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Article ; Online: Comprehensive analysis of downstream transcriptomic features in the competitive relationships between BEH3 and other BES/BZR transcription factors.

Furuya, Tomoyuki / Kondo, Yuki

2023 Volume 98, Issue 2, Page(s) 89–92

Abstract: Members of a plant-specific BES/BZR transcription factor (TF) family including BRI1-EMS-SUPPRESSOR 1 (BES1) and BRASSINAZOLE-RESISTANT 1 (BZR1) regulate various developmental processes and environmental responses. Recently, we reported that BES1/BZR1 ... ...

Abstract	Members of a plant-specific BES/BZR transcription factor (TF) family including BRI1-EMS-SUPPRESSOR 1 (BES1) and BRASSINAZOLE-RESISTANT 1 (BZR1) regulate various developmental processes and environmental responses. Recently, we reported that BES1/BZR1 Homolog 3 (BEH3) exhibited a competitive effect toward other BES/BZR TFs. In this study, we analyzed transcriptome profiles in BEH3-overexpressing plants and compared them with those of BES1 and BZR1 double gain-of-function mutants. We identified 46 differentially expressed genes (DEGs), which were downregulated in the gain-of-function mutants of BES1 and BZR1 but upregulated upon BEH3 overexpression. In these DEGs, putative BES1 and BZR1 direct-targeted genes were highly enriched. In addition, these DEGs contained not only known brassinosteroid biosynthetic enzymes, but also some NAC TFs, which negatively regulate brassinosteroid-inactivating enzymes. Moreover, the iron sensor and the iron-deficient response-related bHLH TFs were also included. Taken together, our findings indicate that a competitive relationship between BEH3 and other BES/BZR TFs exists in various BES/BZR binding target genes.
MeSH term(s)	Transcription Factors/genetics ; Transcription Factors/metabolism ; DNA-Binding Proteins/genetics ; Transcriptome ; Brassinosteroids/metabolism ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Arabidopsis/genetics ; Arabidopsis/metabolism ; Gene Expression Regulation, Plant
Chemical Substances	Transcription Factors ; DNA-Binding Proteins ; Brassinosteroids ; Arabidopsis Proteins ; BES (10191-18-1)
Language	English
Publishing date	2023-06-16
Publishing country	Japan
Document type	Journal Article
ZDB-ID	1323536-9
ISSN	1880-5779 ; 1341-7568
ISSN (online)	1880-5779
ISSN	1341-7568
DOI	10.1266/ggs.23-00029
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Article ; Online: Multiple roles of brassinosteroid signaling in vascular development.

Furuya, Tomoyuki / Ohashi-Ito, Kyoko / Kondo, Yuki

Plant & cell physiology

2024

Abstract: Brassinosteroids (BRs) are plant steroid hormones that control growth and stress responses. In the context of development, BRs play diverse roles in controlling cell differentiation and tissue patterning. The vascular system, which is essential for ... ...

Abstract	Brassinosteroids (BRs) are plant steroid hormones that control growth and stress responses. In the context of development, BRs play diverse roles in controlling cell differentiation and tissue patterning. The vascular system, which is essential for transporting water and nutrients throughout the plant body, initially establishes a tissue pattern during primary development and then dramatically increases the number of vascular cells during secondary development. This complex developmental process is properly regulated by a network consisting of various hormonal signalling pathways. Genetic studies have revealed that mutants defective in BR biosynthesis or the BR signalling cascade exhibit a multifaceted vascular development phenotype. Furthermore, BR crosstalk with other plant hormones, including peptide hormones, coordinately regulates vascular development. Recently, the involvement of BR in vascular development, especially in xylem differentiation, has also been suggested in plant species other than the model plant Arabidopsis thaliana. In this review, we briefly summarize the recent findings on the roles of BR in primary and secondary vascular development in Arabidopsis and other species.
Language	English
Publishing date	2024-04-08
Publishing country	Japan
Document type	Journal Article
ZDB-ID	208907-5
ISSN	1471-9053 ; 0032-0781
ISSN (online)	1471-9053
ISSN	0032-0781
DOI	10.1093/pcp/pcae037
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Article ; Online: Molecular Mechanisms Underlying the Establishment and Maintenance of Vascular Stem Cells in Arabidopsis thaliana.

Shimadzu, Shunji / Furuya, Tomoyuki / Kondo, Yuki

Plant & cell physiology

2022 Volume 64, Issue 3, Page(s) 274–283

Abstract: The vascular system plays pivotal roles in transporting water and nutrients throughout the plant body. Primary vasculature is established as a continuous strand, which subsequently initiates secondary growth through cell division. Key factors regulating ... ...

Abstract	The vascular system plays pivotal roles in transporting water and nutrients throughout the plant body. Primary vasculature is established as a continuous strand, which subsequently initiates secondary growth through cell division. Key factors regulating primary and secondary vascular developments have been identified in numerous studies, and the regulatory networks including these factors have been elucidated through omics-based approaches. However, the vascular system is composed of a variety of cells such as xylem and phloem cells, which are commonly generated from vascular stem cells. In addition, the vasculature is located deep inside the plant body, which makes it difficult to investigate the vascular development while distinguishing between vascular stem cells and developing xylem and phloem cells. Recent technical advances in the tissue-clearing method, RNA-seq analysis and tissue culture system overcome these problems by enabling the cell-type-specific analysis during vascular development, especially with a special focus on stem cells. In this review, we summarize the recent findings on the establishment and maintenance of vascular stem cells.
MeSH term(s)	Arabidopsis ; Arabidopsis Proteins/metabolism ; Cell Division ; Stem Cells/metabolism ; Phloem ; Xylem ; Gene Expression Regulation, Plant
Chemical Substances	Arabidopsis Proteins
Language	English
Publishing date	2022-11-21
Publishing country	Japan
Document type	Review ; Journal Article
ZDB-ID	208907-5
ISSN	1471-9053 ; 0032-0781
ISSN (online)	1471-9053
ISSN	0032-0781
DOI	10.1093/pcp/pcac161
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Article ; Online: Spatio-temporal imaging of cell fate dynamics in single plant cells using luminescence microscope.

Shimadzu, Shunji / Furuya, Tomoyuki / Ozawa, Yasuko / Fukuda, Hiroo / Kondo, Yuki

Quantitative plant biology

2022 Volume 3, Page(s) e15

Abstract: Stem cell fates are spatio-temporally regulated during plant development. Time-lapse imaging of fluorescence reporters is the most widely used method for spatio-temporal analysis of biological processes. However, excitation light for imaging fluorescence ...

Abstract	Stem cell fates are spatio-temporally regulated during plant development. Time-lapse imaging of fluorescence reporters is the most widely used method for spatio-temporal analysis of biological processes. However, excitation light for imaging fluorescence reporters causes autofluorescence and photobleaching. Unlike fluorescence reporters, luminescence proteins do not require excitation light, and therefore offer an alternative reporter for long-term and quantitative spatio-temporal analysis. We established an imaging system for luciferase, which enabled monitoring cell fate marker dynamics during vascular development in a vascular cell induction system called VISUAL. Single cells expressing the cambium marker,
Language	English
Publishing date	2022-07-18
Publishing country	England
Document type	Journal Article
ISSN	2632-8828
ISSN (online)	2632-8828
DOI	10.1017/qpb.2022.12
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Article: A glycogen synthase kinase 3-like kinase MpGSK regulates cell differentiation in

Furuya, Tomoyuki / Nishihama, Ryuichi / Ishizaki, Kimitsune / Kohchi, Takayuki / Fukuda, Hiroo / Kondo, Yuki

Plant biotechnology (Tokyo, Japan)

2022 Volume 39, Issue 1, Page(s) 65–72

Abstract: Plants precisely coordinate the balance between cell proliferation and differentiation to ensure the continuous development. ... ...

Abstract	Plants precisely coordinate the balance between cell proliferation and differentiation to ensure the continuous development. In
Language	English
Publishing date	2022-06-21
Publishing country	Japan
Document type	Journal Article
ZDB-ID	2210142-1
ISSN	1347-6114 ; 1342-4580
ISSN (online)	1347-6114
ISSN	1342-4580
DOI	10.5511/plantbiotechnology.21.1219a
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Article ; Online: Protein Kinase MpYAK1 Is Involved in Meristematic Cell Proliferation, Reproductive Phase Change and Nutrient Signaling in the Liverwort Marchantia polymorpha.

Shinkawa, Haruka / Kajikawa, Masataka / Furuya, Tomoyuki / Nishihama, Ryuichi / Tsukaya, Hirokazu / Kohchi, Takayuki / Fukuzawa, Hideya

Plant & cell physiology

2022 Volume 63, Issue 8, Page(s) 1063–1077

Abstract: Plant growth and development are regulated by environmental factors, including nutrient availability and light conditions, via endogenous genetic signaling pathways. Phosphorylation-dependent protein modification plays a major role in the regulation of ... ...

Abstract	Plant growth and development are regulated by environmental factors, including nutrient availability and light conditions, via endogenous genetic signaling pathways. Phosphorylation-dependent protein modification plays a major role in the regulation of cell proliferation in stress conditions, and several protein kinases have been shown to function in response to nutritional status, including dual-specificity tyrosine phosphorylation-regulated kinases (DYRKs). Although DYRKs are widely conserved in eukaryotes, the physiological functions of DYRKs in land plants are still to be elucidated. In the liverwort Marchantia polymorpha, a model bryophyte, four putative genes encoding DYRK homologous proteins, each of which belongs to the subfamily yet another kinase 1 (Yak1), plant-specific DYRK, DYRK2, or pre-mRNA processing protein 4 kinase, were identified. MpYAK1-defective male and female mutant lines generated by the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9) system showed smaller sizes of thalli than did the wild-type plants and repressed cell divisions in the apical notch regions. The Mpyak1 mutants developed rhizoids from gemmae in the gemma cup before release. The Mpyak1 lines developed sexual organs even in non-inductive short-day photoperiod conditions supplemented with far-red light. In nitrogen (N)-deficient conditions, rhizoid elongation was inhibited in the Mpyak1 mutants. In conditions of aeration with 0.08% CO2 (v/v) and N depletion, Mpyak1 mutants accumulated higher levels of sucrose and lower levels of starch compared to the wild type. Transcriptomic analyses revealed that the expression of peroxidase genes was differentially affected by MpYAK1. These results suggest that MpYAK1 is involved in the maintenance of plant growth and developmental responses to light conditions and nutrient signaling.
MeSH term(s)	Cell Division ; Marchantia/metabolism ; Nutrients ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Protein Kinases/metabolism
Chemical Substances	Plant Proteins ; Protein Kinases (EC 2.7.-)
Language	English
Publishing date	2022-06-08
Publishing country	Japan
Document type	Journal Article
ZDB-ID	208907-5
ISSN	1471-9053 ; 0032-0781
ISSN (online)	1471-9053
ISSN	0032-0781
DOI	10.1093/pcp/pcac076
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Article ; Online: Sucrose Signaling Contributes to the Maintenance of Vascular Cambium by Inhibiting Cell Differentiation.

Narutaki, Aoi / Kahar, Prihardi / Shimadzu, Shunji / Maeda, Shota / Furuya, Tomoyuki / Ishizaki, Kimitsune / Fukaki, Hidehiro / Ogino, Chiaki / Kondo, Yuki

Plant & cell physiology

2023 Volume 64, Issue 12, Page(s) 1511–1522

Abstract: Plants produce sugars by photosynthesis and use them for growth and development. Sugars are transported from source-to-sink organs via the phloem in the vasculature. It is well known that vascular development is precisely controlled by plant hormones and ...

Abstract	Plants produce sugars by photosynthesis and use them for growth and development. Sugars are transported from source-to-sink organs via the phloem in the vasculature. It is well known that vascular development is precisely controlled by plant hormones and peptide hormones. However, the role of sugars in the regulation of vascular development is poorly understood. In this study, we examined the effects of sugars on vascular cell differentiation using a vascular cell induction system named 'Vascular Cell Induction Culture System Using Arabidopsis Leaves' (VISUAL). We found that sucrose has the strongest inhibitory effect on xylem differentiation, among several types of sugars. Transcriptome analysis revealed that sucrose suppresses xylem and phloem differentiation in cambial cells. Physiological and genetic analyses suggested that sucrose might function through the BRI1-EMS-SUPPRESSOR1 transcription factor, which is the central regulator of vascular cell differentiation. Conditional overexpression of cytosolic invertase led to a decrease in the number of cambium layers due to an imbalance between cell division and differentiation. Taken together, our results suggest that sucrose potentially acts as a signal that integrates environmental conditions with the developmental program.
MeSH term(s)	Cambium/genetics ; Cambium/metabolism ; Cell Differentiation/genetics ; Arabidopsis/metabolism ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Phloem/metabolism ; Xylem/metabolism ; Sugars/metabolism
Chemical Substances	Arabidopsis Proteins ; Sugars
Language	English
Publishing date	2023-04-29
Publishing country	Japan
Document type	Journal Article
ZDB-ID	208907-5
ISSN	1471-9053 ; 0032-0781
ISSN (online)	1471-9053
ISSN	0032-0781
DOI	10.1093/pcp/pcad039
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Article: A plant-specific DYRK kinase DYRKP coordinates cell morphology in Marchantia polymorpha

Furuya, Tomoyuki / Shinkawa, Haruka / Kajikawa, Masataka / Nishihama, Ryuichi / Kohchi, Takayuki / Fukuzawa, Hideya / Tsukaya, Hirokazu

Journal of plant research. 2021 Nov., v. 134, no. 6

2021

Abstract: Dual-specificity tyrosine phosphorylation-regulated kinases (DYRKs) are activated via the auto-phosphorylation of conserved tyrosine residues in their activation loop during protein translation, and they then phosphorylate serine/threonine residues on ... ...

Abstract	Dual-specificity tyrosine phosphorylation-regulated kinases (DYRKs) are activated via the auto-phosphorylation of conserved tyrosine residues in their activation loop during protein translation, and they then phosphorylate serine/threonine residues on substrates. The DYRK family is widely conserved in eukaryotes and is composed of six subgroups. In plant lineages, DYRK homologs are classified into four subgroups, DYRK2s, yet another kinase1s, pre-mRNA processing factor 4 kinases, and DYRKPs. Only the DYRKP subgroup is plant-specific and has been identified in a wide array of plant lineages, including land plants and green algae. It has been suggested that in Arabidopsis thaliana DYRKPs are involved in the regulation of centripetal nuclear positioning induced by dark light conditions. However, the molecular functions, such as kinase activity and the developmental and physiological roles of DYRKPs are poorly understood. Here, we focused on a sole DYRKP ortholog in the model bryophyte, Marchantia polymorpha, MpDYRKP. MpDYRKP has a highly conserved kinase domain located in the C-terminal region and shares common sequence motifs in the N-terminal region with other DYRKP members. To identify the roles of MpDYRKP in M. polymorpha, we generated loss-of-function Mpdyrkp mutants via genome editing. Mpdyrkp mutants exhibited abnormal, shrunken morphologies with less flattening in their vegetative plant bodies, thalli, and male reproductive organs, antheridial receptacles. The surfaces of the thalli in the Mpdyrkp mutants appeared uneven and disordered. Moreover, their epidermal cells were drastically altered to a narrower shape when compared to the wild type. These results suggest that MpDYRKP acts as a morphological regulator, which contributes to orderly tissue morphogenesis via the regulation of cell shape.
Keywords	Arabidopsis thaliana ; Bryophyta ; Marchantia polymorpha ; cell structures ; eukaryotic cells ; genome ; loss-of-function mutation ; males ; morphogenesis ; phosphotransferases (kinases) ; research ; serine ; thallus ; threonine ; tyrosine
Language	English
Dates of publication	2021-11
Size	p. 1265-1277.
Publishing place	Springer Singapore
Document type	Article
ZDB-ID	2077362-6
ISSN	1618-0860 ; 0918-9440
ISSN (online)	1618-0860
ISSN	0918-9440
DOI	10.1007/s10265-021-01345-w
Database	NAL-Catalogue (AGRICOLA)

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Article: A Method for Evaluating Three-Dimensional Morphological Features: A Case Study Using

Furuya, Tomoyuki / Kimori, Yoshitaka / Tsukaya, Hirokazu

Frontiers in plant science

2019 Volume 10, Page(s) 1214

Abstract: The description and evaluation of morphological features are essential to many biological studies. Bioimaging and quantification methods have been developed to analyze the morphological features of plants. However, efficient three-dimensional (3D) ... ...

Abstract	The description and evaluation of morphological features are essential to many biological studies. Bioimaging and quantification methods have been developed to analyze the morphological features of plants. However, efficient three-dimensional (3D) imaging and its quantification are still under development, particularly for studies of plant morphology, due to complex organ structure with great flexibility among individuals with the same genotype. In this study, we propose a new approach that combines a 3D imaging technique using micro-computed tomography and a mathematical image-processing method to describe 3D morphological features. As an example, we applied this method to
Language	English
Publishing date	2019-10-02
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2711035-7
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2019.01214
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Article ; Online: A plant-specific DYRK kinase DYRKP coordinates cell morphology in Marchantia polymorpha.

Furuya, Tomoyuki / Shinkawa, Haruka / Kajikawa, Masataka / Nishihama, Ryuichi / Kohchi, Takayuki / Fukuzawa, Hideya / Tsukaya, Hirokazu

Journal of plant research

2021 Volume 134, Issue 6, Page(s) 1265–1277

Abstract	Dual-specificity tyrosine phosphorylation-regulated kinases (DYRKs) are activated via the auto-phosphorylation of conserved tyrosine residues in their activation loop during protein translation, and they then phosphorylate serine/threonine residues on substrates. The DYRK family is widely conserved in eukaryotes and is composed of six subgroups. In plant lineages, DYRK homologs are classified into four subgroups, DYRK2s, yet another kinase1s, pre-mRNA processing factor 4 kinases, and DYRKPs. Only the DYRKP subgroup is plant-specific and has been identified in a wide array of plant lineages, including land plants and green algae. It has been suggested that in Arabidopsis thaliana DYRKPs are involved in the regulation of centripetal nuclear positioning induced by dark light conditions. However, the molecular functions, such as kinase activity and the developmental and physiological roles of DYRKPs are poorly understood. Here, we focused on a sole DYRKP ortholog in the model bryophyte, Marchantia polymorpha, MpDYRKP. MpDYRKP has a highly conserved kinase domain located in the C-terminal region and shares common sequence motifs in the N-terminal region with other DYRKP members. To identify the roles of MpDYRKP in M. polymorpha, we generated loss-of-function Mpdyrkp mutants via genome editing. Mpdyrkp mutants exhibited abnormal, shrunken morphologies with less flattening in their vegetative plant bodies, thalli, and male reproductive organs, antheridial receptacles. The surfaces of the thalli in the Mpdyrkp mutants appeared uneven and disordered. Moreover, their epidermal cells were drastically altered to a narrower shape when compared to the wild type. These results suggest that MpDYRKP acts as a morphological regulator, which contributes to orderly tissue morphogenesis via the regulation of cell shape.
MeSH term(s)	Arabidopsis/genetics ; Marchantia/genetics ; Protein Serine-Threonine Kinases/genetics ; Protein-Tyrosine Kinases/genetics ; Dyrk Kinases
Chemical Substances	Protein-Tyrosine Kinases (EC 2.7.10.1) ; Protein Serine-Threonine Kinases (EC 2.7.11.1)
Language	English
Publishing date	2021-09-21
Publishing country	Japan
Document type	Journal Article
ZDB-ID	2077362-6
ISSN	1618-0860 ; 0918-9440
ISSN (online)	1618-0860
ISSN	0918-9440
DOI	10.1007/s10265-021-01345-w
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