Genomes and Genes
Experts and Doctors on arabidopsis in Yokohama, Kanagawa, Japan
Locale: Yokohama, Kanagawa, Japan
Publications186 found, 100 shown here
- Kondou Y, Nakazawa M, Kawashima M, Ichikawa T, Yoshizumi T, Suzuki K, et al. RETARDED GROWTH OF EMBRYO1, a new basic helix-loop-helix protein, expresses in endosperm to control embryo growth. Plant Physiol. 2008;147:1924-35 pubmed publisher..These data suggest that RGE1 expression in the endosperm at the heart stage of embryo development plays an important role in controlling embryo growth. ..
- Kaminuma E, Yoshizumi T, Wada T, Matsui M, Toyoda T. Quantitative analysis of heterogeneous spatial distribution of Arabidopsis leaf trichomes using micro X-ray computed tomography. Plant J. 2008;56:470-82 pubmed publisher..On the other hand, CPC does affect trichome growth and developmental progression. Hence, quantitative phenotyping based on microCT enables precise phenotypic description for elucidation of gene control in morphological mutants. ..
- Kanno Y, Jikumaru Y, Hanada A, Nambara E, Abrams S, Kamiya Y, et al. Comprehensive hormone profiling in developing Arabidopsis seeds: examination of the site of ABA biosynthesis, ABA transport and hormone interactions. Plant Cell Physiol. 2010;51:1988-2001 pubmed publisher..These data suggest that ABA metabolism depends on developmental stages and tissues, and that ABA interacts with other hormones to regulate seed developmental processes. ..
- Murayama M, Hayashi S, Nishimura N, Ishide M, Kobayashi K, Yagi Y, et al. Isolation of Arabidopsis ahg11, a weak ABA hypersensitive mutant defective in nad4 RNA editing. J Exp Bot. 2012;63:5301-10 pubmed publisher..Presumably, partial impairment of mitochondrial function caused by an amino acid conversion in one of the complex I components induces redox imbalance which, in turn, confers an abnormal response to the plant hormone. ..
- Magome H, Nomura T, Hanada A, Takeda Kamiya N, Ohnishi T, Shinma Y, et al. CYP714B1 and CYP714B2 encode gibberellin 13-oxidases that reduce gibberellin activity in rice. Proc Natl Acad Sci U S A. 2013;110:1947-52 pubmed publisher..Our results suggest that GA 13-oxidases play a role in fine-tuning plant growth by decreasing GA bioactivity in rice and that they also participate in GA homeostasis...
- Hong J, Takeshi Y, Kondou Y, Schachtman D, Matsui M, Shin R. Identification and characterization of transcription factors regulating Arabidopsis HAK5. Plant Cell Physiol. 2013;54:1478-90 pubmed publisher..These results indicate that at least these four transcription factors can bind to the HAK5 promoter in response to K limitation and activate HAK5 expression, thus allowing plants to adapt to nutrient stress...
- Morioka R, Kanaya S, Hirai M, Yano M, Ogasawara N, Saito K. Predicting state transitions in the transcriptome and metabolome using a linear dynamical system model. BMC Bioinformatics. 2007;8:343 pubmed..This general approach can be applied to any time-series data profile from which one wishes to identify elements responsible for state transitions, such as rapid environmental adaptation by an organism. ..
- Nishiyama R, Le D, Watanabe Y, Matsui A, Tanaka M, Seki M, et al. Transcriptome analyses of a salt-tolerant cytokinin-deficient mutant reveal differential regulation of salt stress response by cytokinin deficiency. PLoS ONE. 2012;7:e32124 pubmed publisher..This study highlights the impact of CK regulation on the well-known stress-responsive signaling pathways, which regulate plant adaptation to high salinity as well as other environmental stresses. ..
- Ohama N, Kusakabe K, Mizoi J, Zhao H, Kidokoro S, Koizumi S, et al. The Transcriptional Cascade in the Heat Stress Response of Arabidopsis Is Strictly Regulated at the Level of Transcription Factor Expression. Plant Cell. 2016;28:181-201 pubmed publisher..These complex regulatory mechanisms related to the transcriptional cascade may enable plants to respond resiliently to various heat stress conditions. ..
- Takahashi N, Kuroda H, Kuromori T, Hirayama T, Seki M, Shinozaki K, et al. Expression and interaction analysis of Arabidopsis Skp1-related genes. Plant Cell Physiol. 2004;45:83-91 pubmed..Both histochemical and RT-PCR analysis of eight ASK genes expression revealed unique expression patterns for the respective genes. ..
- Yoshizumi T, Tsumoto Y, Takiguchi T, Nagata N, Yamamoto Y, Kawashima M, et al. Increased level of polyploidy1, a conserved repressor of CYCLINA2 transcription, controls endoreduplication in Arabidopsis. Plant Cell. 2006;18:2452-68 pubmed..Furthermore, loss of CYCA2;1 expression induces an increase in polyploidy in Arabidopsis. We demonstrate that this protein regulates endoreduplication through control of CYCA2 expression in Arabidopsis. ..
- Okamoto M, Tatematsu K, Matsui A, Morosawa T, Ishida J, Tanaka M, et al. Genome-wide analysis of endogenous abscisic acid-mediated transcription in dry and imbibed seeds of Arabidopsis using tiling arrays. Plant J. 2010;62:39-51 pubmed publisher..Our results suggest that transcription in Arabidopsis seeds is more complex and dynamic than previously thought. ..
- Stotz H, Jikumaru Y, Shimada Y, Sasaki E, Stingl N, Mueller M, et al. Jasmonate-dependent and COI1-independent defense responses against Sclerotinia sclerotiorum in Arabidopsis thaliana: auxin is part of COI1-independent defense signaling. Plant Cell Physiol. 2011;52:1941-56 pubmed publisher..Hypersusceptibility of an axr1 mutant to S. sclerotiorum confirmed the contribution of auxin action to defense responses against this fungal pathogen. ..
- Sasaki Sekimoto Y, Jikumaru Y, Obayashi T, Saito H, Masuda S, Kamiya Y, et al. Basic helix-loop-helix transcription factors JASMONATE-ASSOCIATED MYC2-LIKE1 (JAM1), JAM2, and JAM3 are negative regulators of jasmonate responses in Arabidopsis. Plant Physiol. 2013;163:291-304 pubmed publisher..These results show that JAMs negatively regulate the JA responses in a manner that is mostly antagonistic to MYC2...
- Rymen B, Kawamura A, Schäfer S, Breuer C, Iwase A, Shibata M, et al. ABA Suppresses Root Hair Growth via the OBP4 Transcriptional Regulator. Plant Physiol. 2017;173:1750-1762 pubmed publisher..Taken together, our results suggest that OBP4-mediated transcriptional repression of RSL2 contributes to the ABA-dependent inhibition of root hair growth in Arabidopsis. ..
- Kataoka T, Hayashi N, Yamaya T, Takahashi H. Root-to-shoot transport of sulfate in Arabidopsis. Evidence for the role of SULTR3;5 as a component of low-affinity sulfate transport system in the root vasculature. Plant Physiol. 2004;136:4198-204 pubmed
- Yoshida T, Nishimura N, Kitahata N, Kuromori T, Ito T, Asami T, et al. ABA-hypersensitive germination3 encodes a protein phosphatase 2C (AtPP2CA) that strongly regulates abscisic acid signaling during germination among Arabidopsis protein phosphatase 2Cs. Plant Physiol. 2006;140:115-26 pubmed
- Nishimura N, Kitahata N, Seki M, Narusaka Y, Narusaka M, Kuromori T, et al. Analysis of ABA hypersensitive germination2 revealed the pivotal functions of PARN in stress response in Arabidopsis. Plant J. 2005;44:972-84 pubmed..These results suggest that both upregulation and downregulation of gene expression by the mRNA-destabilizing activity of AtPARN are crucial for proper ABA, salicylic acid and stress responses. ..
- Oono Y, Seki M, Satou M, Iida K, Akiyama K, Sakurai T, et al. Monitoring expression profiles of Arabidopsis genes during cold acclimation and deacclimation using DNA microarrays. Funct Integr Genomics. 2006;6:212-34 pubmed..We compared genes that are regulated during deacclimation with those regulated during rehydration after dehydration to discuss the similarity and difference of each recovery process. ..
- Motohashi K, Hisabori T. HCF164 receives reducing equivalents from stromal thioredoxin across the thylakoid membrane and mediates reduction of target proteins in the thylakoid lumen. J Biol Chem. 2006;281:35039-47 pubmed..The data presented here suggest that HCF164 serves as an important transducer of reducing equivalents to proteins in the thylakoid lumen. ..
- Yonekura Sakakibara K, Tohge T, Niida R, Saito K. Identification of a flavonol 7-O-rhamnosyltransferase gene determining flavonoid pattern in Arabidopsis by transcriptome coexpression analysis and reverse genetics. J Biol Chem. 2007;282:14932-41 pubmed..Our present study demonstrates that the integration of transcriptome coexpression analysis with a reverse genetic approach is a versatile tool for understanding a multigene family of a metabolic pathway in Arabidopsis. ..
- Hirai M, Sugiyama K, Sawada Y, Tohge T, Obayashi T, Suzuki A, et al. Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. Proc Natl Acad Sci U S A. 2007;104:6478-83 pubmed..A working model for regulation of GSL production involving these genes, renamed Production of Methionine-Derived Glucosinolate (PMG) 1 and 2, are postulated. ..
- Tominaga R, Iwata M, Okada K, Wada T. Functional analysis of the epidermal-specific MYB genes CAPRICE and WEREWOLF in Arabidopsis. Plant Cell. 2007;19:2264-77 pubmed..Furthermore, we showed by gel mobility shift assays that WER chimera proteins do not bind to the GL2 promoter region. However, a CPC chimera protein, which harbors the WER R3 motif, still binds to the GL2 promoter region. ..
- Yoshimoto N, Inoue E, Watanabe Takahashi A, Saito K, Takahashi H. Posttranscriptional regulation of high-affinity sulfate transporters in Arabidopsis by sulfur nutrition. Plant Physiol. 2007;145:378-88 pubmed..This study suggested the importance of root-specific and sulfur deficiency-inducible accumulation of SULTR1;1 and SULTR1;2 sulfate transporter proteins for the acquisition of sulfate from low-sulfur environment. ..
- Okamoto M, Tanaka Y, Abrams S, Kamiya Y, Seki M, Nambara E. High humidity induces abscisic acid 8'-hydroxylase in stomata and vasculature to regulate local and systemic abscisic acid responses in Arabidopsis. Plant Physiol. 2009;149:825-34 pubmed publisher..Taken together, ABA catabolism in both vascular tissues and guard cells participates in the systemic ABA action that controls stomatal movement in response to high humidity. ..
- Sawada Y, Toyooka K, Kuwahara A, Sakata A, Nagano M, Saito K, et al. Arabidopsis bile acid:sodium symporter family protein 5 is involved in methionine-derived glucosinolate biosynthesis. Plant Cell Physiol. 2009;50:1579-86 pubmed publisher..These results supported the idea that BASS5 plays a role in translocation across the chloroplast membranes of the biosynthetic intermediates of Met-GSLs. ..
- Ishida T, Fujiwara S, Miura K, Stacey N, Yoshimura M, Schneider K, et al. SUMO E3 ligase HIGH PLOIDY2 regulates endocycle onset and meristem maintenance in Arabidopsis. Plant Cell. 2009;21:2284-97 pubmed publisher..These results establish that HPY2-mediated sumoylation modulates the cell cycle progression and meristem development in the PLT-dependent signaling pathway...
- Diaz C, Kusano M, Sulpice R, Araki M, Redestig H, Saito K, et al. Determining novel functions of Arabidopsis 14-3-3 proteins in central metabolic processes. BMC Syst Biol. 2011;5:192 pubmed publisher..Taken together, our findings indicate that 14-3-3 proteins play roles as crucial tuners of multiple primary metabolic processes including TCA cycle and the shikimate pathway. ..
- Nam Y, Tran L, Kojima M, Sakakibara H, Nishiyama R, Shin R. Regulatory roles of cytokinins and cytokinin signaling in response to potassium deficiency in Arabidopsis. PLoS ONE. 2012;7:e47797 pubmed publisher..From these results, we conclude that a reduction in CK levels subsequently allows fast and effective stimulation of low K-induced ROS accumulation, root hair growth and HAK5 expression, leading to plant adaptation to low K conditions. ..
- ..Great promise is seen in metabolic quantitative loci analysis in major crops such as rice and tomato, and identification of novel genes involved in the biosynthesis of bioactive specialized metabolites in medicinal plants. ..
- Harashima H, Sugimoto K. Integration of developmental and environmental signals into cell proliferation and differentiation through RETINOBLASTOMA-RELATED 1. Curr Opin Plant Biol. 2016;29:95-103 pubmed publisher..In this review we will discuss recent findings on cell cycle regulation, highlighting the emerging roles of RBR1 as a key integrator of internal differentiation cues and external stimuli into the cell cycle machinery. ..
- Nakazawa M, Ichikawa T, Ishikawa A, Kobayashi H, Tsuhara Y, Kawashima M, et al. Activation tagging, a novel tool to dissect the functions of a gene family. Plant J. 2003;34:741-50 pubmed..The pck1-D mutants have lost apical dominance, have epinastic leaves and are sterile. These results strongly suggest that activation tagging is a powerful mutant-mining tool especially for genes that make up a gene family. ..
- Tominaga R, Iwata M, Sano R, Inoue K, Okada K, Wada T. Arabidopsis CAPRICE-LIKE MYB 3 (CPL3) controls endoreduplication and flowering development in addition to trichome and root hair formation. Development. 2008;135:1335-45 pubmed publisher..Notably, the CPL3 gene has pleiotropic effects on flowering development, epidermal cell size and trichome branching through the regulation of endoreduplication. ..
- Yamaguchi M, Goué N, Igarashi H, Ohtani M, Nakano Y, Mortimer J, et al. VASCULAR-RELATED NAC-DOMAIN6 and VASCULAR-RELATED NAC-DOMAIN7 effectively induce transdifferentiation into xylem vessel elements under control of an induction system. Plant Physiol. 2010;153:906-14 pubmed publisher..These data demonstrate that the induction systems controlling VND6 and VND7 activities can be used as powerful tools for understanding xylem cell differentiation. ..
- Stotz H, Sawada Y, Shimada Y, Hirai M, Sasaki E, Krischke M, et al. Role of camalexin, indole glucosinolates, and side chain modification of glucosinolate-derived isothiocyanates in defense of Arabidopsis against Sclerotinia sclerotiorum. Plant J. 2011;67:81-93 pubmed publisher..sclerotiorum. This information is important for microbial associations with cruciferous host plants and for metabolic engineering of pathogen defenses in cruciferous plants that produce short-chained aliphatic glucosinolates...
- Kuromori T, Sugimoto E, Shinozaki K. Arabidopsis mutants of AtABCG22, an ABC transporter gene, increase water transpiration and drought susceptibility. Plant J. 2011;67:885-94 pubmed publisher..Also, the atabcg22 mutation enhanced the phenotype of nced3 mutants, which were defective in ABA biosynthesis. Accordingly, the additive roles of AtABCG22 functions in ABA signalling and ABA biosynthesis are discussed...
- Iwase A, Ohme Takagi M, Sugimoto K. WIND1: a key molecular switch for plant cell dedifferentiation. Plant Signal Behav. 2011;6:1943-5 pubmed..Our data show that WIND proteins are required to activate the local cytokinin response at the wound site. ..
- Okazaki Y, Otsuki H, Narisawa T, Kobayashi M, Sawai S, Kamide Y, et al. A new class of plant lipid is essential for protection against phosphorus depletion. Nat Commun. 2013;4:1510 pubmed publisher..Glucuronosyldiacylglycerol was also found in rice, and its concentration increased significantly following phosphorus limitation, suggesting a shared physiological significance of this novel lipid against phosphorus depletion in plants. ..
- Nakayama M, Masuda T, Sato N, Yamagata H, Bowler C, Ohta H, et al. Cloning, subcellular localization and expression of CHL1, a subunit of magnesium-chelatase in soybean. Biochem Biophys Res Commun. 1995;215:422-8 pubmed publisher..CHLI was localized in the soluble fraction in soybean chloroplasts, suggesting that it was a stromal subunit of Mg-chelatase. chlI mRNA in cell culture (SB-P) of soybean was reversibly induced by light...
- Kimura M, Manabe K, Abe T, Yoshida S, Matsui M, Yamamoto Y. Analysis of hydrogen peroxide-independent expression of the high-light-inducible ELIP2 gene with the aid of the ELIP2 promoter-luciferase fusions. Photochem Photobiol. 2003;77:668-74 pubmed
- Masuda T, Fusada N, Oosawa N, Takamatsu K, Yamamoto Y, Ohto M, et al. Functional analysis of isoforms of NADPH: protochlorophyllide oxidoreductase (POR), PORB and PORC, in Arabidopsis thaliana. Plant Cell Physiol. 2003;44:963-74 pubmed
- Nakamura A, Goda H, Shimada Y, Yoshida S. Brassinosteroid selectively regulates PIN gene expression in Arabidopsis. Biosci Biotechnol Biochem. 2004;68:952-4 pubmed..This suggests that BL selectively regulates the PIN gene in a complex manner. ..
- Takahashi N, Nakazawa M, Shibata K, Yokota T, Ishikawa A, Suzuki K, et al. shk1-D, a dwarf Arabidopsis mutant caused by activation of the CYP72C1 gene, has altered brassinosteroid levels. Plant J. 2005;42:13-22 pubmed..Unlike BAS1/CYP734A1 the expression of CYP72C1 was not changed by application of exogenous brassinolide. We propose that CYP72C1 controls BR homeostasis by modulating the concentration of BRs. ..
- Ishida T, Hattori S, Sano R, Inoue K, Shirano Y, Hayashi H, et al. Arabidopsis TRANSPARENT TESTA GLABRA2 is directly regulated by R2R3 MYB transcription factors and is involved in regulation of GLABRA2 transcription in epidermal differentiation. Plant Cell. 2007;19:2531-43 pubmed
- Mizusawa K, Masuda S, Ohta H. Expression profiling of four RelA/SpoT-like proteins, homologues of bacterial stringent factors, in Arabidopsis thaliana. Planta. 2008;228:553-62 pubmed publisher..These results suggest that expression of the four RSH genes is coordinately regulated and that the ppGpp-dependent plastid stringent response has certain roles in the physiology of higher plants. ..
- Sawada Y, Kuwahara A, Nagano M, Narisawa T, Sakata A, Saito K, et al. Omics-based approaches to methionine side chain elongation in Arabidopsis: characterization of the genes encoding methylthioalkylmalate isomerase and methylthioalkylmalate dehydrogenase. Plant Cell Physiol. 2009;50:1181-90 pubmed publisher..As shown here, an omics-based approach is an efficient strategy for the functional elucidation of genes involved in metabolism. ..
- Yano R, Kanno Y, Jikumaru Y, Nakabayashi K, Kamiya Y, Nambara E. CHOTTO1, a putative double APETALA2 repeat transcription factor, is involved in abscisic acid-mediated repression of gibberellin biosynthesis during seed germination in Arabidopsis. Plant Physiol. 2009;151:641-54 pubmed publisher..These results indicate that CHO1 acts downstream of ABA to repress GA biosynthesis during seed germination. ..
- Kusano M, Fukushima A, Redestig H, Kobayashi M, Otsuki H, Onouchi H, et al. Comparative metabolomics charts the impact of genotype-dependent methionine accumulation in Arabidopsis thaliana. Amino Acids. 2010;39:1013-21 pubmed publisher..The findings suggest that our metabolomics approach not only can reveal the impact of Met over-accumulation on metabolism, but also may provide clues to identify crucial pathways for regulation of metabolism in plants. ..
- Shin R, Jez J, Basra A, Zhang B, Schachtman D. 14-3-3 proteins fine-tune plant nutrient metabolism. FEBS Lett. 2011;585:143-7 pubmed publisher..Using a combination of methods, this work elucidates how 14-3-3s function as modulators of plant N and S metabolic pathways. ..
- To T, Kim J, Matsui A, Kurihara Y, Morosawa T, Ishida J, et al. Arabidopsis HDA6 regulates locus-directed heterochromatin silencing in cooperation with MET1. PLoS Genet. 2011;7:e1002055 pubmed publisher..We propose that HDA6 regulates locus-directed heterochromatin silencing in cooperation with MET1, possibly recruiting MET1 to specific loci, thus forming the foundation of silent chromatin structure for subsequent non-CG methylation. ..
- Ohtani M, Nishikubo N, Xu B, Yamaguchi M, Mitsuda N, Gou N, et al. A NAC domain protein family contributing to the regulation of wood formation in poplar. Plant J. 2011;67:499-512 pubmed publisher..These results suggest that wood formation in poplar is regulated by cooperative functions of the NAC domain proteins...
- Ueda N, Kojima M, Suzuki K, Sakakibara H. Agrobacterium tumefaciens tumor morphology root plastid localization and preferential usage of hydroxylated prenyl donor is important for efficient gall formation. Plant Physiol. 2012;159:1064-72 pubmed publisher..Tmr is thus specialized for plastid localization and preferential usage of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate in vivo and is important for efficient gall formation. ..
- Araki R, Hasumi A, Nishizawa O, Sasaki K, Kuwahara A, Sawada Y, et al. Novel bioresources for studies of Brassica oleracea: identification of a kale MYB transcription factor responsible for glucosinolate production. Plant Biotechnol J. 2013;11:1017-27 pubmed publisher..Our results indicate that these biological resources can facilitate further identification of genes useful for modifications of GSL profiles and accumulation in kale. ..
- Ko D, Kang J, Kiba T, Park J, Kojima M, Do J, et al. Arabidopsis ABCG14 is essential for the root-to-shoot translocation of cytokinin. Proc Natl Acad Sci U S A. 2014;111:7150-5 pubmed publisher..Our results provide molecular evidence for the long-distance transport of cytokinin and show that this transport is necessary for normal shoot development. ..
- Nakazawa M, Matsui M. Selection of hygromycin-resistant Arabidopsis seedlings. Biotechniques. 2003;34:28-30 pubmed
- Ohtani M, Demura T, Sugiyama M. Particular significance of SRD2-dependent snRNA accumulation in polarized pattern generation during lateral root development of Arabidopsis. Plant Cell Physiol. 2010;51:2002-12 pubmed publisher..These findings suggest that high-level accumulation of snRNA involving the SRD2 function is particularly important for expression of PINs in polarized pattern generation during the development of lateral root primordia. ..
- Goda H, Sawa S, Asami T, Fujioka S, Shimada Y, Yoshida S. Comprehensive comparison of auxin-regulated and brassinosteroid-regulated genes in Arabidopsis. Plant Physiol. 2004;134:1555-73 pubmed
- Hara S, Motohashi K, Arisaka F, Romano P, Hosoya Matsuda N, Kikuchi N, et al. Thioredoxin-h1 reduces and reactivates the oxidized cytosolic malate dehydrogenase dimer in higher plants. J Biol Chem. 2006;281:32065-71 pubmed..These results demonstrate that the oxidized form cytMDH dimer is a preferable target protein of the reduced form thioredoxin-h1 as suggested by thioredoxin affinity chromatography. ..
- Nagashima A, Suzuki G, Uehara Y, Saji K, Furukawa T, Koshiba T, et al. Phytochromes and cryptochromes regulate the differential growth of Arabidopsis hypocotyls in both a PGP19-dependent and a PGP19-independent manner. Plant J. 2008;53:516-29 pubmed..These data suggest that the control of auxin transport by phytochromes and cryptochromes is a critical regulatory component of hypocotyl growth in response to light. ..
- Yamaguchi M, Kubo M, Fukuda H, Demura T. Vascular-related NAC-DOMAIN7 is involved in the differentiation of all types of xylem vessels in Arabidopsis roots and shoots. Plant J. 2008;55:652-64 pubmed publisher..Together these data suggest that VND7 regulates the differentiation of all types of vessels in roots and shoots, possibly in cooperation with VND2 to VND5 and other regulatory proteins. ..
- Seo M, Nambara E, Choi G, Yamaguchi S. Interaction of light and hormone signals in germinating seeds. Plant Mol Biol. 2009;69:463-72 pubmed publisher..Several key components that link the perception of light and the modulation of hormone levels and responsiveness have been identified. Complex regulatory loops between light, GA and ABA signaling pathways have been uncovered. ..
- Kurihara Y, Matsui A, Hanada K, Kawashima M, Ishida J, Morosawa T, et al. Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis. Proc Natl Acad Sci U S A. 2009;106:2453-8 pubmed publisher..This finding demonstrates that one of the most important roles of NMD is the genome-wide suppression of the aberrant mlncRNAs including nat-RNAs. ..
- Yamaguchi M, Ohtani M, Mitsuda N, Kubo M, Ohme Takagi M, Fukuda H, et al. VND-INTERACTING2, a NAC domain transcription factor, negatively regulates xylem vessel formation in Arabidopsis. Plant Cell. 2010;22:1249-63 pubmed publisher..These data suggest that VNI2 regulates xylem cell specification as a transcriptional repressor that interacts with VND proteins and possibly also with other NAC domain proteins. ..
- Suzuki M, Kamide Y, Nagata N, Seki H, Ohyama K, Kato H, et al. Loss of function of 3-hydroxy-3-methylglutaryl coenzyme A reductase 1 (HMG1) in Arabidopsis leads to dwarfing, early senescence and male sterility, and reduced sterol levels. Plant J. 2004;37:750-61 pubmed..These findings suggest that HMG1 plays a critical role in triterpene biosynthesis, and that sterols and/or triterpenoids contribute to cell elongation, senescence, and fertility. ..
- Ohgishi M, Saji K, Okada K, Sakai T. Functional analysis of each blue light receptor, cry1, cry2, phot1, and phot2, by using combinatorial multiple mutants in Arabidopsis. Proc Natl Acad Sci U S A. 2004;101:2223-8 pubmed..Microarray analysis suggested that cry1 and cry2 independently function as key regulators of early blue light-induced genes, whereas phot1 and phot2 play subsidiary roles in transcriptional regulation by blue light. ..
- Niinuma K, Someya N, Kimura M, Yamaguchi I, Hamamoto H. Circadian rhythm of circumnutation in inflorescence stems of Arabidopsis. Plant Cell Physiol. 2005;46:1423-7 pubmed..These results highlight for the first time a role for a circadian clock in the regulation of circumnutation based on genetic analysis of Arabidopsis. ..
- Sakakibara H, Kasahara H, Ueda N, Kojima M, Takei K, Hishiyama S, et al. Agrobacterium tumefaciens increases cytokinin production in plastids by modifying the biosynthetic pathway in the host plant. Proc Natl Acad Sci U S A. 2005;102:9972-7 pubmed..These results demonstrate that A. tumefaciens modifies CK biosynthesis by sending a key enzyme into plastids of the host plant to promote tumorigenesis. ..
- Kikuchi J, Hirayama T. Practical aspects of uniform stable isotope labeling of higher plants for heteronuclear NMR-based metabolomics. Methods Mol Biol. 2007;358:273-86 pubmed..In this chapter, we describe the practical aspects of two key NMR technologies: uniform stable labeling of plants and in vitro heteronuclear NMR...
- Maruyama Nakashita A, Nakamura Y, Tohge T, Saito K, Takahashi H. Arabidopsis SLIM1 is a central transcriptional regulator of plant sulfur response and metabolism. Plant Cell. 2006;18:3235-51 pubmed
- Demura T, Fukuda H. Transcriptional regulation in wood formation. Trends Plant Sci. 2007;12:64-70 pubmed
- Nagai S, Koide M, Takahashi S, Kikuta A, Aono M, Sasaki Sekimoto Y, et al. Induction of isoforms of tetrapyrrole biosynthetic enzymes, AtHEMA2 and AtFC1, under stress conditions and their physiological functions in Arabidopsis. Plant Physiol. 2007;144:1039-51 pubmed
- Yonekura Sakakibara K, Tohge T, Matsuda F, Nakabayashi R, Takayama H, Niida R, et al. Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene-metabolite correlations in Arabidopsis. Plant Cell. 2008;20:2160-76 pubmed publisher..The precise identification of flavonoids in conjunction with transcriptomics thus led to the identification of a gene function and a more complete understanding of a plant metabolic network. ..
- Trujillo M, Ichimura K, Casais C, Shirasu K. Negative regulation of PAMP-triggered immunity by an E3 ubiquitin ligase triplet in Arabidopsis. Curr Biol. 2008;18:1396-401 pubmed publisher..Our data provide novel insights into the regulation of immunity in plants and links ubiquitination as a mechanism of negative regulation of PTI. ..
- Okazaki Y, Shimojima M, Sawada Y, Toyooka K, Narisawa T, Mochida K, et al. A chloroplastic UDP-glucose pyrophosphorylase from Arabidopsis is the committed enzyme for the first step of sulfolipid biosynthesis. Plant Cell. 2009;21:892-909 pubmed publisher..A comparative genomics study on UGP3 homologs across different plant species suggested the structural and functional conservation of the proteins and, thus, a committing role for UGP3 in sulfolipid synthesis. ..
- Narise T, Kobayashi K, Baba S, Shimojima M, Masuda S, Fukaki H, et al. Involvement of auxin signaling mediated by IAA14 and ARF7/19 in membrane lipid remodeling during phosphate starvation. Plant Mol Biol. 2010;72:533-44 pubmed publisher..These results demonstrate a requirement of auxin signaling mediated by IAA14 and ARF7/19 for low-Pi adaptation in Arabidopsis. ..
- Nagata T, Niyada E, Fujimoto N, Nagasaki Y, Noto K, Miyanoiri Y, et al. Solution structures of the trihelix DNA-binding domains of the wild-type and a phosphomimetic mutant of Arabidopsis GT-1: mechanism for an increase in DNA-binding affinity through phosphorylation. Proteins. 2010;78:3033-47 pubmed publisher..On the basis of our findings, we propose a mechanism by which the DNA-binding activity toward BoxII of the phosphorylated GT-1 could be enhanced. ..
- Konishi S, Sasakuma T, Sasanuma T. Identification of novel Mlo family members in wheat and their genetic characterization. Genes Genet Syst. 2010;85:167-75 pubmed..This result suggested that the organ specific expression of individual Mlo members occurred relatively recently in their evolution...
- Shimojima M, Ohta H. Critical regulation of galactolipid synthesis controls membrane differentiation and remodeling in distinct plant organs and following environmental changes. Prog Lipid Res. 2011;50:258-66 pubmed publisher..Here we review progress made in the last decade towards a better understanding of the pathways regulating plant galactolipid biosynthesis. ..
- Nishiyama R, Watanabe Y, Fujita Y, Le D, Kojima M, Werner T, et al. Analysis of cytokinin mutants and regulation of cytokinin metabolic genes reveals important regulatory roles of cytokinins in drought, salt and abscisic acid responses, and abscisic acid biosynthesis. Plant Cell. 2011;23:2169-83 pubmed publisher
- Tran L, Nishiyama R, Yamaguchi Shinozaki K, Shinozaki K. Potential utilization of NAC transcription factors to enhance abiotic stress tolerance in plants by biotechnological approach. GM Crops. 2010;1:32-9 pubmed publisher..In this review the NAC TF family will be described and the potential use of NAC TFs in development of improved stress tolerant transgenic crops will be discussed. ..
- Mashiguchi K, Tanaka K, Sakai T, Sugawara S, Kawaide H, Natsume M, et al. The main auxin biosynthesis pathway in Arabidopsis. Proc Natl Acad Sci U S A. 2011;108:18512-7 pubmed publisher..Indole-3-acetaldehyde is probably not a precursor of IAA in the IPA pathway. Our results indicate that YUC proteins catalyze a rate-limiting step of the IPA pathway, which is the main IAA biosynthesis pathway in Arabidopsis. ..
- Kawade K, Horiguchi G, Usami T, Hirai M, Tsukaya H. ANGUSTIFOLIA3 signaling coordinates proliferation between clonally distinct cells in leaves. Curr Biol. 2013;23:788-92 pubmed publisher..Taking these findings together, we present a novel model emphasizing the role of mesophyll cells as a signaling source coordinating proliferation between clonally independent leaf cells. ..
- Matsui A, Nguyen A, Nakaminami K, Seki M. Arabidopsis non-coding RNA regulation in abiotic stress responses. Int J Mol Sci. 2013;14:22642-54 pubmed publisher..In this review, we summarize recent progress that has been made on ncRNA research in plant abiotic stress response. ..
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