shows a dwarf phenotype associated with excess xylem differentiation. SAC51 was identified from a dominant suppressor of acl5, sac51-d, and encodes a basic helix-loop-helix protein. The sac51-d mutant has a premature termination codon in an upstream open reading frame (uORF) that is conserved among all four members of the SAC51 family, SAC51 and SACL1-SACL3 This suggests that thermospermine cancels the inhibitory effect of the uORF in main ORF translation. Another suppressor, sac57-d, has a mutation in the conserved uORF of SACL3 To define further the function of the SAC51 family in the thermospermine response, we analyzed T-DNA insertion mutants of each gene. Although sacl1-1 may not be a null allele, the quadruple mutant showed a semi-dwarf phenotype but with an increased level of thermospermine and decreased sensitivity to exogenous thermospermine that normally represses xylem differentiation. The sac51-1 sacl3-1 double mutant was also insensitive to thermospermine. These results suggest that SAC51 and SACL3 play a key role in thermospermine-dependent negative control of thermospermine biosynthesis and xylem differentiation. Using 5' leader-GUS (β-glucuronidase) fusion constructs, however, we detected a significant enhancement of the GUS activity by thermospermine only in SAC51 and SACL1 constructs. Furthermore, while acl5-1 sac51-1 showed the acl5 dwarf phenotype, acl5-1 sacl3-1 exhibited an extremely tiny-plant phenotype. These results suggest a complex regulatory network for the thermospermine response in which SAC51 and SACL3 function in parallel pathways.
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- 2016
24. Transcriptional Framework of Male Gametogenesis in the LiverwortMarchantia polymorphaL
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Takayuki Kohchi, Tetsuya Kurata, Katsuyuki T. Yamato, Masaki Niwa, Katsushi Yamaguchi, Shuji Shigenobu, Motomu Endo, Ryuichi Nishihama, Hitoshi Sawada, Tomoaki Sakamoto, Lixy Yamada, Kimitsune Ishizaki, Asuka Higo, Takashi Araki, and Makoto Shirakawa
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0301 basic medicine ,Egg cell ,Transcription, Genetic ,Physiology ,Plant Science ,Biology ,Genes, Plant ,Real-Time Polymerase Chain Reaction ,Chromosomes, Plant ,Histones ,Transcriptome ,Open Reading Frames ,03 medical and health sciences ,Marchantia polymorpha ,Gene Expression Regulation, Plant ,Marchantia ,medicine ,RNA, Messenger ,Gene ,Gametogenesis, Plant ,Gene Expression Profiling ,Reproducibility of Results ,food and beverages ,Cell Biology ,General Medicine ,biology.organism_classification ,Sexual reproduction ,Cell biology ,030104 developmental biology ,medicine.anatomical_structure ,Antheridium ,Gamete ,Pollen tube ,Signal Transduction ,Transcription Factors - Abstract
In land plants, there are two types of male gametes: one is a non-motile sperm cell which is delivered to the egg cell by a pollen tube, and the other is a motile sperm cell with flagella. The molecular mechanism underlying the sexual reproduction with the egg and pollen-delivered sperm cell is well understood from studies using model plants such as Arabidopsis and rice. On the other hand, the sexual reproduction with motile sperm has remained poorly characterized, due to the lack of suitable models. Marchantia polymorpha L. is a model basal land plant with sexual reproduction involving an egg cell and bi-flagellated motile sperm. To understand the differentiation process of plant motile sperm, we analyzed the gene expression profile of developing antheridia of M. polymorpha. We performed RNA-sequencing experiments and compared transcript profiles of the male sexual organ (antheridiophore and antheridium contained therein), female sexual organ (archegoniophore) and a vegetative organ (thallus). Transcriptome analysis showed that the antheridium expresses nearly half of the protein-coding genes predicted in the genome, but it also has unique features. The antheridium transcriptome shares some common features with male gamete transcriptomes of angiosperms and animals, and homologs of genes involved in male gamete formation and function in angiosperms and animals were identified. In addition, we showed that some of them had distinct expression patterns in the spermatogenous tissue of developing antheridia. This study provides a transcriptional framework on which to study the molecular mechanism of plant motile sperm development in M. polymorpha as a model.
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- 2016
25. BELL1-like homeobox genes regulate inflorescence architecture and meristem maintenance in rice
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Takuyuki Ikeda, Toshihiko Shiroishi, Masayuki Murai, Tetsuya Kurata, Chie Suzuki, Taiyo Toriba, Hiro-Yuki Hirano, Hiroaki Matsusaka, Toshihiro Kumamaru, Tomoaki Sakamoto, Katsutoshi Tsuda, Akiteru Maeno, and Wakana Tanaka
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0106 biological sciences ,0301 basic medicine ,Mutant ,Meristem ,Plant Science ,01 natural sciences ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Arabidopsis ,Genetics ,Inflorescence ,Plant Proteins ,Internode patterning ,biology ,fungi ,food and beverages ,Oryza ,Cell Biology ,Meristem maintenance ,Phyllotaxis ,biology.organism_classification ,Cell biology ,030104 developmental biology ,Homeobox ,010606 plant biology & botany - Abstract
Inflorescence architecture is diverse in angiosperms, and is mainly determined by the arrangement of the branches and flowers, known as phyllotaxy. In rice (Oryza sativa), the main inflorescence axis, called the rachis, generates primary branches in a spiral phyllotaxy, and flowers (spikelets) are formed on these branches. Here, we have studied a classical mutant, named verticillate rachis (ri), which produces branches in a partially whorled phyllotaxy. Gene isolation revealed that RI encodes a BELL1-type homeodomain transcription factor, similar to Arabidopsis PENNYWISE/BELLRINGER/REPLUMLESS, and is expressed in the specific regions within the inflorescence and branch meristems where their descendant meristems would soon initiate. Genetic combination of an ri homozygote and a mutant allele of RI-LIKE1 (RIL1) (designated ri ril1/+ plant), a close paralog of RI, enhanced the ri inflorescence phenotype, including the abnormalities in branch phyllotaxy and rachis internode patterning. During early inflorescence development, the timing and arrangement of primary branch meristem (pBM) initiation were disturbed in both ri and ri ril1/+ plants. These findings suggest that RI and RIL1 were involved in regulating the phyllotactic pattern of the pBMs to form normal inflorescences. In addition, both RI and RIL1 seem to be involved in meristem maintenance, because the ri ril1 double-mutant failed to establish or maintain the shoot apical meristem during embryogenesis.
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- 2018
26. DNA methylation is reconfigured at the onset of reproduction in rice shoot apical meristem
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Yoko Higashi, Yoichiro Fukao, Shojiro Tamaki, Takashi Ito, Tomoaki Sakamoto, Fumihito Miura, Ko Shimamoto, Tetsuya Kurata, Asuka Higo, Tetsuji Kakutani, Toshinori Kinoshita, Hiroyuki Tsuji, Tasuku Ito, Rie Terada, Noriko Saihara, Satoru Moritoh, Megumi Yamada, Yoshiaki Tarutani, and Masayuki Fujiwara
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0301 basic medicine ,Epigenomics ,Science ,Population ,Meristem ,General Physics and Astronomy ,02 engineering and technology ,Flowers ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,Plant reproduction ,Gene Expression Regulation, Plant ,Developmental biology ,medicine ,Epigenetics ,Inflorescence ,education ,lcsh:Science ,Plant Proteins ,education.field_of_study ,Multidisciplinary ,fungi ,food and beverages ,Oryza ,General Chemistry ,Methylation ,DNA Methylation ,021001 nanoscience & nanotechnology ,Cell biology ,Plant Leaves ,030104 developmental biology ,medicine.anatomical_structure ,DNA methylation ,DNA Transposable Elements ,lcsh:Q ,0210 nano-technology ,Germ cell ,Plant Shoots - Abstract
DNA methylation is an epigenetic modification that specifies the basic state of pluripotent stem cells and regulates the developmental transition from stem cells to various cell types. In flowering plants, the shoot apical meristem (SAM) contains a pluripotent stem cell population which generates the aerial part of plants including the germ cells. Under appropriate conditions, the SAM undergoes a developmental transition from a leaf-forming vegetative SAM to an inflorescence- and flower-forming reproductive SAM. While SAM characteristics are largely altered in this transition, the complete picture of DNA methylation remains elusive. Here, by analyzing whole-genome DNA methylation of isolated rice SAMs in the vegetative and reproductive stages, we show that methylation at CHH sites is kept high, particularly at transposable elements (TEs), in the vegetative SAM relative to the differentiated leaf, and increases in the reproductive SAM via the RNA-dependent DNA methylation pathway. We also show that half of the TEs that were highly methylated in gametes had already undergone CHH hypermethylation in the SAM. Our results indicate that changes in DNA methylation begin in the SAM long before germ cell differentiation to protect the genome from harmful TEs., The shoot apical meristem of flowering plants transitions from forming leaves to floral organs. Here Higo et al. show that DNA methylation of many transposons that are hypermethylated in gametes is established in the SAM before flowering, suggesting it protects against harmful transposition long before germ cell differentiation.
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- 2018
27. Gametangia Development in the Moss Physcomitrella Patens
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Rumiko Kofuji, Takeshi Yoshimura, Haruko Inoue, Keiko Sakakibara, Yuji Hiwatashi, Tetsuya Kurata, Tsuyoshi Aoyama, Kunihiko Ueda, and Mitsuyasu Hasebe
- Published
- 2018
28. Comparative transcriptomics with self-organizing map reveals cryptic photosynthetic differences between two accessions of North American Lake cress
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Tetsuya Kurata, Yuki Okegawa, Yasunori Ichihashi, Ken Motohashi, Hokuto Nakayama, Neelima Sinha, Ihsan A. Al-Shehbaz, Manabu Fujie, Seisuke Kimura, Kaori Kaminoyama, and Tomoaki Sakamoto
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0106 biological sciences ,0301 basic medicine ,Physiological ,lcsh:Medicine ,Sequence assembly ,Growing season ,01 natural sciences ,Article ,Transcriptome ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Phylogenetics ,Botany ,Genetics ,Adaptation ,Photosynthesis ,lcsh:Science ,Phylogeny ,Local adaptation ,Multidisciplinary ,biology ,lcsh:R ,Temperature ,Brassicaceae ,Plant ,15. Life on land ,biology.organism_classification ,Adaptation, Physiological ,United States ,Plant Leaves ,Rorippa ,030104 developmental biology ,Gene Expression Regulation ,lcsh:Q ,010606 plant biology & botany - Abstract
Because natural variation in wild species is likely the result of local adaptation, it provides a valuable resource for understanding plant-environmental interactions. Rorippa aquatica (Brassicaceae) is a semi-aquatic North American plant with morphological differences between several accessions, but little information available on any physiological differences. Here, we surveyed the transcriptomes of two R. aquatica accessions and identified cryptic physiological differences between them. We first reconstructed a Rorippa phylogeny to confirm relationships between the accessions. We performed large-scale RNA-seq and de novo assembly; the resulting 87,754 unigenes were then annotated via comparisons to different databases. Between-accession physiological variation was identified with transcriptomes from both accessions. Transcriptome data were analyzed with principal component analysis and self-organizing map. Results of analyses suggested that photosynthetic capability differs between the accessions. Indeed, physiological experiments revealed between-accession variation in electron transport rate and the redox state of the plastoquinone pool. These results indicated that one accession may have adapted to differences in temperature or length of the growing season.
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- 2018
29. Identifying the target genes of SUPPRESSOR OF GAMMA RESPONSE 1, a master transcription factor controlling DNA damage response in Arabidopsis
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Motoaki Seki, Naoki Takahashi, Yuko Makita, Maho Tanaka, Tomoaki Sakamoto, Yusuke Saijo, Nobuo Ogita, Masaaki Umeda, Minami Matsui, Mutsutomo Tokizawa, Tetsuya Kurata, Yoshiharu Y. Yamamoto, Kaoru Okamoto‐Yoshiyama, Yoko Okushima, and Kei Hiruma
- Subjects
p53 ,0106 biological sciences ,0301 basic medicine ,Chromatin Immunoprecipitation ,DNA Repair ,Arabidopsis thaliana ,DNA damage ,DNA repair ,NAC transcription factor ,Arabidopsis ,Plant Science ,Biology ,DNA damage response ,Genes, Plant ,01 natural sciences ,immune response ,ChIP-Seq ,03 medical and health sciences ,chemistry.chemical_compound ,SOG1 ,Genetics ,Phosphorylation ,Transcription factor ,Gene ,Oligonucleotide Array Sequence Analysis ,Plant Proteins ,Microarray analysis techniques ,Arabidopsis Proteins ,Inverted Repeat Sequences ,Cell Biology ,Genes, p53 ,cis-element ,Cell biology ,030104 developmental biology ,chemistry ,Homologous recombination ,Chromatin immunoprecipitation ,DNA ,010606 plant biology & botany ,DNA Damage ,Transcription Factors - Abstract
In mammalian cells, the transcription factor p53 plays a crucial role in transmitting DNA damage signals to maintain genome integrity. However, in plants, orthologous genes for p53 and checkpoint proteins are absent. Instead, the plant-specific transcription factor SUPPRESSOR OF GAMMA RADIATION 1 (SOG1) controls most of the genes induced by gamma irradiation and promotes DNA repair, cell cycle arrest, and stem cell death. Thus far, the genes directly controlled by SOG1 remain largely unknown, limiting the understanding of DNA damage signaling in plants. Here, we conducted a microarray analysis and chromatin immunoprecipitation (ChIP)-sequencing, and identified 146 Arabidopsis genes as direct targets of SOG1. By using the ChIP-sequencing data, we extracted the palindromic motif [CTT(N)7AAG] as a consensus SOG1-binding sequence, which mediates target gene induction in response to DNA damage. Furthermore, DNA damage-triggered phosphorylation of SOG1 is required for efficient binding to SOG1-binding sequence. Comparison between SOG1 and p53 target genes showed that both transcription factors control genes responsible for cell cycle regulation, such as CDK inhibitors, and DNA repair proteins, whereas SOG1 preferentially targets genes involved in homologous recombination. We also found that defense-related genes were enriched in the SOG1 target genes. Consistent with this, SOG1 is required for resistance against the hemi-biotrophic fungus Colletotrichum higginsianum, suggesting that SOG1 has a unique function in controlling immune response. This article is protected by copyright. All rights reserved.
- Published
- 2018
30. A Missense Mutation in the NSF Gene Causes Abnormal Golgi Morphology in Arabidopsis thaliana
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Sayuri, Tanabashi, Keiko, Shoda, Chieko, Saito, Tomoaki, Sakamoto, Tetsuya, Kurata, Tomohiro, Uemura, and Akihiko, Nakano
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Adenosine Triphosphatases ,Binding Sites ,Microscopy, Confocal ,Arabidopsis Proteins ,Arabidopsis ,Mutation, Missense ,Golgi Apparatus ,Membrane Fusion ,Microscopy, Electron ,Phenotype ,Animals ,Humans ,Amino Acid Sequence ,N-Ethylmaleimide-Sensitive Proteins ,Sequence Alignment - Abstract
The Golgi apparatus is a key station of glycosylation and membrane traffic. It consists of stacked cisternae in most eukaryotes. However, the mechanisms how the Golgi stacks are formed and maintained are still obscure. The model plant Arabidopsis thaliana provides a nice system to observe Golgi structures by light microscopy, because the Golgi in A. thaliana is in the form of mini-stacks that are distributed throughout the cytoplasm. To obtain a clue to understand the molecular basis of Golgi morphology, we took a forward-genetic approach to isolate A. thaliana mutants that show abnormal structures of the Golgi under a confocal microscope. In the present report, we describe characterization of one of such mutants, named #46-3. The #46-3 mutant showed pleiotropic Golgi phenotypes. The Golgi size was in majority smaller than the wild type, but varied from very small ones, sometimes without clear association of cis and trans cisternae, to abnormally large ones under a confocal microscope. At the ultrastructual level by electron microscopy, queer-shaped large Golgi stacks were occasionally observed. By positional mapping, genome sequencing, and complementation and allelism tests, we linked the mutant phenotype to the missense mutation D374N in the NSF gene, encoding the N-ethylmaleimide-sensitive factor (NSF), a key component of membrane fusion. This residue is near the ATP-binding site of NSF, which is very well conserved in eukaryotes, suggesting that the biochemical function of NSF is important for maintaining the normal morphology of the Golgi.Key words: Golgi morphology, N-ethylmaleimide-sensitive factor (NSF), Arabidopsis thaliana.
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- 2018
31. Constitutive BiP protein accumulation in Arabidopsis mutants defective in a gene encoding chloroplast-resident stearoyl-acyl carrier protein desaturase
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Tetsuya Kurata, Toshihiro Matsunami, Kei-ichiro Mishiba, Yuji Iwata, Nozomu Koizumi, Takumi Ogawa, Tsukasa Iida, and Yu Yamada
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0106 biological sciences ,0301 basic medicine ,Fatty Acid Desaturases ,Chloroplasts ,Mutant ,Arabidopsis ,Endoplasmic Reticulum ,01 natural sciences ,03 medical and health sciences ,chemistry.chemical_compound ,Gene Expression Regulation, Plant ,Gene expression ,Genetics ,Arabidopsis thaliana ,biology ,Arabidopsis Proteins ,Endoplasmic reticulum ,Binding protein ,fungi ,Fatty Acids ,food and beverages ,Cell Biology ,Tunicamycin ,biology.organism_classification ,Plants, Genetically Modified ,Cell biology ,030104 developmental biology ,Basic-Leucine Zipper Transcription Factors ,Phenotype ,chemistry ,Mutation ,Unfolded protein response ,Unfolded Protein Response ,010606 plant biology & botany ,Molecular Chaperones - Abstract
The unfolded protein response (UPR) occurs when protein folding and maturation are disturbed in the endoplasmic reticulum (ER). During the UPR, a number of genes including those encoding ER-resident molecular chaperones are induced. In Arabidopsis, BiP3 has been used as a UPR marker gene whose expression is strongly induced in response to ER stress. In this study, we mutagenized Arabidopsis plants expressing β-glucuronidase (GUS) gene under the control of BiP3 promoter and isolated a mutant that exhibits strong GUS activity without treatment with ER stress inducers. By whole genome sequencing, we identified a causal gene in the mutant as SUPPRESSOR OF SALICYLIC ACID INSENSITIVITY2 (SSI2), which encodes stearoyl-acyl carrier protein desaturase that converts stearic acids to oleic acids in the chloroplasts. In addition to GUS proteins, the ssi2 mutant accumulates endogenous BiP3 proteins without treatment by any stress reagents. Interestingly, although the degree of endogenous BiP3 protein accumulation in the ssi2 mutant was comparable to that in wild-type plants treated with the ER stress inducer tunicamycin, much less BiP3 transcripts were detected in the ssi2 mutant compared to tunicamycin-treated wild-type plants. Our finding suggests a genetic link between fatty acid metabolism in the chloroplasts and ER functions.
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- 2017
32. A plant U-box protein, PUB4, regulates asymmetric cell division and cell proliferation in the root meristem
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Shuji Shigenobu, Mitsunori Seo, Mitsuyasu Hasebe, Renze Heidstra, Takashi Ishida, Katsushi Yamaguchi, Takuji Wada, Ben Scheres, Hiroo Fukuda, Ryo Tabata, Colette A. ten Hove, Satoshi Iuchi, Noriko Shimizu, Masatomo Kobayashi, Yuji Kamiya, Shinichiro Sawa, Atsuko Kinoshita, Masashi Yamada, Tetsuya Kurata, Ikram Blilou, and Yumiko Takebayashi
- Subjects
Cell division ,Ubiquitin-Protein Ligases ,growth ,Meristem ,Arabidopsis ,Plant Developmental Biology ,Biochemie ,Cell Cycle Proteins ,Biology ,Biochemistry ,repeat protein ,Gene Expression Regulation, Plant ,Cyclins ,Two-Hybrid System Techniques ,Asymmetric cell division ,thaliana ,Cloning, Molecular ,cle peptides ,Molecular Biology ,Cell Proliferation ,Microscopy, Confocal ,Arabidopsis Proteins ,of-function phenotypes ,Cell growth ,Gene Expression Profiling ,Asymmetric Cell Division ,fungi ,differentiation ,organization ,Cell cycle ,Plants, Genetically Modified ,gene-expression ,Cortex (botany) ,Cell biology ,receptor-like kinase ,arabidopsis shoot meristem ,Endodermis ,Stem cell ,Signal Transduction ,Developmental Biology - Abstract
The root meristem (RM) is a fundamental structure that is responsible for postembryonic root growth. The RM contains the quiescent center (QC), stem cells and frequently dividing meristematic cells, in which the timing and the frequency of cell division are tightly regulated. In Arabidopsis thaliana, several gain-of-function analyses have demonstrated that peptide ligands of the CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION-RELATED (CLE) family are important for maintaining RM size. Here, we demonstrate that a plant U-box E3 ubiquitin ligase, PUB4, is a novel downstream component of CLV3/CLE signaling in the RM. Mutations in PUB4 reduced the inhibitory effect of exogenous CLV3/CLE peptide on root cell proliferation and columella stem cell maintenance. Moreover, pub4 mutants grown without exogenous CLV3/CLE peptide exhibited characteristic phenotypes in the RM, such as enhanced root growth, increased number of cortex/endodermis stem cells and decreased number of columella layers. Our phenotypic and gene expression analyses indicated that PUB4 promotes expression of a cell cycle regulatory gene, CYCD6;1, and regulates formative periclinal asymmetric cell divisions in endodermis and cortex/endodermis initial daughters. These data suggest that PUB4 functions as a global regulator of cell proliferation and the timing of asymmetric cell division that are important for final root architecture.
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- 2015
33. Subtilase activity in intrusive cells mediates haustorium maturation in parasitic plants.
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Satoshi Ogawa, Takanori Wakatake, Spallek, Thomas, Ishida, Juliane K., Ryosuke Sano, Tetsuya Kurata, Taku Demura, Satoko Yoshida, Yasunori Ichihashi, Andreas Schaller, and Ken Shirasu
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- 2021
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34. Localization of the CAPRICE-ENHANCER OF TRY AND CPC1 chimera protein in Arabidopsis root epidermis
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Takuji Wada, Tetsuya Kurata, and Rumi Tominaga-Wada
- Subjects
0106 biological sciences ,0301 basic medicine ,Recombinant Fusion Proteins ,Arabidopsis ,Biology ,Root hair ,01 natural sciences ,Applied Microbiology and Biotechnology ,Biochemistry ,Plant Roots ,Analytical Chemistry ,Green fluorescent protein ,Plant Epidermis ,03 medical and health sciences ,Proto-Oncogene Proteins c-myb ,MYB ,Amino Acid Sequence ,Enhancer ,Molecular Biology ,Gene ,Transcription factor ,Genetics ,Cell Nucleus ,Arabidopsis Proteins ,Organic Chemistry ,General Medicine ,Trichomes ,biology.organism_classification ,Cell biology ,DNA-Binding Proteins ,Protein Transport ,030104 developmental biology ,Phenotype ,Nuclear localization sequence ,010606 plant biology & botany ,Biotechnology - Abstract
The CAPRICE (CPC) encodes an R3-type MYB transcription factor, which promotes root-hair differentiation. Previously, we showed that the CPC protein moves from the non-hair cell to the neighboring cell and induces root-hair differentiation in Arabidopsis. In addition, we proposed two cell-to-cell movement signal sequences, S1 and S2, in CPC. However, an S1:2xGFP:S2 chimera protein did not move between root epidermal cells. Here, we show that the S1 and S2 sequences do not confer cell-to-cell movement or nuclear localization ability to a GFP protein. The ENHANCER OF TRY AND CPC1 (ETC1) gene encodes the CPC homolog R3 MYB; this protein does not possess cell-to-cell movement ability or the S1 sequence. To elucidate whether the S1 sequence can induce cell-to-cell movement ability in ETC1, CPCp:S1:ETC1:2xGFP was constructed and introduced into Arabidopsis. Our results indicate that the addition of the S1 sequence was not sufficient for ETC1 to acquire cell-to-cell movement ability.
- Published
- 2017
35. Protein S-Nitrosylation Regulates Xylem Vessel Cell Differentiation in Arabidopsis
- Author
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Tetsuya Kurata, Tomoaki Sakamoto, Taku Demura, Misato Ohtani, and Harunori Kawabe
- Subjects
0106 biological sciences ,0301 basic medicine ,Physiology ,Cellular differentiation ,Mutant ,Arabidopsis ,Mutagenesis (molecular biology technique) ,Plant Science ,Nitric Oxide ,01 natural sciences ,03 medical and health sciences ,Transactivation ,Xylem ,Botany ,Cysteine ,Transcription factor ,biology ,Chemistry ,Arabidopsis Proteins ,Cell Differentiation ,Cell Biology ,General Medicine ,S-Nitrosylation ,biology.organism_classification ,Plants, Genetically Modified ,Cell biology ,030104 developmental biology ,Glutathione Reductase ,Mutation ,Protein Processing, Post-Translational ,010606 plant biology & botany ,Transcription Factors - Abstract
Post-translational modifications of proteins have important roles in the regulation of protein activity. One such modification, S-nitrosylation, involves the covalent binding of nitric oxide (NO)-related species to a cysteine residue. Recent work showed that protein S-nitrosylation has crucial functions in plant development and environmental responses. In the present study, we investigated the importance of protein S-nitrosylation for xylem vessel cell differentiation using a forward genetics approach. We performed ethyl methanesulfonate mutagenesis of a transgenic Arabidopsis 35S::VND7-VP16-GR line in which the activity of VASCULAR-RELATED NAC-DOMAIN7 (VND7), a key transcription factor involved in xylem vessel cell differentiation, can be induced post-translationally by glucocorticoid treatment, with the goal of obtaining suppressor mutants that failed to differentiate ectopic xylem vessel cells; we named these mutants suppressor of ectopic vessel cell differentiation induced by VND7 (seiv) mutants. We found the seiv1 mutant to be a recessive mutant in which ectopic xylem cell differentiation was inhibited, especially in aboveground organs. In seiv1 mutants, a single nucleic acid substitution (G to A) leading to an amino acid substitution (E36K) was present in the gene encoding S-NITROSOGLUTATHIONE REDUCTASE 1 (GSNOR1), which regulates the turnover of the natural NO donor, S-nitrosoglutathione. An in vitro S-nitrosylation assay revealed that VND7 can be S-nitrosylated at Cys264 and Cys320 located near the transactivation activity-related domains, which were shown to be important for transactivation activity of VND7 by transient reporter assay. Our results suggest crucial roles for GSNOR1-regulated protein S-nitrosylation in xylem vessel cell differentiation, partly through the post-translational modification of VND7.
- Published
- 2017
36. Toxic Substances in Jatropha Seeds: Biosynthesis of the Most Problematic Compounds, Phorbol Esters
- Author
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Ryosuke Sano, Misato Ohtani, Tetsuya Kurata, Yoshimi Nakano, and Taku Demura
- Subjects
0106 biological sciences ,0301 basic medicine ,Biodiesel ,Protease ,medicine.medical_treatment ,Euphorbiaceae ,food and beverages ,Jatropha ,Biology ,biology.organism_classification ,01 natural sciences ,03 medical and health sciences ,030104 developmental biology ,Bioenergy ,Botany ,medicine ,biology.protein ,Thymelaeaceae ,Food science ,Jatropha curcas ,010606 plant biology & botany ,Casbene synthase - Abstract
Jatropha (Jatropha curcas L.) is considered to be an important oilseed crop. Its seed oil can be used as a biodiesel in existing diesel engines without special modifications, making this plant an attractive bioresource for the production of sustainable bioenergy. Additionally, it is possible that, after extracting the oil from Jatropha seed cakes, they can be used as animal feed because they contain high amounts of proteins. However, the toxic and antinutritional substances in the seeds and oils, such as a lectin, protease inhibitors, saponins, and phorbol esters, have generated a serious safety concern for further utilization of Jatropha. In this chapter, we review the toxic substances found in Jatropha seeds, focusing on the most problematic toxic substance, phorbol ester, one of the characteristic tetracyclic diterpenoids in Thymelaeaceae and Euphorbiaceae plants. Recent advances in genome-wide Jatropha research using toxic and non-toxic varieties have identified the genetic locus related to the phorbol ester content and the genes responsible for casbane-type diterpenoid biosynthesis. Based on these findings, Jatropha genomic research should help to achieve the practical utilization of Jatropha as a multipurpose crop.
- Published
- 2017
37. WOX13-like genes are required for reprogramming of leaf and protoplast cells into stem cells in the moss Physcomitrella patens
- Author
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Pascal Reisewitz, Sayuri Ando, Tetsuya Kurata, Tsuyoshi Aoyama, Hironori Deguchi, Thomas D. Friedrich, Mitsuyasu Hasebe, Wolfgang Werr, Tomoaki Nishiyama, Yosuke Tamada, Yuji Hiwatashi, Masaki Ishikawa, Thomas Laux, Takashi Murata, Yoshikatsu Sato, Keiko Sakakibara, and Stefan A. Rensing
- Subjects
Plant stem cell ,Zygote ,Cellular differentiation ,Physcomitrella ,Meristem ,Molecular Sequence Data ,Arabidopsis ,Biology ,Genes, Plant ,Physcomitrella patens ,Cell Wall ,Gene Expression Regulation, Plant ,Regeneration ,Amino Acid Sequence ,Molecular Biology ,Cell Proliferation ,Plant Proteins ,Genetics ,Arabidopsis Proteins ,Cell growth ,Protoplasts ,Stem Cells ,food and beverages ,Plant cell ,biology.organism_classification ,Bryopsida ,Up-Regulation ,Cell biology ,Plant Leaves ,Stem cell ,Reprogramming ,Gene Deletion ,Developmental Biology - Abstract
Many differentiated plant cells can dedifferentiate into stem cells, reflecting the remarkable developmental plasticity of plants. In the moss Physcomitrella patens, cells at the wound margin of detached leaves become reprogrammed into stem cells. Here, we report that two paralogous P. patens WUSCHEL-related homeobox 13-like (PpWOX13L) genes, homologs of stem cell regulators in flowering plants, are transiently upregulated and required for the initiation of cell growth during stem cell formation. Concordantly, Δppwox13l deletion mutants fail to upregulate genes encoding homologs of cell wall loosening factors during this process. During the moss life cycle, most of the Δppwox13l mutant zygotes fail to expand and initiate an apical stem cell to form the embryo. Our data show that PpWOX13L genes are required for the initiation of cell growth specifically during stem cell formation, in analogy to WOX stem cell functions in seed plants, but using a different cellular mechanism.
- Published
- 2014
38. Contribution of NAC Transcription Factors to Plant Adaptation to Land
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Ryosuke Sano, Yoshimi Nakano, Kiminori Toyooka, Taku Demura, Mayumi Wakazaki, Misato Ohtani, Yuji Hiwatashi, Tetsuya Kurata, Arata Yoneda, Ko Kato, Takashi Murata, Mitsuyasu Hasebe, Bo Xu, Masatoshi Yamaguchi, Minoru Kubo, and Mayuko Sato
- Subjects
Regulation of gene expression ,Multidisciplinary ,Plant Stems ,Transcription, Genetic ,Molecular Sequence Data ,Mutant ,Arabidopsis ,Water ,Sporophyte ,Biology ,Physcomitrella patens ,biology.organism_classification ,Adaptation, Physiological ,Bryopsida ,Cell biology ,Gene Expression Regulation, Plant ,Genetic Loci ,Transcription (biology) ,Trans-Activators ,Transcriptional regulation ,Amino Acid Sequence ,Gene ,Transcription factor ,Genome, Plant ,Plant Proteins - Abstract
From Drips to Tubes In the evolutionary transition from aquatic to terrestrial habitats, plants acquired internal systems to transport water and provide structural support. Xu et al. (p. 1505 , published online 20 March) studied a family of genes and the cells they control to better understand the innovations required to adapt to dry land. In Arabidopsis , specific transcription factors regulate development of xylem—the plant tissue that transports water. The moss Physcomitrella patens has similar genes, which regulate development of hydroids and stereids, cells specialized in water transport and structural support. The similarity in the genes and their functions suggests the evolutionary origins of land-plant vascular systems.
- Published
- 2014
39. High-Resolution Mapping of In vivo Genomic Transcription Factor Binding Sites Using In situ DNase I Footprinting and ChIP-seq
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Jon L. Hobman, Shu Ishikawa, Kensuke Nakamura, Taku Oshima, Onuma Chumsakul, Naotake Ogasawara, Tetsuya Kurata, and Tomoaki Sakamoto
- Subjects
Chromatin Immunoprecipitation ,Molecular Sequence Data ,genetic processes ,DNA Footprinting ,GeF-seq ,DNA footprinting ,Computational biology ,Biology ,Bacterial Proteins ,Genetics ,Deoxyribonuclease I ,Nucleotide Motifs ,Molecular Biology ,Conserved Sequence ,Binding Sites ,fungi ,DNase-I Footprinting ,High-Throughput Nucleotide Sequencing ,Sequence Analysis, DNA ,General Medicine ,Bacterial nucleoid ,Full Papers ,AbrB ,Molecular biology ,Footprinting ,DNA-Binding Proteins ,ChIP-seq ,DNA binding site ,DNase I hypersensitive site ,DNase footprinting assay ,Hypersensitive site ,Protein Binding ,Transcription Factors ,Bacillus subtilis - Abstract
Accurate identification of the DNA-binding sites of transcription factors and other DNA-binding proteins on the genome is crucial to understanding their molecular interactions with DNA. Here, we describe a new method: Genome Footprinting by high-throughput sequencing (GeF-seq), which combines in vivo DNase I digestion of genomic DNA with ChIP coupled with high-throughput sequencing. We have determined the in vivo binding sites of a Bacillus subtilis global regulator, AbrB, using GeF-seq. This method shows that exact DNA-binding sequences, which were protected from in vivo DNase I digestion, were resolved at a comparable resolution to that achieved by in vitro DNase I footprinting, and this was simply attained without the necessity of prediction by peak-calling programs. Moreover, DNase I digestion of the bacterial nucleoid resolved the closely positioned AbrB-binding sites, which had previously appeared as one peak in ChAP-chip and ChAP-seq experiments. The high-resolution determination of AbrB-binding sites using GeF-seq enabled us to identify bipartite TGGNA motifs in 96% of the AbrB-binding sites. Interestingly, in a thousand binding sites with very low-binding intensities, single TGGNA motifs were also identified. Thus, GeF-seq is a powerful method to elucidate the molecular mechanism of target protein binding to its cognate DNA sequences.
- Published
- 2013
40. Primary Metabolism during Biosynthesis of Secondary Wall Polymers of Protoxylem Vessel Elements
- Author
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Yuji Sawada, Misato Ohtani, Tetsuya Kurata, Yoshimi Nakano, Tomohisa Hasunuma, Taku Demura, Keiko Morisaki, Masami Yokota Hirai, Shiro Suzuki, Abigail Loren Tung Uy, Ryosuke Sano, Mami Matsuda, and Atsushi Yamamoto
- Subjects
0106 biological sciences ,0301 basic medicine ,Physiology ,Polymers ,Cellular differentiation ,Shikimic Acid ,Plant Science ,Biology ,01 natural sciences ,Lignin ,03 medical and health sciences ,chemistry.chemical_compound ,Biosynthesis ,Cell Wall ,Gene Expression Regulation, Plant ,Xylem ,Tobacco ,Genetics ,Shikimate pathway ,Metabolomics ,Amino Acids ,Amino acid synthesis ,chemistry.chemical_classification ,Principal Component Analysis ,Gene Expression Profiling ,Cell Differentiation ,Metabolism ,Articles ,Amino acid ,Biosynthetic Pathways ,030104 developmental biology ,chemistry ,Biochemistry ,Metabolome ,Phosphoenolpyruvate carboxykinase ,Secondary cell wall ,Glycolysis ,010606 plant biology & botany - Abstract
Xylem vessels, the water-conducting cells in vascular plants, undergo characteristic secondary wall deposition and programmed cell death. These processes are regulated by the VASCULAR-RELATED NAC-DOMAIN (VND) transcription factors. Here, to identify changes in metabolism that occur during protoxylem vessel element differentiation, we subjected tobacco (Nicotiana tabacum) BY-2 suspension culture cells carrying an inducible VND7 system to liquid chromatography-mass spectrometry-based wide-target metabolome analysis and transcriptome analysis. Time-course data for 128 metabolites showed dynamic changes in metabolites related to amino acid biosynthesis. The concentration of glyceraldehyde 3-phosphate, an important intermediate of the glycolysis pathway, immediately decreased in the initial stages of cell differentiation. As cell differentiation progressed, specific amino acids accumulated, including the shikimate-related amino acids and the translocatable nitrogen-rich amino acid arginine. Transcriptome data indicated that cell differentiation involved the active up-regulation of genes encoding the enzymes catalyzing fructose 6-phosphate biosynthesis from glyceraldehyde 3-phosphate, phosphoenolpyruvate biosynthesis from oxaloacetate, and phenylalanine biosynthesis, which includes shikimate pathway enzymes. Concomitantly, active changes in the amount of fructose 6-phosphate and phosphoenolpyruvate were detected during cell differentiation. Taken together, our results show that protoxylem vessel element differentiation is associated with changes in primary metabolism, which could facilitate the production of polysaccharides and lignin monomers and, thus, promote the formation of the secondary cell wall. Also, these metabolic shifts correlate with the active transcriptional regulation of specific enzyme genes. Therefore, our observations indicate that primary metabolism is actively regulated during protoxylem vessel element differentiation to alter the cell's metabolic activity for the biosynthesis of secondary wall polymers.
- Published
- 2016
41. WIND1 Promotes Shoot Regeneration through Transcriptional Activation of
- Author
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Akira, Iwase, Hirofumi, Harashima, Momoko, Ikeuchi, Bart, Rymen, Mariko, Ohnuma, Shinichiro, Komaki, Kengo, Morohashi, Tetsuya, Kurata, Masaru, Nakata, Masaru, Ohme-Takagi, Erich, Grotewold, and Keiko, Sugimoto
- Subjects
Transcriptional Activation ,Microscopy, Confocal ,Arabidopsis Proteins ,Reverse Transcriptase Polymerase Chain Reaction ,fungi ,Arabidopsis ,food and beverages ,Plants, Genetically Modified ,Tissue Culture Techniques ,Gene Expression Regulation, Plant ,Regeneration ,Promoter Regions, Genetic ,Plant Shoots ,Research Articles ,Protein Binding ,Signal Transduction ,Transcription Factors - Abstract
Many plant species display remarkable developmental plasticity and regenerate new organs after injury. Local signals produced by wounding are thought to trigger organ regeneration but molecular mechanisms underlying this control remain largely unknown. We previously identified an AP2/ERF transcription factor WOUND INDUCED DEDIFFERENTIATION1 (WIND1) as a central regulator of wound-induced cellular reprogramming in plants. In this study, we demonstrate that WIND1 promotes callus formation and shoot regeneration by upregulating the expression of the
- Published
- 2016
42. FLC: A Hidden Polycomb Response Element Shows Up in Silence
- Author
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Tetsuya Kurata, Diana Mihaela Buzas, and Yosuke Tamada
- Subjects
Regulation of gene expression ,Genetics ,animal structures ,biology ,Physiology ,fungi ,Response element ,Polycomb-Group Proteins ,Repressor ,MADS Domain Proteins ,Cell Biology ,Plant Science ,General Medicine ,Response Elements ,biology.organism_classification ,Repressor Proteins ,Gene Expression Regulation, Plant ,hemic and lymphatic diseases ,Flowering Locus C ,Polycomb-group proteins ,Animals ,Coding region ,Gene Silencing ,Drosophila melanogaster ,Homeotic gene - Abstract
A sizeable fraction of eukaryotic genomes is regulated by Polycomb group (PcG) and trithorax group (trxG) proteins, which play key roles in epigenetic repression and activation, respectively. In Drosophila melanogaster, homeotic genes are well-documented PcG targets; they are known to contain cis-acting elements termed Polycomb response elements (PREs), which bind PcG proteins and satisfy three defined criteria, and also often contain binding sites for the trithorax (trx) protein. However, the presence of PREs, or an alternative mode for PcG/trxG interaction with the genome, has not been well documented outside Drosophila. In Arabidopsis thaliana, PcG/trxG regulation has been studied extensively for the flowering repressor gene FLOWERING LOCUS C (FLC). Here we evaluate how PRE-like activities that reside within the FLC locus may satisfy the defined Drosophila criteria, by analyzing four FLC transcription states. When the FLC locus is not transcribed, the intrinsic PcG recruitment ability of the coding region can be attributed to two redundant cis-acting elements (Modules IIA and IIB). When FLC is highly expressed, trxG recruitment is to a region overlapping the transcription start site (Module I). Exposure to prolonged cold converts the active FLC state into a repressed state that is maintained after the cold period finishes. These two additional transcriptional states also rely on the same three modules for PcG/trxG regulation. We conclude that each of Modules I, IIA and IIB partially fulfills the PRE function criteria, and that together they represent the functional FLC PRE, which differs structurally from canonical PREs in Drosophila.
- Published
- 2011
43. Identification of EMS-Induced Causal Mutations in a Non-Reference Arabidopsis thaliana Accession by Whole Genome Sequencing
- Author
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Tomoaki Sakamoto, Masao Tasaka, Tetsuya Kurata, and Naoyuki Uchida
- Subjects
Cancer genome sequencing ,Candidate gene ,DNA, Plant ,Genetic Linkage ,Physiology ,DNA Mutational Analysis ,Arabidopsis ,Locus (genetics) ,Plant Science ,Biology ,Polymorphism, Single Nucleotide ,Genome ,Crosses, Genetic ,Exome sequencing ,Genetics ,Whole genome sequencing ,Arabidopsis Proteins ,Homozygote ,Chromosome Mapping ,High-Throughput Nucleotide Sequencing ,Methane sulfonate ,Sequence Analysis, DNA ,Cell Biology ,General Medicine ,Phenotype ,Genetic Loci ,Ethyl Methanesulfonate ,Mutation ,Chromosomal region ,Carrier Proteins ,Genome, Plant ,Genome-Wide Association Study ,Mutagens - Abstract
The most frequently used method to identify mutations induced by a commonly used mutagen, EMS (ethyl methane sulfonate), in Arabidopsis thaliana has been map-based cloning. The first step of this method is crossing a mutant with a plant of another accession as it requires polymorphisms between accessions for linkage analysis. Therefore, to perform the method routinely, it is greatly preferred to use accession combinations between which enough polymorphisms are already known. Further, it requires laborious examination of a large number of F₂ recombinants using many markers to detect each polymorphism. After linkage analysis narrows down the chromosomal region containing the causal mutation, sequencing candidate genes one by one within the region is necessary until the mutation is finally identified. Overall, this method is generally time-consuming and labor intensive, and it becomes harder when multiple loci are involved in phenotypes. A few recent reports showed that causal mutations induced by EMS could be identified by deep-sequencing technologies with less labor compared with the conventional method when mutants were generated in the Arabidopsis reference Columbia background whose genome organization is well known. Here we report that we succeeded in rapid identification of EMS-induced causal mutations in a non-reference accession background, whose whole genome sequence is not publicly available, using one round of whole genome sequencing. Moreover, in our case, we could monitor the causal locus and the transgenic reporter locus simultaneously, implying that this methodology could theoretically be applicable to analyzing even complex traits. We describe the pipeline of this methodology and discuss its characteristics.
- Published
- 2011
44. FE, a phloem-specific Myb-related protein, promotes flowering through transcriptional activation of FLOWERING LOCUS T and FLOWERING LOCUS T INTERACTING PROTEIN 1
- Author
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Ayako Watanabe-Taneda, Carlos Alonso-Blanco, Hidetaka Kaya, Ayako Yamaguchi, Mitsutomo Abe, Takashi Araki, Tetsuya Kurata, Israel Ausin, Mio Shibuta, and Tomoaki Sakamoto
- Subjects
Mutant ,Arabidopsis ,Plant Science ,Flowers ,Phloem ,chemistry.chemical_compound ,Gene Expression Regulation, Plant ,Botany ,Genetics ,MYB ,photoperiodism ,biology ,Arabidopsis Proteins ,fungi ,food and beverages ,Membrane Proteins ,Cell Biology ,Meristem ,biology.organism_classification ,Plants, Genetically Modified ,Transport protein ,Cell biology ,Plant Leaves ,Protein Transport ,chemistry ,Mutation ,Florigen ,Plant Shoots ,Transcription Factors - Abstract
In many flowering plants, the transition to flowering is primarily affected by seasonal changes in day length (photoperiod). An inductive photoperiod promotes flowering via synthesis of a floral stimulus, called florigen. In Arabidopsis thaliana, the FLOWERING LOCUS T (FT) protein is an essential component of florigen, which is synthesized in leaf phloem companion cells and is transported through phloem tissue to the shoot apical meristem where floral morphogenesis is initiated. However, the molecular mechanism involved in the long-distance transport of FT protein remains elusive. In this study, we characterized the classic Arabidopsis mutant fe, which is involved in the photoperiodic induction of flowering, and showed that FE encodes a phloem-specific Myb-related protein that was previously reported as ALTERED PHLOEM DEVELOPMENT. Phenotypic analyses of the fe mutant showed that FT expression is reduced in leaf phloem companion cells. In addition, the transport of FT protein from leaves to the shoot apex is impaired in the fe mutant. Expression analyses further demonstrated that FE is also required for transcriptional activation of FLOWERING LOCUS T INTERACTING PROTEIN 1 (FTIP1), an essential regulator for selective trafficking of the FT protein from companion cells to sieve elements. These findings indicate that FE plays a dual role in the photoperiodic induction of flowering: as a transcriptional activator of FT on the one hand, and its transport machinery component, FTIP1, on the other hand. Thus, FE is likely to play a role in regulating FT by coordinating FT synthesis and FT transport in phloem companion cells.
- Published
- 2015
45. A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads
- Author
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Takeshi Furuhashi, Daisuke Ikeue, Tetsuya Kurata, Tomoaki Sakamoto, Yoshiyuki Ogata, Koh Aoki, Wenna Zhang, Christian Schudoma, and Friedrich Kragler
- Subjects
Cuscuta japonica ,Cuscuta reflexa ,biology ,Parasitic plant ,Host (biology) ,Methodology ,UniGene ,food and beverages ,RNA-Seq ,Plant Science ,biology.organism_classification ,Bioinformatics ,Classification ,Haustorium ,Genetics ,Parasite-host interaction ,Cuscuta ,Transcriptome ,Biotechnology - Abstract
Background The genus Cuscuta is a group of parasitic plants that are distributed world-wide. The process of parasitization starts with a Cuscuta plant coiling around the host stem. The parasite’s haustorial organs then establish a vascular connection allowing for access to the phloem content. The host and the parasite form new cellular connections, suggesting coordination of developmental and biochemical processes. Simultaneous monitoring of gene expression in the parasite’s and host’s tissues may shed light on the complex events occurring between the parasitic and host cells and may help to overcome experimental limitations (i.e. how to separate host tissue from Cuscuta tissue at the haustorial connection). A novel approach is to use bioinformatic analysis to classify sequencing reads as either belonging to the host or to the parasite and to characterize the expression patterns. Owing to the lack of a comprehensive genomic dataset from Cuscuta spp., such a classification has not been performed previously. Results We first classified RNA-Seq reads from an interface region between the non-model parasitic plant Cuscuta japonica and the non-model host plant Impatiens balsamina. Without established reference sequences, we classified reads as originating from either of the plants by stepwise similarity search against de novo assembled transcript sets of C. japonica and I. balsamina, unigene sets of the same genus, and cDNA sequences of the same family. We then assembled de novo transcriptomes from the classified read sets. We assessed the quality of the classification by mapping reads to contigs of both plants, achieving a misclassification rate low enough (0.22-0.39%) to be used reliably for differential gene expression analysis. Finally, we applied our read classification method to RNA-Seq data from the interface between the non-model parasitic plant C. japonica and the model host plant Glycine max. Analysis of gene expression profiles at 5 parasitizing stages revealed differentially expressed genes from both C. japonica and G. max, and uncovered the coordination of cellular processes between the two plants. Conclusions We demonstrated that reliable identification of differentially expressed transcripts in undissected interface region of the parasite-host association is feasible and informative with respect to differential-expression patterns. Electronic supplementary material The online version of this article (doi:10.1186/s13007-015-0066-6) contains supplementary material, which is available to authorized users.
- Published
- 2015
46. FT-like proteins induce transposon silencing in the shoot apex during floral induction in rice
- Author
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Ayana Matsumoto, Rie Terada, Hiroyuki Tsuji, Akiko Fujita, Shojiro Tamaki, Tomoaki Sakamoto, Tetsuya Kurata, Zenpei Shimatani, and Ko Shimamoto
- Subjects
Organogenesis ,Meristem ,Down-Regulation ,Flowers ,Biology ,Genes, Plant ,chemistry.chemical_compound ,Gene Expression Regulation, Plant ,Gene Silencing ,Inflorescence ,Transcription factor ,Gene ,Florigen ,Plant Proteins ,Genetics ,Multidisciplinary ,Oryza sativa ,Base Sequence ,Reproduction ,fungi ,food and beverages ,Reproducibility of Results ,Oryza ,Up-Regulation ,Protein Transport ,Phenotype ,chemistry ,PNAS Plus ,Shoot ,DNA Transposable Elements - Abstract
Floral induction is a crucial developmental step in higher plants. Florigen, a mobile floral activator that is synthesized in the leaf and transported to the shoot apex, was recently identified as a protein encoded by FLOWERING LOCUS T (FT) and its orthologs; the rice florigen is Heading date 3a (Hd3a) protein. The 14-3-3 proteins mediate the interaction of Hd3a with the transcription factor OsFD1 to form a ternary structure called the florigen activation complex on the promoter of OsMADS15, a rice APETALA1 ortholog. However, crucial information, including the spatiotemporal overlap among FT-like proteins and the components of florigen activation complex and downstream genes, remains unclear. Here, we confirm that Hd3a coexists, in the same regions of the rice shoot apex, with the other components of the florigen activation complex and its transcriptional targets. Unexpectedly, however, RNA-sequencing analysis of shoot apex from wild-type and RNA-interference plants depleted of florigen activity revealed that 4,379 transposable elements (TEs; 58% of all classifiable rice TEs) were expressed collectively in the vegetative and reproductive shoot apex. Furthermore, in the reproductive shoot apex, 214 TEs were silenced by florigen. Our results suggest a link between floral induction and regulation of TEs.
- Published
- 2015
47. Correction: The Tinkerbell (Tink) Mutation Identifies the Dual-Specificity MAPK Phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) as a Novel Regulator of Organ Size in Arabidopsis
- Author
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Sascha Ramm, Ottoline Leyser, Michael W. Bevan, Kim L. Johnson, Sally Ward, Tetsuya Kurata, Michael Lenhard, Tomoaki Sakamoto, and Christian Kappel
- Subjects
Multidisciplinary ,biology ,Science ,Regulator ,Organ Size ,Indole-3-butyric acid ,biology.organism_classification ,Molecular biology ,chemistry.chemical_compound ,chemistry ,Arabidopsis ,Mutation (genetic algorithm) ,MAPK phosphatase ,Medicine - Published
- 2015
48. Intercellular movement of transcription factors
- Author
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Kiyotaka Okada, Tetsuya Kurata, and Takuji Wada
- Subjects
Arabidopsis ,Gene Expression Regulation, Developmental ,Organogenesis ,Plant Science ,Plasmodesma ,Biology ,Cell biology ,Protein Transport ,Gene Expression Regulation, Plant ,Botany ,Extracellular Space ,Transcription factor ,Intracellular ,Transcription Factors - Abstract
Intercellular communication by the direct trafficking of transcription factors has been reported in plant developmental events such as root radial or epidermal cell patterning and shoot organogenesis. Investigations of this novel communication system have just begun and have highlighted the structural requirements for and mechanisms of transcription factor movement. Early studies suggest that plants employ both targeted (selective) and non-targeted (non-selective) intercellular movement of transcription factors. Factors that affect the intercellular movement of transcription factors through plasmodesmata have been explored.
- Published
- 2005
49. TheYORE-YOREgene regulates multiple aspects of epidermal cell differentiation inArabidopsis
- Author
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Kiyotaka Okada, Takuji Wada, Eiji Sakuradani, Tetsuya Kurata, Sakayu Shimizu, and Chie Kawabata-Awai
- Subjects
Molecular Sequence Data ,Mutant ,Arabidopsis ,Epidermal cell differentiation ,Plant Science ,Plant Epidermis ,Epicuticular wax ,Gene Expression Regulation, Plant ,Botany ,Genetics ,Arabidopsis thaliana ,Amino Acid Sequence ,Sequence Homology, Amino Acid ,biology ,Arabidopsis Proteins ,Lateral root ,Gene Expression Regulation, Developmental ,Cell Differentiation ,Cell Biology ,Meristem ,Plants, Genetically Modified ,biology.organism_classification ,Trichome ,Cell biology ,Phenotype ,Waxes ,Mutation ,RNA Interference ,Cell Surface Extensions - Abstract
Summary We have identified a new Arabidopsis mutant, yore-yore (yre), which has small trichomes and glossy stems. Adhesion between epidermal cells was observed in the organs of the yre shoot. The cloned YRE had high homology to plant genes involved in epicuticular wax synthesis, such as ECERIFERUM1 (CER1) and maize GLOSSY1. The phenotype of transgenic plants harboring double-stranded RNA interference (dsRNAi) YRE was quite similar to that of the yre mutant. The amount of epicuticular wax extracted from leaves and stems of yre-1 was approximately one-sixth of that from the wild type. YRE promoter::GUS and in situ hybridization revealed that YRE was specifically expressed in cells of the L1 layer of the shoot apical meristem and young leaves, stems, siliques, and lateral root primordia. Strong expression was detected in developing trichomes. The trichome structure of cer1 was normal, whereas that of the yre cer1 double mutant was heavily deformed, indicating that epicuticular wax is required for normal growth of trichomes. Double mutants of yre and trichome-morphology mutants, glabra 2 (gl2) and transparent testa glabra1 (ttg1), showed that the phenotype of the trichome structure was additive, suggesting that the wax-requiring pathway is distinct from the trichome development pathway controlled by GL2 and TTG1.
- Published
- 2003
50. Role of a positive regulator of root hair development,CAPRICE,inArabidopsisroot epidermal cell differentiation
- Author
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Yoshihiro Koshino-Kimura, Rumi Tominaga, Tetsuya Kurata, M. David Marks, Koji Goto, Kiyotaka Okada, Takuji Wada, Tatsuhiko Tachibana, and Yoshiro Shimura
- Subjects
Recombinant Fusion Proteins ,Arabidopsis ,Regulator ,macromolecular substances ,Root hair ,Biology ,Genes, Plant ,Plant Roots ,Plant Epidermis ,Trichome patterning ,Proto-Oncogene Proteins c-myb ,Gene Expression Regulation, Plant ,Genes, Reporter ,Two-Hybrid System Techniques ,otorhinolaryngologic diseases ,MYB ,Promoter Regions, Genetic ,Molecular Biology ,In Situ Hybridization ,Plant Proteins ,Homeodomain Proteins ,Genetics ,integumentary system ,Epidermis (botany) ,Arabidopsis Proteins ,technology, industry, and agriculture ,Cell Differentiation ,Plants, Genetically Modified ,biology.organism_classification ,Hairless ,Cell biology ,Phenotype ,sense organs ,Root epidermal cell differentiation ,Protein Binding ,Developmental Biology - Abstract
In Arabidopsis, root hairs are formed only from a set of epidermal cells named trichoblasts or hair-forming cells. Previous studies showedCAPRICE (CPC) promotes differentiation of hair-forming cells by controlling a negative regulator, GLABRA2 (GL2), which is preferentially expressed in hairless cells. Here, we show that CPC is also predominantly expressed in the hairless cells, but not in the neighboring hair-forming cells, and that CPC protein moves to the hair-forming cells and represses the GL2 expression. We also show that the N terminus of bHLH protein interacts with CPC and is responsible for the GL2expression. We propose a model in which CPC plays a key role in the fate-determination of hair-forming cells.
- Published
- 2002
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