14 results on '"Akie Shimotohno"'
Search Results
2. CLE2 regulates light-dependent carbohydrate metabolism in Arabidopsis shoots
- Author
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Hiroo Fukuda, Dichao Ma, Shigeyuki Betsuyaku, Akie Shimotohno, and Satoshi Endo
- Subjects
0106 biological sciences ,0301 basic medicine ,Light ,Transgene ,Mutant ,Arabidopsis ,Plant Science ,Carbohydrate metabolism ,01 natural sciences ,03 medical and health sciences ,Protein Domains ,Gene Expression Regulation, Plant ,Genetics ,Arabidopsis thaliana ,Gene ,biology ,Arabidopsis Proteins ,Gene Expression Profiling ,General Medicine ,Darkness ,Plants, Genetically Modified ,biology.organism_classification ,Cell biology ,030104 developmental biology ,Shoot ,Carbohydrate Metabolism ,Gene-Environment Interaction ,CRISPR-Cas Systems ,Agronomy and Crop Science ,Plant Shoots ,Function (biology) ,Signal Transduction ,010606 plant biology & botany - Abstract
This study focused on the role of CLE1-CLE7 peptides as environmental mediators and indicated that root-induced CLE2 functions systemically in light-dependent carbohydrate metabolism in shoots. Plants sense environmental stimuli and convert them into cellular signals, which are transmitted to distinct cells and tissues to induce adequate responses. Plant hormones and small secretory peptides often function as environmental stress mediators. In this study, we investigated whether CLAVATA3/EMBRYO SURROUNDING REGION-RELATED proteins, CLE1-CLE7, which share closely related CLE domains, mediate environmental stimuli in Arabidopsis thaliana. Expression analysis of CLE1-CLE7 revealed that these genes respond to different environmental stimuli, such as nitrogen deprivation, nitrogen replenishment, cold, salt, dark, and sugar starvation, in a sophisticated manner. To further investigate the function of CLE2, we generated transgenic Arabidopsis lines expressing the β-glucuronidase gene under the control of the CLE2 promoter or expressing the CLE2 gene under the control of an estradiol-inducible promoter. We also generated cle2-1 and cle2-2 mutants using the CRISPR/Cas9 technology. In these transgenic lines, dark induced the expression of CLE2 in the root vasculature. Additionally, induction of CLE2 in roots induced the expression of various genes not only in roots but also in shoots, and genes related to light-dependent carbohydrate metabolism were particularly induced in shoots. In addition, cle2 mutant plants showed chlorosis when subjected to a shade treatment. These results suggest that root-induced CLE2 functions systemically in light-dependent carbohydrate metabolism in shoots.
- Published
- 2020
3. Correction to: CLE2 regulates light-dependent carbohydrate metabolism in Arabidopsis shoots
- Author
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Hiroo Fukuda, Akie Shimotohno, Shigeyuki Betsuyaku, Dichao Ma, and Satoshi Endo
- Subjects
Arabidopsis ,Shoot ,Botany ,Genetics ,Plant Science ,General Medicine ,Biology ,Carbohydrate metabolism ,biology.organism_classification ,Agronomy and Crop Science - Published
- 2021
4. CDK Phosphorylation
- Author
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Akie Shimotohno and Masaaki Umeda
- Published
- 2018
5. Root stem cell niche organizer specification by molecular convergence of PLETHORA and SCARECROW transcription factor modules
- Author
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Ikram Blilou, Ben Scheres, Akie Shimotohno, and Renze Heidstra
- Subjects
0301 basic medicine ,Somatic cell ,Arabidopsis ,Gene Expression ,Plant Developmental Biology ,Plant Roots ,03 medical and health sciences ,Genetics ,Arabidopsis thaliana ,Laboratorium voor Moleculaire Biologie ,Protein Interaction Domains and Motifs ,Organizer ,PLT-TCP-SCR complexes ,Gene ,Transcription factor ,Homeodomain Proteins ,biology ,Arabidopsis Proteins ,Stem cell niche ,biology.organism_classification ,Cell biology ,030104 developmental biology ,Quiescent center ,Mutation ,Homeobox ,WUSCHEL-RELATED HOMEOBOX 5 ,Laboratory of Molecular Biology ,Stem cell ,EPS ,Function (biology) ,Developmental Biology ,Transcription Factors - Abstract
Continuous formation of somatic tissues in plants requires functional stem cell niches where undifferentiated cells are maintained. In Arabidopsis thaliana, PLETHORA (PLT) and SCARECROW (SCR) genes are outputs of apical–basal and radial patterning systems, and both are required for root stem cell specification and maintenance. The WUSCHEL-RELATED HOMEOBOX 5 (WOX5) gene is specifically expressed in and required for functions of a small group of root stem cell organizer cells, also called the quiescent center (QC). PLT and SCR are required for QC function, and their expression overlaps in the QC; however, how they specify the organizer has remained unknown. We show that PLT and SCR genetically and physically interact with plant-specific teosinte-branched cycloidea PCNA (TCP) transcription factors to specify the stem cell niche during embryogenesis and maintain organizer cells post-embryonically. PLT–TCP–SCR complexes converge on PLT-binding sites in the WOX5 promoter to induce expression.
- Published
- 2018
6. Mathematical Modeling and Experimental Validation of the Spatial Distribution of Boron in the Root of Arabidopsis thaliana Identify High Boron Accumulation in the Tip and Predict a Distinct Root Tip Uptake Function
- Author
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Micol De Ruvo, Naoyuki Sotta, Verônica A. Grieneisen, Takafumi Sato, Toru Fujiwara, Athanasius F. M. Marée, and Akie Shimotohno
- Subjects
inorganic chemicals ,Arabidopsis thaliana ,Physiology ,Diffusion ,Meristem ,Polar localization ,Arabidopsis ,chemistry.chemical_element ,Plant Science ,Transporter ,Models, Biological ,Cell wall ,Botany ,Computer Simulation ,Special Focus Issue – Regular Papers ,LA-ICP-MS ,Boron ,biology ,Arabidopsis Proteins ,Chemistry ,Lasers ,Spectrophotometry, Atomic ,Reproducibility of Results ,Biological Transport ,Cell Biology ,General Medicine ,biology.organism_classification ,Membrane ,Solubility ,Shoot ,Biophysics ,Mathematical modeling - Abstract
Boron, an essential micronutrient, is transported in roots of Arabidopsis thaliana mainly by two different types of transporters, BORs and NIPs (nodulin26-like intrinsic proteins). Both are plasma membrane localized, but have distinct transport properties and patterns of cell type-specific accumulation with different polar localizations, which are likely to affect boron distribution. Here, we used mathematical modeling and an experimental determination to address boron distributions in the root. A computational model of the root is created at the cellular level, describing the boron transporters as observed experimentally. Boron is allowed to diffuse into roots, in cells and cell walls, and to be transported over plasma membranes, reflecting the properties of the different transporters. The model predicts that a region around the quiescent center has a higher concentration of soluble boron than other portions. To evaluate this prediction experimentally, we determined the boron distribution in roots using laser ablation-inductivity coupled plasma-mass spectrometry. The analysis indicated that the boron concentration is highest near the tip and is lower in the more proximal region of the meristem zone, similar to the pattern of soluble boron distribution predicted by the model. Our model also predicts that upward boron flux does not continuously increase from the root tip toward the mature region, indicating that boron taken up in the root tip is not efficiently transported to shoots. This suggests that root tip-absorbed boron is probably used for local root growth, and that instead it is the more mature root regions which have a greater role in transporting boron toward the shoots.
- Published
- 2015
7. The PLETHORA Gene Regulatory Network Guides Growth and Cell Differentiation in Arabidopsis Roots
- Author
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Ben Scheres, Kenzo Nakamura, Gabino F. Sanchez-Perez, Renze Heidstra, Lidija Berke, Luca Santuari, Dongping Bao, Berend Snel, Inez Terpstra, Kenichiro Maeo, Maartje Gorte, Ari Pekka Mähönen, Ondřej Novák, Dick de Ridder, Edwin Cuppen, Akie Shimotohno, Marijn Luijten, Bas Rutjens, Wolfgang Lukowitz, Karin Ljung, Viola Willemsen, Ales Pencik, Ewart de Bruijn, Sebastiaan van Heesch, Kalika Prasad, Johanna L.P.M. Timmermans-Hereijgers, Sub Bioinformatics, and Theoretical Biology and Bioinformatics
- Subjects
0301 basic medicine ,congenital, hereditary, and neonatal diseases and abnormalities ,Bioinformatics ,Cellular differentiation ,Cell ,Gene regulatory network ,Arabidopsis ,Plant Developmental Biology ,Plant Science ,Biology ,Plant Roots ,03 medical and health sciences ,BIOS Applied Bioinformatics ,Gene Expression Regulation, Plant ,Bioinformatica ,medicine ,Journal Article ,Life Science ,Gene Regulatory Networks ,Transcription factor ,Research Articles ,Regulation of gene expression ,Cell growth ,Arabidopsis Proteins ,Cell Differentiation ,Cell Biology ,biology.organism_classification ,humanities ,Biosystematiek ,Cell biology ,030104 developmental biology ,medicine.anatomical_structure ,Biosystematics ,Stem cell ,EPS ,Transcription Factors - Abstract
Organ formation in animals and plants relies on precise control of cell state transitions to turn stem cell daughters into fully differentiated cells. In plants, cells cannot rearrange due to shared cell walls. Thus, differentiation progression and the accompanying cell expansion must be tightly coordinated across tissues. PLETHORA (PLT) transcription factor gradients are unique in their ability to guide the progression of cell differentiation at different positions in the growing Arabidopsis thaliana root, which contrasts with well-described transcription factor gradients in animals specifying distinct cell fates within an essentially static context. To understand the output of the PLT gradient, we studied the gene set transcriptionally controlled by PLTs. Our work reveals how the PLT gradient can regulate cell state by region-specific induction of cell proliferation genes and repression of differentiation. Moreover, PLT targets include major patterning genes and autoregulatory feedback components, enforcing their role as master regulators of organ development.
- Published
- 2016
8. Control of Cell Division and Transcription by Cyclin-dependent Kinase-activating Kinases in Plants
- Author
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Akie Shimotohno, Masaaki Umeda, and Masatoshi Yamaguchi
- Subjects
Cyclin-dependent kinase 1 ,Transcription, Genetic ,Physiology ,Cyclin-dependent kinase 2 ,Cyclin-dependent kinase 3 ,Cell Biology ,Plant Science ,General Medicine ,Plants ,Cell cycle ,Biology ,Cyclin-Dependent Kinases ,CDK-activating kinase ,Cell biology ,Phosphorylation cascade ,Biochemistry ,Cyclin-dependent kinase ,biology.protein ,Protein phosphorylation ,Cell Division ,Cyclin-Dependent Kinase-Activating Kinase - Abstract
Cyclin-dependent protein kinases (CDKs) play key roles in the progression of the cell cycle in eukaryotes. A CDK-activating kinase (CAK) catalyzes the phosphorylation of CDKs to activate their enzyme activity; thus, it is involved in activation of cell proliferation. In plants, two distinct classes of CAK have been identified; CDKD is functionally related to vertebrate-type CAKs, while CDKF is a plant-specific CAK having unique enzymatic characteristics. Recently, CDKF was shown to phosphorylate and activate CDKDs in Arabidopsis. This led to a proposal that CDKD and CDKF constitute a phosphorylation cascade that mediates environmental or hormonal signals to molecular machineries that control the cell cycle and transcription. In this review, we have summarized the biochemical features of plant CAKs and discussed the manner in which they diverge from animal and yeast orthologs. We have introduced several transgenic studies in which CAK genes were used as a tool to modify the CDK activity and to analyze cell division and differentiation during organ development.
- Published
- 2005
9. The Plant-Specific Kinase CDKF;1 Is Involved in Activating Phosphorylation of Cyclin-Dependent Kinase-Activating Kinases in Arabidopsis
- Author
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Akie Shimotohno, Chikage Umeda-Hara, Masaaki Umeda, Hirofumi Uchimiya, and Katerina Bisova
- Subjects
Cyclin H ,Insecta ,Macromolecular Substances ,Cyclin D ,Molecular Sequence Data ,Cyclin A ,Arabidopsis ,Saccharomyces cerevisiae ,Plant Science ,Protein Serine-Threonine Kinases ,Cyclin-dependent kinase ,Cyclins ,Schizosaccharomyces ,Animals ,Phosphorylation ,Cells, Cultured ,Research Articles ,Cyclin-dependent kinase 1 ,biology ,Arabidopsis Proteins ,Protoplasts ,Cell Biology ,Cyclin-Dependent Kinases ,Protein Structure, Tertiary ,Cell biology ,Enzyme Activation ,enzymes and coenzymes (carbohydrates) ,biology.protein ,Cyclin-dependent kinase complex ,Cyclin-dependent kinase 7 ,Protein Kinases ,Cyclin-Dependent Kinase-Activating Kinase ,Cyclin A2 - Abstract
Cyclin-dependent kinases (CDKs) play essential roles in coordinate control of cell cycle progression. Activation of CDKs requires interaction with specific cyclin partners and phosphorylation of their T-loops by CDK-activating kinases (CAKs). The Arabidopsis thaliana genome encodes four potential CAKs. CAK2At (CDKD;3) and CAK4At (CDKD;2) are closely related to the vertebrate CAK, CDK7/p40MO15; they interact with cyclin H and phosphorylate CDKs, as well as the C-terminal domain (CTD) of the largest subunit of RNA polymerase II. CAK1At (CDKF;1) shows cyclin H-independent CDK-kinase activity and can activate a heterologous CAK, Mcs6, in fission yeast. In Arabidopsis, CAK1At is a subunit of a protein complex of 130 kD, which phosphorylates the T-loop of CAK2At and CAK4At and activates the CTD-kinase activity of CAK4At in vitro and in root protoplasts. These results suggest that CAK1At is a novel CAK-activating kinase that modulates the activity of CAK2At and CAK4At, thereby controlling CDK activities and basal transcription in Arabidopsis.
- Published
- 2004
10. CDK Phosphorylation
- Author
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Akie Shimotohno and Masaaki Umeda
- Published
- 2007
11. Demonstration of the importance and usefulness of manipulating non-active-site residues in protein design
- Author
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Seiki Kuramitsu, Hiroyuki Kagamiyama, Takato Yano, Akie Shimotohno, and Shinya Oue
- Subjects
Models, Molecular ,Stereochemistry ,Protein design ,Mutagenesis (molecular biology technique) ,Context (language use) ,Biochemistry ,Catalysis ,Structure-Activity Relationship ,Protein structure ,Escherichia coli ,Aspartate Aminotransferases ,Binding site ,Amino Acids ,Molecular Biology ,Binding Sites ,biology ,Chemistry ,Active site ,General Medicine ,Protein engineering ,Directed evolution ,Protein Structure, Tertiary ,Kinetics ,Amino Acid Substitution ,Mutation ,biology.protein ,Mutagenesis, Site-Directed ,Thermodynamics ,Directed Molecular Evolution - Abstract
Do non-active-site residues participate in protein function in a more direct way than just by holding the static framework of the protein molecule? If so, how important are they? As a model to answer these questions, ATB17, which is a mutant of aspartate aminotransferase created by directed evolution, is an ideal system because it shows a 10(6)-fold increase in the catalytic efficiency for valine but most of its 17 mutated residues are non-active-site residues. To analyze the roles of the mutations in the altered function, we divided the mutations into four groups, namely, three clusters and the remainder, based on their locations in the three-dimensional structure. Mutants with various combinations of the clusters were constructed and analyzed, and the data were interpreted in the context of the structure-function relationship of this enzyme. Each cluster shows characteristic effects: for example, one cluster appears to enhance the catalytic efficiency by fixing the conformation of the enzyme to that of the substrate-bound form. The effects of the clusters are largely additive and independent of each other. The present results illustrate how a protein function is dramatically modified by the accumulation of many seemingly inert mutations of non-active-site residues.
- Published
- 2001
12. Mathematical Modeling and Experimental Validation of the Spatial Distribution of Boron in the Root of Arabidopsis thaliana Identify High Boron Accumulation in the Tip and Predict a Distinct Root Tip Uptake Function.
- Author
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Akie Shimotohno, Naoyuki Sotta, Takafumi Sato, De Ruvo, Micol, Marée, Athanasius F. M., Grieneisen, Verônica A., and Toru Fujiwara
- Subjects
- *
BORON , *ARABIDOPSIS thaliana , *PLANT root physiology , *BIOACCUMULATION in plants , *PLANT nutrients , *MICRONUTRIENTS , *MATHEMATICAL models , *PHYSIOLOGY - Abstract
Boron, an essential micronutrient, is transported in roots of Arabidopsis thaliana mainly by two different types of transporters, BORs and NIPs (nodulin26-like intrinsic proteins). Both are plasma membrane localized, but have distinct transport properties and patterns of cell type-specific accumulation with different polar localizations, which are likely to affect boron distribution. Here, we used mathematical modeling and an experimental determination to address boron distributions in the root. A computational model of the root is created at the cellular level, describing the boron transporters as observed experimentally. Boron is allowed to diffuse into roots, in cells and cell walls, and to be transported over plasma membranes, reflecting the properties of the different transporters. The model predicts that a region around the quiescent center has a higher concentration of soluble boron than other portions. To evaluate this prediction experimentally, we determined the boron distribution in roots using laser ablation-inductivity coupled plasmamass spectrometry. The analysis indicated that the boron concentration is highest near the tip and is lower in the more proximal region of the meristem zone, similar to the pattern of soluble boron distribution predicted by the model. Our model also predicts that upward boron flux does not continuously increase from the root tip toward the mature region, indicating that boron taken up in the root tip is not efficiently transported to shoots. This suggests that root tip-absorbed boron is probably used for local root growth, and that instead it is the more mature root regions which have a greater role in transporting boron toward the shoots. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
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13. Diverse phosphoregulatory mechanisms controlling cyclin-dependent kinase-activating kinases in Arabidopsis
- Author
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Jirong Huang, Norihiro Sakaguchi, Csaba Koncz, Hirofumi Uchimiya, Masaaki Umeda, Katerina Bisova, Akie Shimotohno, and Ryoko Ohno
- Subjects
Cyclin binding ,Cyclin H ,biology ,Kinase ,Cell Biology ,Plant Science ,CDK-activating kinase ,enzymes and coenzymes (carbohydrates) ,Wee1 ,Biochemistry ,Cyclin-dependent kinase ,Genetics ,biology.protein ,Phosphorylation ,Kinase activity - Abstract
*Summary For the full activation of cyclin-dependent kinases (CDKs), not only cyclin binding but also phosphorylation of a threonine (Thr) residue within the T-loop is required. This phosphorylation is catalyzed by CDK-activating kinases (CAKs). In Arabidopsis three D-type CDK genes (CDKD;1–CDKD;3) encode vertebrate-type CAK orthologues, of which CDKD;2 exhibits high phosphorylation activity towards the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II. Here, we show that CDKD;2 forms a stable complex with cyclin H and is downregulated by the phosphorylation of the ATP-binding site by WEE1 kinase. A knockout mutant of CDKD;3, which has a higher CDK kinase activity, displayed no defect in plant development. Instead, another type of CAK – CDKF;1 – exhibited significant activity towards CDKA;1 in Arabidopsis root protoplasts, and the activity was dependent on the T-loop phosphorylation of CDKF;1. We propose that two distinct types of CAK, namely CDKF;1 and CDKD;2, play a major role in CDK and CTD phosphorylation, respectively, in Arabidopsis.
- Published
- 2006
14. Differential phosphorylation activities of CDK-activating kinases in Arabidopsis thaliana
- Author
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Masatoshi Yamaguchi, Masaaki Umeda, Satoko Matsubayashi, Akie Shimotohno, and Hirofumi Uchimiya
- Subjects
Arabidopsis thaliana ,Molecular Sequence Data ,Arabidopsis ,Biophysics ,RNA polymerase II ,Cell cycle ,Biochemistry ,environment and public health ,CDK-activating kinase ,Structural Biology ,Cyclin-dependent kinase ,Transcription (biology) ,Yeasts ,Genetics ,Amino Acid Sequence ,Phosphorylation ,Molecular Biology ,Cells, Cultured ,biology ,Arabidopsis Proteins ,Kinase ,Genetic Complementation Test ,Cell Biology ,biology.organism_classification ,Cyclin-Dependent Kinases ,enzymes and coenzymes (carbohydrates) ,biology.protein ,RNA Polymerase II ,Cyclin-dependent kinase 7 ,Protein Kinases ,Transcription ,Cyclin-Dependent Kinase-Activating Kinase - Abstract
Activation of cyclin-dependent kinases (CDKs) requires phosphorylation of a threonine residue within the T-loop by a CDK-activating kinase (CAK). Here we isolated an Arabidopsis cDNA (CAK4At) whose predicted product shows a high similarity to vertebrate CDK7/p40MO15. Northern blot analysis showed that expressions of the four Arabidopsis CAKs (CAK1At–CAK4At) were not dependent on cell division. CAK2At- and CAK4At-immunoprecipitates of Arabidopsis crude extract phosphorylated CDK and the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II with different preferences. These results suggest the existence of differential mechanisms in Arabidopsis that control CDK and CTD phosphorylation by multiple CAKs.
- Full Text
- View/download PDF
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