Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

Agriculture is particularly vulnerable to climate change. To cope with the risks posed by climate-related stressors to agricultural production, global population growth, and changes in food preferences, it is imperative to develop new climate-smart crop varieties with increased yield and environmental resilience. Molecular genetics and genomic analyses have revealed that allelic variations in genes involved in phytohormone-mediated growth regulation have greatly improved productivity in major crops. Plant science has remarkably advanced our understanding of the molecular basis of various phytohormone-mediated events in plant life. These findings provide essential information for improving the productivity of crops growing in changing climates. In this review, we highlight the recent advances in plant hormonomics (multiple phytohormone profiling) and discuss their application to crop improvement. We present plant hormonomics as a key tool for deep physiological phenotyping, focusing on representative plant growth regulators associated with the improvement of crop productivity. Specifically, we review advanced methodologies in plant hormonomics, highlighting mass spectrometry- and nanosensor-based plant hormone profiling techniques. We also discuss the applications of plant hormonomics in crop improvement through breeding and agricultural management practices.

DOI： 10.1093/pcp/pcac067

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Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：{MDPI} {AG}  

DOI： 10.3390/ijms221910776

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Publishing type：Research paper (scientific journal)   Publisher：{MDPI} {AG}  

Climate resilience of crops is critical for global food security. Understanding the genetic basis of plant responses to ambient environmental changes is key to developing resilient crops. To detect genetic factors that set flowering time according to seasonal temperature conditions, we evaluated differences of flowering time over years by using chromosome segment substitution lines (CSSLs) derived from japonica rice cultivars “Koshihikari” × “Khao Nam Jen”, each with different robustness of flowering time to environmental fluctuations. The difference of flowering times in 9 years’ field tests was large in “Khao Nam Jen” (36.7 days) but small in “Koshihikari” (9.9 days). Part of this difference was explained by two QTLs. A CSSL with a “Khao Nam Jen” segment on chromosome 11 showed 28.0 days’ difference; this QTL would encode a novel flowering-time gene. Another CSSL with a segment from “Khao Nam Jen” in the region around Hd16 on chromosome 3 showed 23.4 days” difference. A near-isogenic line (NIL) for Hd16 showed 21.6 days’ difference, suggesting Hd16 as a candidate for this QTL. RNA-seq analysis showed differential expression of several flowering-time genes between early and late flowering seasons. Low-temperature treatment at panicle initiation stage significantly delayed flowering in the CSSL and NIL compared with “Koshihikari”. Our results unravel the molecular control of flowering time under ambient temperature fluctuations.

DOI： 10.3390/ijms22031024

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Publishing type：Research paper (scientific journal)   Publisher：eLife Sciences Publications, Ltd  

Although mechanisms that activate organogenesis in plants are well established, much less is known about the subsequent fine-tuning of cell proliferation, which is crucial for creating properly structured and sized organs. Here we show, through analysis of temperature-dependent fasciation (TDF) mutants of Arabidopsis, <italic>root redifferentiation defective 1</italic> (<italic>rrd1</italic>), <italic>rrd2</italic>, and <italic>root initiation defective 4</italic> (<italic>rid4</italic>), that mitochondrial RNA processing is required for limiting cell division during early lateral root (LR) organogenesis. These mutants formed abnormally broadened (i.e. fasciated) LRs under high-temperature conditions due to extra cell division. All TDF proteins localized to mitochondria, where they were found to participate in RNA processing: RRD1 in mRNA deadenylation, and RRD2 and RID4 in mRNA editing. Further analysis suggested that LR fasciation in the TDF mutants is triggered by reactive oxygen species generation caused by defective mitochondrial respiration. Our findings provide novel clues for the physiological significance of mitochondrial activities in plant organogenesis.

DOI： 10.7554/elife.61611

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Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

<title>Abstract</title>Genetic diversity is key to crop improvement. Owing to pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence diversity of a crop species (known as the ‘pan-genome’¹). Multiple high-quality sequence assemblies are an indispensable component of a pan-genome infrastructure. Barley (<italic>Hordeum vulgare</italic> L.) is an important cereal crop with a long history of cultivation that is adapted to a wide range of agro-climatic conditions². Here we report the construction of chromosome-scale sequence assemblies for the genotypes of 20 varieties of barley—comprising landraces, cultivars and a wild barley—that were selected as representatives of global barley diversity. We catalogued genomic presence/absence variants and explored the use of structural variants for quantitative genetic analysis through whole-genome shotgun sequencing of 300 gene bank accessions. We discovered abundant large inversion polymorphisms and analysed in detail two inversions that are frequently found in current elite barley germplasm; one is probably the product of mutation breeding and the other is tightly linked to a locus that is involved in the expansion of geographical range. This first-generation barley pan-genome makes previously hidden genetic variation accessible to genetic studies and breeding.

DOI： 10.1038/s41586-020-2947-8

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

Rhizoctonia solani is a soil-borne necrotrophic fungus that causes sheath blight in grasses. The basal resistance of compatible interactions between R. solani and rice is known to be modulated by some WRKY transcription factors (TFs). However, genes and defense responses involved in incompatible interaction with R. solani remain unexplored, because no such interactions are known in any host plants. Recently, we demonstrated that Bd3-1, an accession of the model grass Brachypodium distachyon, is resistant to R. solani and, upon inoculation with the fungus, undergoes rapid induction of genes responsive to the phytohormone salicylic acid (SA) that encode the WRKY TFs BdWRKY38 and BdWRKY44. Here, we show that endogenous SA and these WRKY TFs positively regulate this accession-specific R. solani resistance. In contrast to a susceptible accession (Bd21), the infection process in the resistant accessions Bd3-1 and Tek-3 was suppressed at early stages before the development of fungal biomass and infection machinery. A comparative transcriptome analysis during pathogen infection revealed that putative WRKY-dependent defense genes were induced faster in the resistant accessions than in Bd21. A gene regulatory network (GRN) analysis based on the transcriptome dataset demonstrated that BdWRKY38 was a GRN hub connected to many target genes specifically in resistant accessions, whereas BdWRKY44 was shared in the GRNs of all three accessions. Moreover, overexpression of BdWRKY38 increased R. solani resistance in Bd21. Our findings demonstrate that these resistant accessions can activate an incompatible host response to R. solani, and BdWRKY38 regulates this response by mediating SA signaling.

DOI： 10.1111/tpj.14976

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Other Link： https://onlinelibrary.wiley.com/doi/full-xml/10.1111/tpj.14976

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

DOI： 10.1093/pcp/pcaa087

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Other Link： http://academic.oup.com/pcp/article-pdf/61/8/1381/33662834/pcaa087.pdf

Language：English   Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

<title>Abstract</title>To ensure food security in the face of increasing global demand due to population growth and progressive urbanization, it will be crucial to integrate emerging technologies in multiple disciplines to accelerate overall throughput of gene discovery and crop breeding. Plant agronomic traits often appear during the plants’ later growth stages due to the cumulative effects of their lifetime interactions with the environment. Therefore, decoding plant–environment interactions by elucidating plants’ temporal physiological responses to environmental changes throughout their lifespans will facilitate the identification of genetic and environmental factors, timing and pathways that influence complex end-point agronomic traits, such as yield. Here, we discuss the expected role of the life-course approach to monitoring plant and crop health status in improving crop productivity by enhancing the understanding of plant–environment interactions. We review recent advances in analytical technologies for monitoring health status in plants based on multi-omics analyses and strategies for integrating heterogeneous datasets from multiple omics areas to identify informative factors associated with traits of interest. In addition, we showcase emerging phenomics techniques that enable the noninvasive and continuous monitoring of plant growth by various means, including three-dimensional phenotyping, plant root phenotyping, implantable/injectable sensors and affordable phenotyping devices. Finally, we present an integrated review of analytical technologies and applications for monitoring plant growth, developed across disciplines, such as plant science, data science and sensors and Internet-of-things technologies, to improve plant productivity.

DOI： 10.1093/pcp/pcaa064

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Other Link： http://academic.oup.com/pcp/article-pdf/61/8/1408/33662755/pcaa064.pdf

Authorship：Lead author,　Last author   Language：English   Publishing type：Research paper (scientific journal)  

Agronomically important traits often develop during the later stages of crop growth as consequences of various plant-environment interactions. Therefore, the temporal physiological states that change and accumulate during the crop's life course can significantly affect the eventual phenotypic differences in agronomic traits among crop varieties. Thus, to improve productivity, it is important to elucidate the associations between temporal physiological responses during the growth of different crop varieties and their agronomic traits. However, data representing the dynamics and diversity of physiological states in plants grown under field conditions is sparse. In this study, we quantified the endogenous levels of five phytohormones-auxin, cytokinins, abscisic acid, jasmonate, and salicylic acid-in the leaves of eight diverse barley (Hordeum vulgare) accessions grown under field conditions sampled weekly over their life course to assess the ongoing fluctuations in hormone levels in the different accessions under field growth conditions. Notably, we observed enormous changes over time in the development-related plant hormones, such as auxin and cytokinins. Using 3' RNA-seq-based transcriptome data from the same samples, we investigated the expression of barley genes orthologous to known hormone-related genes of Arabidopsis throughout the life course. These data illustrated the dynamics and diversity of the physiological states of these field-grown barley accessions. Together our findings provide new insights into plant-environment interaction, highlighting that there is cultivar diversity in physiological responses during growth under field conditions.

DOI： 10.1093/pcp/pcaa046

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media {LLC}  

Black pepper (Piper nigrum L.) is one of the most popular and oldest spices in the world with culinary uses and various pharmacological properties. In order to satisfy the growing worldwide demand for black pepper, improved productivity of pepper is highly desirable. A primary constraint in black pepper production is the non-synchronous nature of flower development and non-uniform fruit ripening within a spike. The uneven ripening of pepper berries results in a high labour requirement for selective harvesting contributes to low productivity and affects the quality of the pepper products. In Malaysia, there are a few recommended varieties for black pepper planting, each having some limitations in addition to the useful characteristics. Therefore, a comparative study of different black pepper varieties will provide a better understanding of the mechanisms regulates fruit development and ripening. Plant hormones are known to influence the fruit development process and their roles in black pepper flower and fruit development were inferred based on the probe-based gene expression analysis and the quantification of the multiple plant hormones using high-performance liquid chromatography coupled to tandem mass spectrometry (HPLC-MS/MS). In this study, jasmonic acid and salicylic acid were found to play roles in flowering and fruit setting, whereas auxin, gibberellin and cytokinins are important for fruit growth. Abscisic acid has positive role in fruit maturation and ripening in the development process. Distinct pattern of plant hormones related gene expression profiles with the hormones accumulation profiles suggested a complex network of regulation is involved in the signaling process and crosstalk between plant hormones was another layer of regulation in the black pepper fruit development mechanisms. The current study provides clues to help in elucidating the timing of the action of each specific plant hormone during fruit development and ripening which could be applied to enhance our ability to control the ripening process, leading to improving procedures for the production and post-harvest handling of pepper fruits.

DOI： 10.1007/s10265-019-01156-0

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This study examined contents of nine plant hormones in developing seeds of field-grown wheat varieties (Triticum aestivum L.) with different seed dormancy using liquid chromatography-mass spectrometry. The varieties showed marked diversity in germination indices at 15°C and 20°C. Contents of the respective hormones in seeds showed a characteristic pattern during seed maturation from 30-day post anthesis to 60-day post anthesis. Principal component analysis and hierarchical clustering analysis revealed that plant hormone profiles were not correlated with dormancy levels, indicating that hormone contents were not associated with preharvest sprouting (PHS) susceptibility. Indole acetic acid (IAA) contents of mature seeds showed positive correlation with the germination index, but no other hormone. Response of embryo-half seeds to exogenous abscisic acid (ABA) indicates that ABA sensitivity is correlated with whole-seed germinability, which can be explained in part by genotypes of MOTHER OF FT AND TFL (MFT) allele modulating ABA signaling of wheat seeds. These results demonstrate that variation in wheat seed dormancy is attributable to ABA sensitivity of mature seeds, but not to ABA contents in developing seeds.

DOI： 10.1270/jsbbs.19030

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Authorship：Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

<title>Abstract</title>
Regulation of the stability and the quality of mitochondrial RNA is essential for the maintenance of mitochondrial and cellular functions in eukaryotes. We have previously reported that the eukaryotic poly(A)-specific ribonuclease (PARN) and the prokaryotic poly(A) polymerase encoded by AHG2 and AGS1, respectively, coordinately regulate the poly(A) status and the stability of mitochondrial mRNA in Arabidopsis. Mitochondrial function of PARN has not been reported in any other eukaryotes. To know how much this PARN-based mitochondrial mRNA regulation is conserved among plants, we studied the AHG2 and AGS1 counterparts of the liverwort, Marchantia polymorpha, a member of basal land plant lineage. We found that M. polymorpha has one ortholog each for AHG2 and AGS1, named MpAHG2 and MpAGS1, respectively. Their Citrine-fused proteins were detected in mitochondria of the liverwort. Molecular genetic analysis showed that MpAHG2 is essential and functionally interacts with MpAGS1 as observed in Arabidopsis. A recombinant MpAHG2 protein had a deadenylase activity in vitro. Overexpression of MpAGS1 and the reduced expression of MpAHG2 caused an accumulation of polyadenylated Mpcox1 mRNA. Furthermore, MpAHG2 suppressed Arabidopsis ahg2-1 mutant phenotype. These results suggest that the PARN-based mitochondrial mRNA regulatory system is conserved in land plants.

DOI： 10.1093/pcp/pcz212

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Other Link： http://academic.oup.com/pcp/article-pdf/61/3/470/32891632/pcz212.pdf

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

DOI： 10.1104/pp.18.01426

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PUBLIC LIBRARY SCIENCE  

Most deciduous fruit trees cultivated in the temperate zone require a genotype-dependent amounts of chilling exposure for dormancy release and bud break. In Japanese apricot (Prunus mume), DORMANCY-ASSOCIATED MADS-box 6 (PmDAM6) may influence chilling-mediated dormancy release and bud break. In this study, we attempted to elucidate the biological functions of PmDAM6 related to dormancy regulation by analyzing PmDAM6-overexpressing transgenic apple (Malusspp.). We generated 35S:PmDAM6 lines and chemically inducible overexpression lines, 35S:PmDAM6-GR. In both overexpression lines, shoot growth was inhibited and early bud set was observed. In addition, PmDAM6 expression repressed bud break competency during dormancy and delayed bud break. Moreover, PmDAM6 expression increased abscisic acid levels and decreased cytokinins contents during the late dormancy and bud break stages in both 35S:PmDAM6 and 35S:PmDAM6-GR. Our analysis also suggested that abscisic acid levels increased during dormancy but subsequently decreased during dormancy release whereas cytokinins contents increased during the bud break stage in dormant Japanese apricot buds. We previously revealed that PmDAM6 expression is continuously down-regulated during dormancy release toward bud break in Japanese apricot. The PmDAM6 expression pattern was concurrent with a decrease and increase in the abscisic acid and cytokinins contents, respectively, in dormant Japanese apricot buds. Therefore, we hypothesize that PmDAM6 represses the bud break competency during dormancy and bud break stages in Japanese apricot by modulating abscisic acid and cytokinins accumulation in dormant buds.

DOI： 10.1371/journal.pone.0214788

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Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

DOI： 10.1093/gigascience/giy153

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Nature Publishing Group  

Abscisic acid (ABA) regulates abiotic stress and developmental responses including regulation of seed dormancy to prevent seeds from germinating under unfavorable environmental conditions. ABA HYPERSENSITIVE GERMINATION1 (AHG1) encoding a type 2C protein phosphatase (PP2C) is a central negative regulator of ABA response in germination
however, the molecular function and regulation of AHG1 remain elusive. Here we report that AHG1 interacts with DELAY OF GERMINATION1 (DOG1), which is a pivotal positive regulator in seed dormancy. DOG1 acts upstream of AHG1 and impairs the PP2C activity of AHG1 in vitro. Furthermore, DOG1 has the ability to bind heme. Binding of DOG1 to AHG1 and heme are independent processes, but both are essential for DOG1 function in vivo. Our study demonstrates that AHG1 and DOG1 constitute an important regulatory system for seed dormancy and germination by integrating multiple environmental signals, in parallel with the PYL/RCAR ABA receptor-mediated regulatory system.

DOI： 10.1038/s41467-018-04437-9

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：BMC  

BackgroundThe ureides allantoin and allantoate are major metabolic intermediates of purine catabolism with high nitrogen-to-carbon ratios. Ureides play a key role in nitrogen utilization in ureide-type legumes, but their effects on growth and development in non-legume plants are poorly understood. Here, we examined the effects of knocking out genes encoding ureide-degrading enzymes, allantoinase (ALN) and allantoate amidohydrolase (AAH), on the vegetative-to-reproductive transition and subsequent growth of Arabidopsis plants.ResultsThe ureide-degradation mutants (aln and aah) showed symptoms similar to those of nitrogen deficiency: early flowering, reduced size at maturity, and decreased fertility. Consistent with these phenotypes, carbon-to-nitrogen ratios and nitrogen-use efficiencies were significantly decreased in ureide-degradation mutants; however, adding nitrogen to irrigation water did not alleviate the reduced growth of these mutants. In addition to nitrogen status, levels of indole-3-acetic acid and gibberellin in five-week-old plants were also affected by the aln mutations. To test the possibility that ureides are remobilized from source to sink organs, we measured ureide levels in various organs. In wild-type plants, allantoate accumulated predominantly in inflorescence stems and siliques; this accumulation was augmented by disruption of its catabolism. Mutants lacking ureide transporters, ureide permeases 1 and 2 (UPS1 and UPS2), exhibited phenotypes similar to those of the ureide-degradation mutants, but had decreased allantoate levels in the reproductive organs. Transcript analysis in wild-type plants suggested that genes involved in allantoate synthesis and ureide transport were coordinately upregulated in senescing leaves.ConclusionsThis study demonstrates that ureide degradation plays an important role in supporting healthy growth and development in non-legume Arabidopsis during and after transition from vegetative to reproductive stages.

DOI： 10.1186/s12870-018-1491-2

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DOI： 10.1093/pcp/pcy161

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：OXFORD UNIV PRESS  

Iron is an essential element for all organisms, and plants have developed sophisticated systems to acquire iron and maintain iron homeostasis. We found that an Arabidopsis thaliana ABA-hypersensitive mutant, aba hypersensitive germination2-1 (ahg2-1), that is known to be defective in mitochondrial mRNA regulation, had increased expression of iron deficiency response genes. The ahg2-1 mutant had lower heme levels than the wild type. Transcriptome data further revealed that novel genes encoding short polypeptides were highly expressed in this mutant. The expression of one of these genes, which we named FE-UPTAKE-INDUCING PEPTIDE 1 (FEP1), was induced under iron-deficient conditions and was observed in the vascular tissues of the leaves and roots, as well as in leaf mesophyll cells. Notably, deletion or insertion mutations of FEN exhibited impaired iron accumulation in shoots but normal iron levels in roots. Artificially induced expression of FEP1 was sufficient to induce iron deficiency response genes, such as basic HELIX- LOOP-HELIX 38 (bHLH38), bHLH39, IRON-REGULATED TRANSPORTERI (IRT1) and FERRIC REDUCTION OXIDASE2 (FRO2), and led to iron accumulation in planta. Further analysis confirmed that the encoded peptide, but not the FEP1 RNA, was responsible for this activity. Remarkably, the activation of bHLH39 by FEP1 was independent of FER-LIKE IRON DEFICIENCY INDUCED (FIT), a key transcription factor in the iron deficiency response. Taken together, our results indicate that FEP1 functions in iron homeostasis through a previously undescribed regulatory mechanism for iron acquisition in Arabidopsis.

DOI： 10.1093/pcp/pcy145

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Plants closing stomata in the presence of harmful gases is believed to be a stress avoidance mechanism. SO2 , one of the major airborne pollutants, has long been reported to induce stomatal closure, yet the mechanism remains unknown. Little is known about the stomatal response to airborne pollutants besides O3 . SLOW ANION CHANNEL-ASSOCIATED 1 (SLAC1) and OPEN STOMATA 1 (OST1) were identified as genes mediating O3 -induced closure. SLAC1 and OST1 are also known to mediate stomatal closure in response to CO2 , together with RESPIRATORY BURST OXIDASE HOMOLOGs (RBOHs). The overlaying roles of these genes in response to O3 and CO2 suggested that plants share their molecular regulators for airborne stimuli. Here, we investigated and compared stomatal closure event induced by a wide concentration range of SO2 in Arabidopsis through molecular genetic approaches. O3 - and CO2 -insensitive stomata mutants did not show significant differences from the wild type in stomatal sensitivity, guard cell viability, and chlorophyll content revealing that SO2 -induced closure is not regulated by the same molecular mechanisms as for O3 and CO2 . Nonapoptotic cell death is shown as the reason for SO2 -induced closure, which proposed the closure as a physicochemical process resulted from SO2 distress, instead of a biological protection mechanism.

DOI： 10.1111/pce.13406

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Blackwell Publishing Ltd  

Rhizoctonia solani is a soil-borne fungus causing sheath blight. In consistent with its necrotrophic life style, no rice cultivars fully resistant to R. solani are known, and agrochemical plant defense activators used for rice blast, which upregulate a phytohormonal salicylic acid (SA)-dependent pathway, are ineffective towards this pathogen. As a result of the unavailability of genetics, the infection process of R. solani remains unclear. We used the model monocotyledonous plants Brachypodium distachyon and rice, and evaluated the effects of phytohormone-induced resistance to R. solani by pharmacological, genetic and microscopic approaches to understand fungal pathogenicity. Pretreatment with SA, but not with plant defense activators used in agriculture, can unexpectedly induce sheath blight resistance in plants. SA treatment inhibits the advancement of R. solani to the point in the infection process in which fungal biomass shows remarkable expansion and specific infection machinery is developed. The involvement of SA in R. solani resistance is demonstrated by SA-deficient NahG transgenic rice and the sheath blight-resistant B. distachyon accessions, Bd3-1 and Gaz-4, which activate SA-dependent signaling on inoculation. Our findings suggest a hemi-biotrophic nature of R. solani, which can be targeted by SA-dependent plant immunity. Furthermore, B. distachyon provides a genetic resource that can confer disease resistance against R. solani to plants.

DOI： 10.1111/nph.14849

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Language：English   Publisher：OXFORD UNIV PRESS  

DOI： 10.1093/jxb/erw289

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WALTER DE GRUYTER GMBH  

Emerging studies suggest that seaweeds contain phytohormones; however, their chemical entities, biosynthetic pathways, signal transduction mechanisms, and physiological roles are poorly understood. Until recently, it was difficult to conduct comprehensive analysis of phytohormones in seaweeds because of the interfering effects of cellular constituents on fine quantification. In this review, we discuss the details of the latest method allowing simultaneous profiling of multiple phytohormones in red seaweeds, while avoiding the effects of cellular factors. Recent studies have confirmed the presence of indole-3-acetic acid (IAA), N-6-(Delta(2)-isopentenyl) adenine (iP), (+)-abscisic acid (ABA), and salicylic acid, but not of gibberellins and jasmonate, in Pyropia yezoensis and Bangia fuscopurpurea. In addition, an in silico genome-wide homology search indicated that red seaweeds synthesize iP and ABA via pathways similar to those in terrestrial plants, although genes homologous to those involved in IAA biosynthesis in terrestrial plants were not found, suggesting the epiphytic origin of IAA. It is noteworthy that these seaweeds also lack homologues of known factors involved in the perception and signal transduction of IAA, iP, and ABA. Thus, the modes of action of these phytohormones in red seaweeds are unexpectedly dissimilar to those in terrestrial plants.

DOI： 10.1515/bot-2016-0056

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER  

Emerging work has suggested the existence of phytohormones in seaweeds, although chemical species, endogenous biosynthetic pathways, and signal transduction machineries remain poorly understood. We performed profiling of nine phytohormones with liquid chromatography-mass spectrometry and in silico genome-wide homology search to identify genes involved in biosynthesis and signal transduction of hormones in red algae. It was demonstrated that two Bangiophycean algae, Bangia fuscopurpurea and Pyropia yezoensis, possessed indoleacetic acid (IAA), N-6-(Delta(2)-isopentenyl) adenine (iP), abscisic acid (ABA), and salicylic acid, although trans-zeatin, dihydrozeatin, gibberellin A(1) and A(4), and jasmonate were not detected. Results of genome-wide survey demonstrated that Bangiophycean algae produce iP and ABA via pathways similar to those in terrestrial plants. However, these seaweeds lack homologues of already known factors participating in perception and signal transduction of IAA, iP, ABA and SA, indicating that the action modes of these phytohormones in red seaweeds differ from those elucidated in terrestrial plants. These findings shed lights on evolutional divergence of signal transduction pathways of phytohormones in plants.

DOI： 10.1007/s10811-015-0759-2

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Other Link： http://orcid.org/0000-0002-3868-2380

Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATURE PUBLISHING GROUP  

The ubiquitin-proteasome system is fundamentally involved in myriad biological phenomena of eukaryotes. In plants, this regulated protein degradation system has a pivotal role in the cellular response mechanisms for both internal and external stimuli, such as plant hormones and environmental stresses. Information about substrate selection by the ubiquitination machinery has accumulated, but there is very little information about selectivity for substrates at the proteasome. Here, we report characterization of a novel abscisic acid (ABA)-hypersensitive mutant named ABA hypersensitive germination12 (ahg12) in Arabidopsis. The ahg12 mutant showed a unique pleiotropic phenotype, including hypersensitivity to ABA and ethylene, and hyposensitivity to light. Map-based cloning identified the ahg12 mutation to cause an amino acid conversion in the L23 loop of RPT5a, which is predicted to form the pore structure of the 19S RP complex of the proteasome. Transient expression assays demonstrated that some plant-specific signaling components accumulated at higher levels in the ahg12 mutant. These results suggest that the ahg12 mutation led to changes in the substrate preference of the 26S proteasome. The discovery of the ahg12 mutation thus will contribute to elucidate the characteristics of the regulated protein degradation system.

DOI： 10.1038/srep25351

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：OXFORD UNIV PRESS  

Allantoin, a stress-related purine metabolite, can activate JA responses via ABA in Arabidopsis, suggesting its possible involvement in the homeostasis of these phytohormones and their interplay in stress signaling.Allantoin is a metabolic intermediate of purine catabolism that often accumulates in stressed plants. Recently, we used Arabidopsis knockout mutants (aln) of ALLANTOINASE to show that this purine metabolite activates abscisic acid (ABA) production, thereby stimulating stress-related gene expression and enhancing seedling tolerance to abiotic stress. A detailed re-examination of the microarray data of an aln mutant (aln-1) confirmed the increased expression of ABA-related genes and also revealed altered expression of genes involved in jasmonic acid (JA) responses, probably under the control of MYC2, a master switch in the JA signaling pathway. Consistent with the transcriptome profiles, the aln-1 mutant displayed increased JA levels and enhanced responses to mechanical wounding and exogenous JA. Moreover, aln mutants demonstrated modestly increased susceptibility to Pseudomonas syringae and Pectobacterium carotovorum, probably reflecting the antagonistic action of MYC2 on the defense against these bacterial phytopathogens. Exogenously administered allantoin elicited the expression of JA-responsive genes, including MYC2, in wild-type plants, supporting the idea that allantoin might be responsible for the observed JA-related phenotypes of aln mutants. However, mutants deficient in bioactive JA (jar1-1), insensitive to JA (myc2-3), or deficient in ABA (aba2-1 and bglu18) suppressed the effect of exogenous allantoin. The suppression was further confirmed in aln-1 jar1-1 and aln-1 bglu18 double mutants. These results indicate that allantoin can activate the MYC2-regulated JA signaling pathway through ABA production. Overall, this study suggests a possible connection of purine catabolism with stress hormone homeostasis and signaling, and highlights the potential importance of allantoin in these interactions.

DOI： 10.1093/jxb/erw071

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：FRONTIERS MEDIA SA  

Crops are exposed to various environmental stresses in the field throughout their life cycle. Modern plant science has provided remarkable insights into the molecular networks of plant stress responses in laboratory conditions, but the responses of different crops to environmental stresses in the field need to be elucidated. Recent advances in omics analytical techniques and information technology have enabled us to integrate data from a spectrum of physiological metrics of field crops. The interdisciplinary efforts of plant science and data science enable us to explore factors that affect crop productivity and identify stress tolerance-related genes and alleles. Here, we describe recent advances in technologies that are key components for data driven crop design, such as population genomics, chronological omics analyses, and computer-aided molecular network prediction. Integration of the outcomes from these technologies will accelerate our understanding of crop phenology under practical field situations and identify key characteristics to represent crop stress status. These elements would help us to genetically engineer "designed crops" to prevent yield shortfalls because of environmental fluctuations due to future climate change.

DOI： 10.3389/fpls.2015.00740

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Language：English   Publisher：OXFORD UNIV PRESS  

DOI： 10.1093/jxb/erv264

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATURE PUBLISHING GROUP  

Abscisic acid (ABA) regulates seed maturation, germination and various stress responses in plants. The roles of ABA in cellular growth and morphogenesis, however, remain to be explored. Here, we report that ABA induces the ectopic outgrowth of epidermal cells in Arabidopsis thaliana. Seedlings of A. thaliana germinated and grown in the presence of ABA developed ectopic protrusions in the epidermal cells of hypocotyls, petioles and cotyledons. One protrusion was formed in the middle of each epidermal cell. In the hypocotyl epidermis, two types of cell files are arranged alternately into non-stoma cell files and stoma cell files, ectopic protrusions being restricted to the non-stoma cell files. This suggests the presence of a difference in the degree of sensitivity to ABA or in the capacity of cells to form protrusions between the two cell files. The ectopic outgrowth was suppressed in ABA insensitive mutants, whereas it was enhanced in ABA hypersensitive mutants. Interestingly, ABA-induced ectopic outgrowth was also suppressed in mutants in which microtubule organization was compromised. Furthermore, cortical microtubules were disorganized and depolymerized by the ABA treatment. These results suggest that ABA signaling induces ectopic outgrowth in epidermal cells through microtubule reorganization.

DOI： 10.1038/srep11364

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DOI： 10.1093/jxb/erv086

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Landes Bioscience  

Poly(A) status is the major determinant of mRNA stability, even in endosymbiotic organelles. Poly(A) specific ribonuclease (PARN) is distributed widely among eukaryotes and has been shown to regulate the poly(A) status of cytoplasmic mRNA in various organisms. Surprisingly, our recent study revealed that PARN also directly regulates poly (A) status of mitochondrial mRNA in Arabidopsis. In this addendum, we discuss whether this mitochondrial function of PARN is common in plants and why PARN has been assigned such a unique function.

DOI： 10.4161/15592324.2014.973809

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Pentatricopeptide repeat (PPR) proteins are eukaryotic RNA-binding proteins that are commonly found in plants. Organelle transcript processing and stability are mediated by PPR proteins in a gene-specific manner through recognition by tandem arrays of degenerate 35-amino-acid repeating units, the PPR motifs. However, the sequence-specific RNA recognition mechanism of the PPR protein remains largely unknown. Here, we show the principle underlying RNA recognition for PPR proteins involved in RNA editing. The distance between the PPR-RNA alignment and the editable C was shown to be conserved. Amino acid variation at 3 particular positions within the motif determined recognition of a specific RNA in a programmable manner, with a 1-motif to 1-nucleotide correspondence, with no gap sequence. Data from the decoded nucleotide frequencies for these 3 amino acids were used to assign accurate interacting sites to several PPR proteins for RNA editing and to predict the target site for an uncharacterized PPR protein.

DOI： 10.1371/journal.pone.0057286

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

Coordination of gene expression in the organelles and the nucleus is important for eukaryotic cell function. Transcriptional and post-transcriptional gene regulation in mitochondria remains incompletely understood in most eukaryotes, including plants. Here we show that poly(A)-specific ribonuclease, which influences the poly(A) status of cytoplasmic mRNA in many eukaryotes, directly regulates the poly(A) tract of mitochondrial mRNA in conjunction with a bacterial-type poly(A) polymerase, AGS1, in Arabidopsis. An Arabidopsis poly(A)-specific ribonuclease-deficient mutant, ahg2-1, accumulates polyadenylated mitochondrial mRNA and shows defects in mitochondrial protein complex levels. Mutations of AGS1 suppress the ahg2-1 phenotype. Mitochondrial localizations of AHG2 and AGS1 are required for their functions in the regulation of the poly(A) tract of mitochondrial mRNA. Our findings suggest that AHG2 and AGS1 constitute a regulatory system that controls mitochondrial mRNA poly(A) status in Arabidopsis.

DOI： 10.1038/ncomms3247

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The phytohormone abscisic acid (ABA) plays pivotal roles in the regulation of developmental and environmental responses in plants. Identification of cytoplasmic ABA receptors enabled the elucidation of the main ABA signalling pathway, connecting ABA perception to either nuclear events or the action of several transporters. However, the physiological functions of ABA in cellular processes largely remain unknown. To obtain greater insight into the ABA response, genetic screening was performed to isolate ABA-related mutants of Arabidopsis and several novel ABA-hypersensitive mutants were isolated. One of those mutantsahg11was characterized further. Map-based cloning showed that AHG11 encodes a PPR type protein, which has potential roles in RNA editing. An AHG11-GFP fusion protein indicated that AHG11 mainly localized to the mitochondria. Consistent with this observation, the nad4 transcript, which normally undergoes RNA editing, lacks a single RNA editing event conferring a conversion of an amino acid residue in ahg11 mutants. The geminating ahg11 seeds have higher levels of reactive-oxygen-species-responsive genes. 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.

DOI： 10.1093/jxb/ers188

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPANESE SOC PLANT CELL & MOLECULAR BIOL  

Phytohormones have vigorous crosstalk relationships. For example, abscisic acid (ABA), a hormone involved in abiotic stress responses, has antagonistic interactions with plant hormones that play pivotal roles in defense responses, including salicylic acid (SA) and methyl-jasmonic acid (MeJA). Evidence indicates that the relationships among these plant hormones extend beyond simple antagonism. To explore the interplay between hormones in detail, we analyzed the effects of double hormone treatment on gene expression. By contrast to the antagonistic effects reported previously, our data indicates that ABA interacts with SA and MeJA cooperatively as well. Particularly many genes responded only to double hormone treatment, and, interestingly, the loci that responded to ABA+SA also responded to ABA+MeJA. The expression of early-response genes following double hormone treatment did not fit the linear superposition of individual hormone treatments, in contrast to mammalian and prokaryotic cell responses to multiple chemical stimuli. Thus, synergies in these plant hormone signalings are not simply the sum of individual responses. ABA and SA collaboratively down-regulated the expression of genes involved in cell cycle progression at G2/M phase. Presumably, plants interpret combined hormone signals differently from individual signals in order to respond appropriately to their environmental conditions.

DOI： 10.5511/plantbiotechnology.11.1130a

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In plants, osmotic stress-responsive transcriptional regulation depends mainly on two major classes of cis-acting elements found in the promoter regions of stress-inducible genes: ABA-responsive elements (ABREs) and dehydration-responsive elements (DREs). ABRE has been shown to perceive ABA-mediated osmotic stress signals, whereas DRE is known to be involved in an ABA-independent pathway. Previously, we reported that the transcription factor DRE-BINDING PROTEIN 2A (DREB2A) regulates DRE-mediated transcription of target genes under osmotic stress conditions in Arabidopsis (Arabidopsis thaliana). However, the transcriptional regulation of DREB2A itself remains largely uncharacterized. To elucidate the transcriptional mechanism associated with the DREB2A gene under osmotic stress conditions, we generated a series of truncated and base-substituted variants of the DREB2A promoter and evaluated their transcriptional activities individually. We found that both ABRE and coupling element 3 (CE3)-like sequences located approximately -100 bp from the transcriptional initiation site are necessary for the dehydration-responsive expression of DREB2A. Coupling our transient expression analyses with yeast one-hybrid and chromatin immunoprecipitation (ChIP) assays indicated that the ABRE-BINDING PROTEIN 1 (AREB1), AREB2 and ABRE-BINDING FACTOR 3 (ABF3) bZIP transcription factors can bind to and activate the DREB2A promoter in an ABRE-dependent manner. Exogenous ABA application induced only a modest accumulation of the DREB2A transcript when compared with the osmotic stress treatment. However, the osmotic stress-induced DREB2A expression was found to be markedly impaired in several ABA-deficient and ABA-insensitive mutants. These results suggest that in addition to an ABA-independent pathway, the ABA-dependent pathway plays a positive role in the osmotic stress-responsive expression of DREB2A.

DOI： 10.1093/pcp/pcr143

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Language：English   Publishing type：Part of collection (book)   Publisher：ACADEMIC PRESS LTD-ELSEVIER SCIENCE LTD  

Abscisic acid (ABA), one of the major plant hormones, is involved in various biological processes in plants, especially in the regulation of seed maturation, dormancy and abiotic stress responses, which have strong relationships with crop yields. For these reasons, ABA has been extensively studied for many years. Very recently, several breakthrough studies were published in ABA research. One was the identification of ABA receptors and the establishment of a major ABA signalling pathway. The other was the discovery of the transport activity of ABA among tissues. These findings open new avenues to understanding hormonal response, not only in cells, but also in the whole organism, and for the improvement of crop yields. In this chapter, we will summarise and discuss our knowledge of ABA and provide a perspective led by those processes.

DOI： 10.1016/B978-0-12-387692-8.00006-0

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

Meiotic recombination is initiated by DNA double-stranded breaks introduced by the SPO11 protein. Despite a decade of research, the biochemical functions of SPO11 remain largely unknown, perhaps because of difficulties in studying the functionally active SPO11. Arabidopsis thaliana encodes three SPO11-related proteins, two of which (SPO11-1 and SPO11-2) are required for, and cooperate in, meiosis. We isolated soluble SPO11-1, fused with or free of a trigger factor-tag at its N terminus. The tag-free SPO11-1 needed to interact physically with soluble SPO11-1 to maintain its solubility, suggesting a multimeric active form including a solubilizing protein cofactor. An N-terminal fragment of PRD1, a SPO11-1-interacting protein required for normal meiosis, but not SPO11-2, forms a soluble complex with trigger factor-tagged SPO11-1, but the trigger factor-tag was required for the solubility. Formation of the complex is not sufficient to express endonuclease activity. Trigger factor-tagged SPO11-1 exhibited DNA-binding activities: Glu substitutions of the invariant Gly215 and Arg222 and of the nonconserved Arg223 and Arg226 in a conserved motif (G215E, R222E, R223E, R226E) reduced the DNA-binding ability in vitro, but substitutions of the conserved Arg130 and invariant Tyr103 (a residue in the putative endonuclease-active center) and of Arg residues outside conserved motifs by Glu or Phe (R130E, Y103F, R207E and R254E), did not. Tests for the ability of mutant spo11-1 proteins to complement the silique-defective phenotype of a spo11-1-homozygous mutant in vivo revealed that R222E and G215E induced serious deficiencies, while R130E caused a partial defect in silique formation. Thus, the Gly215, Arg222 and Arg223 residues of SPO11-1 form a DNA-binding surface that is functional in meiosis.

DOI： 10.1111/j.1742-4658.2010.07651.x

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Language：English   Publishing type：Part of collection (book)   Publisher：Wiley-VCH  

Analysis of genetic mutations is one of the most effective techniques for investigating gene function.We now have methods that allow for mass production of mutant lines and cells created by gene disruption or silencing in model organisms, and great progress is being made in the use of those tools for comprehensive phenotypic analysis. In plants, insertion mutations can be produced using T-DNA or transposons, making it possible to monitor the effects of a defect in a single gene. Through bulk storage of mutations in the form of seeds, which is not an option in animal models, it is now feasible to use insertion mutations to analyze every gene in a model plant genome, especially Arabidopsis. This makes Arabidopsis useful not only as a model organism for plant research, but also as the only multicellular organism in which it is currently possible to perform "saturation mutagenesis" to create knockout strains for every gene. Transposon-tagged lines are generated as a gene knockout mutant resource for a wide variety of functional genomics studies in model plants. This chapter introduces a mutagenesis method using the transposon Ac/Ds system. © 2010 Wiley-VCH Verlag GmbH &amp
Co. KGaA.

DOI： 10.1002/9783527629398.ch2

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P&gt;Understanding abiotic stress responses in plants is an important and challenging topic in plant research. Physiological and molecular biological analyses have allowed us to draw a picture of abiotic stress responses in various plants, and determination of the Arabidopsis genome sequence has had a great impact on this research field. The availability of the complete genome sequence has facilitated access to essential information for all genes, e.g. gene products and their function, transcript levels, putative cis-regulatory elements, and alternative splicing patterns. These data have been obtained from comprehensive transcriptome analyses and studies using full-length cDNA collections and T-DNA- or transposon-tagged mutant lines, which were also enhanced by genome sequence information. Moreover, studies on novel regulatory mechanisms involving use of small RNA molecules, chromatin modulation and genomic DNA modification have enabled us to recognize that plants have evolved complicated and sophisticated systems in response to complex abiotic stresses. Integrated data obtained with various &apos;omics&apos; approaches have provided a more comprehensive picture of abiotic stress responses. In addition, research on stress responses in various plant species other than Arabidopsis has increased our knowledge regarding the mechanisms of plant stress tolerance in nature. Based on this progress, improvements in crop stress tolerance have been attempted by means of gene transfer and marker-assisted breeding. In this review, we summarize recent progress in abiotic stress studies, especially in the post-genomic era, and offer new perspectives on research directions for the next decade.

DOI： 10.1111/j.1365-313X.2010.04124.x

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DOI： 10.4161/psb.5.2.10460

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：OXFORD UNIV PRESS  

ABA and salicylic acid (SA) are believed to act antagonistically. We previously reported that an ABA-hypersensitive mutant ahg2-1, which had reduced expression of poly(A)-specific ribonuclease (PARN), exhibited pleiotropic phenotypes including unique enhanced ABA- and SA-sensitive phenotypes. In this study, we characterized the increased SA-sensitive phenotype of this mutant in detail and addressed its relationship with ABA-related and dwarf phenotypes. We found that the ahg2-1 mutant had a high endogenous SA level and an elevated resistance to bacterial pathogens. Double mutant analyses showed that Arabidopsis plants defective in the SA signaling pathway (npr1 and pad4 mutants and nahG transgenic plants) could suppress neither the ABA hypersensitivity nor the dwarf phenotypes. These results indicate that ABA-related, SA-related and dwarf phenotypes of the ahg2-1 mutant are independent of each other. To obtain more insight into the molecular basis of the effect of ahg2-1, microarray analyses were conducted not only for ahg2-1 but also for ahg2sid2 or ahg2abi1 so as to reduce the secondary effects of SA or ABA. The resulting data indicate that ahg2-1 has a unique gene expression profile, consistent with the novel phenotype of this mutant. Detailed comparison of the expression profiles of up- or down-regulated genes implied that ahg2-1 somehow affects mitochondrial function. Our data suggest that a partial loss of PARN activity affects ABA, SA and mitochondrial function independently, and that the regulation of mRNA levels is deeply implicated in diverse cellular functions.

DOI： 10.1093/pcp/pcp146

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Abscisic acid (ABA) signaling is important for stress responses and developmental processes in plants. A subgroup of protein phosphatase 2C (group A PP2C) or SNF1-related protein kinase 2 (subclass III SnRK2) have been known as major negative or positive regulators of ABA signaling, respectively. Here, we demonstrate the physical and functional linkage between these two major signaling factors. Group A PP2Cs interacted physically with SnRK2s in various combinations, and efficiently inactivated ABA-activated SnRK2s via dephosphorylation of multiple Ser/Thr residues in the activation loop. This step was suppressed by the RCAR/PYR ABA receptors in response to ABA. However the abi1 -1 mutated PP2C did not respond to the receptors and constitutively inactivated SnRK2. Our results demonstrate that group A PP2Cs act as ` gatekeepers' of subclass III SnRK2s, unraveling an important regulatory mechanism of ABA signaling.

DOI： 10.1073/pnas.0907095106

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Authorship：Corresponding author   Language：English   Publisher：Japanese Society for Plant Cell and Molecular Biology  

Plant hormones are known to play important roles for maintenance of internal conditions under various environmental stresses. Recent studies revealed that there is a significant cross-talk between abiotic and biotic stress responses. To understand such complex mechanisms, comprehensive analyses at multiple levels are required. In this study, to examine the dynamic interactions between plant hormone responses, we analyzed the metabolic movements of Arabidopsis thaliana cultured cells during hormone treatments by NMR metabolic profiling. First, we verified the effect of plant hormone treatments on intracellular metabolites, and detected that the abscisic acid (ABA), salicylic acid (SA), auxin, and brassinosteroid treatment caused metabolic changes. Secondly, since SA and ABA act antagonistically against each other, we monitored dynamic metabolic movements during ABA and SA combined treatments. The response to ABA-only treatment suggested that sugars and amino acids significantly increased. Although SA alone caused fewer metabolic changes, SA caused remarkable metabolic changes when applied in combination with ABA. In addition, our NMR data implied that salicylate glucoside (SAG), which is major metabolite converted from SA, significantly increased in the SA-only treatment but decreased with ABA in a dose dependent manner. These results suggest that ABA and SA cross-talk at the metabolite level in a complicate manner and that the combination of various conditions will provide us with a holistic view of plant stress response mechanisms.

DOI： 10.5511/plantbiotechnology.26.551

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Background: Metabolic phenotyping has become an important &apos;bird&apos;s-eye-view&apos; technology which can be applied to higher organisms, such as model plant and animal systems in the post-genomics and proteomics era. Although genotyping technology has expanded greatly over the past decade, metabolic phenotyping has languished due to the difficulty of &apos;top-down&apos; chemical analyses. Here, we describe a systematic NMR methodology for stable isotope-labeling and analysis of metabolite mixtures in plant and animal systems.
Methodology/Principal Findings: The analysis method includes a stable isotope labeling technique for use in living organisms; a systematic method for simultaneously identifying a large number of metabolites by using a newly developed HSQC-based metabolite chemical shift database combined with heteronuclear multidimensional NMR spectroscopy; Principal Components Analysis; and a visualization method using a coarse-grained overview of the metabolic system. The database contains more than 1000 (1)H and (13)C chemical shifts corresponding to 142 metabolites measured under identical physicochemical conditions. Using the stable isotope labeling technique in Arabidopsis T87 cultured cells and Bombyx mori, we systematically detected &gt;450 HSQC peaks in each (13)C-HSQC spectrum derived from model plant, Arabidopsis T87 cultured cells and the invertebrate animal model Bombyx mori. Furthermore, for the first time, efficient (13)C labeling has allowed reliable signal assignment using analytical separation techniques such as 3D HCCH-COSY spectra in higher organism extracts.
Conclusions/Significance: Overall physiological changes could be detected and categorized in relation to a critical developmental phase change in B. mori by coarse-grained representations in which the organization of metabolic pathways related to a specific developmental phase was visualized on the basis of constituent changes of 56 identified metabolites. Based on the observed intensities of (13)C atoms of given metabolites on development-dependent changes in the 56 identified (13)C-HSQC signals, we have determined the changes in metabolic networks that are associated with energy and nitrogen metabolism.

DOI： 10.1371/journal.pone.0003805

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Despite the importance of extracellular events in cell wall organization and biogenesis, the mechanisms and related factors are largely unknown. We isolated an allele of the shaven3 (shv3) mutant of Arabidopsis thaliana, which exhibits ruptured root hair cells during tip growth. SHV3 encodes a novel protein with two tandemly repeated glycerophosphoryl diester phosphodiesterase-like domains and a glycosylphosphatidylinositol anchor, and several of its paralogs are found in Arabidopsis. Here, we report the detailed characterization of mutants of SHV3 and one of its paralogs, SVL1. The shv3 and svl1 double mutant exhibited additional defects, including swollen guard cells, aberrant expansion of the hypocotyl epidermis and ectopic lignin deposits, suggesting decreased rigidity of the cell wall. Fourier-transform infrared spectroscopy and measurement of the cell wall components indicated an altered cellulose content and pectin modification with cross-linking in the double mutant. Furthermore, we found that the ruptured root hair phenotype of shv3 was suppressed by increasing the amount of borate, which is supposed to be involved in pectic polysaccharide cross-linking, in the medium. These findings indicate that SHV3 and its paralogs are novel important factors involved in primary cell wall organization.

DOI： 10.1093/pcp/pcn120

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：OXFORD UNIV PRESS  

In transposon-tagged lines of Arabidopsis we found two new mutants, cof1-1 and cof1-2 (uticular defect and organ fusion), that show the phenotype of wilting when grown in soil, organ fusion of rosette leaves and infertility. Toluidine blue testing and scanning electron microscopy observation revealed that these mutants had cuticular defects in the stems and adult leaves, but not in cotyledones. Transmission electron microscopy observation revealed thinner cuticle layers in the mutants, and cuticular materials interspersed between the two fused epidermal layers were observed in the mutant rosette leaves. These two mutants had a transposon insertion in the coding regions of WBC11, which was classified as a member of ABC transporter genes in Arabidopsis. WBC11 showed high sequence similarity to CER5 (also called WBC12), which was involved in cuticular lipid export. Gas chromatographic analysis revealed that C29 alkane extracted from the stem surface of cof1 mutants was reduced whereas C29 ketone was accumulated, which was different from the case of cer5 mutants. While cer5 mutants had fairly normal morphology, cof1 mutants had pleiotropic phenotypes so that COF1/WBC11 could have important roles different from those of CER5/WBC12. We also found that C29 alkane was accumulated in the intracellular extract of cof1 mutants, suggesting a function for WBC11 in the direct transport of lipid molecules. Pollen observation showed that mutant pollen grains were irregularly shaped. The function of COF1/WBC11 in lipid transport for the construction of cuticle layers and pollen coats for normal organ formation is discussed.

DOI： 10.1093/pcp/pcm139

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Authorship：Lead author   Language：English   Publisher：ELSEVIER SCIENCE LONDON  

During the past decade, much progress has been made toward understanding the mechanisms underlying plant hormone activity, from perception to nuclear events. However, the signaling mechanisms for abscisic acid (ABA) have remained largely obscure. Recent breakthroughs identifying FCA, which is an RNA-binding protein, the Mg-chelatase H subunit, and a G protein-coupled receptor as receptors for ABA provide a major leap forward in understanding the initial steps of ABA signaling mechanisms. Recent studies have also revealed the molecular mechanisms of second messenger production, protein modifications such as phosphorylation, and regulatory mechanisms of gene expression in the ABA response. Therefore, the connections between these events are also beginning to be determined. Here, e review recent progress and discuss the overall scheme of the ABA response mechanisms.

DOI： 10.1016/j.tplants.2007.06.013

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：BLACKWELL PUBLISHING  

The phytohormone abscisic acid (ABA) regulates physiologically important stress and developmental responses in plants. To reveal the mechanism of response to ABA, we isolated several novel ABA-hypersensitive Arabidopsis thaliana mutants, named ahg ((A) under bar ABA-(h) under bar ypersensitive (g) under bar ermination). ahg1-1 mutants showed hypersensitivity to ABA, NaCl, KCl, mannitol, glucose and sucrose during germination and post-germination growth, but did not display any significant phenotypes in adult plants. ahg1-1 seeds accumulated slightly more ABA before stratification and showed increased seed dormancy. Map-based cloning of AHG1 revealed that ahg1-1 has a nonsense mutation in a gene encoding a novel protein phosphatase 2C (PP2C). We previously showed that the ahg3-1 mutant has a point mutation in the AtPP2CA gene, which encodes another PP2C that has a major role in the ABA response in seeds (Yoshida et al., 2006b). The levels of AHG1 mRNA were higher in dry seeds and increased during late seed maturation - an expression pattern similar to that of ABI5. Transcriptome analysis revealed that, in ABA-treated germinating seeds, many seed-specific genes and ABA-inducible genes were highly expressed in ahg1-1 and ahg3-1 mutants compared with the wild-type. Detailed analysis suggested differences between the functions of AHG1 and AHG3. Dozens of genes were expressed more strongly in the ahg1-1 mutant than in ahg3-1. Promoter-GUS analyses demonstrated both overlapping and distinct expression patterns in seed. In addition, the ahg1-1 ahg3-1 double mutant was more hypersensitive than either monogenic mutant. These results suggest that AHG1 has specific functions in seed development and germination, shared partly with AHG3.

DOI： 10.1111/j.1365-313X.2007.03107.x

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：25  

Elucidating the function of each gene in a genome is important for understanding the whole organism. We previously constructed 4000 disruptant mutants of Arabidopsis by insertion of Ds transposons. Here, we describe a top-down phenomics approach based on metabolic profiling that uses one-dimensional H-1 and two-dimensional H-1, C-13 NMR analyses and transcriptome analysis of albino mutant lines of Arabidopsis. One-dimensional H-1 NMR metabolic fingerprinting revealed global metabolic changes in the albino mutants, notably a decrease in aromatic metabolites and changes in aliphatic metabolites. NMRmeasurements of plants fed with C-13(6)-glucose showed that the albino lines had dramatically different C-13-labeling patterns and increased levels of several (am)ino acids, especially Asn and Gln. Microarray analysis of one of the albino lines revealed a unique expression profile and showed that changes in the expression of genes encoding metabolic enzymes did not correspond with changes in the levels of metabolites. Collectively, these results suggest that albino mutants lose the normal carbon/nitrogen balance, presumably mainly through lack ofphotosynthesis. Our study offers an idea of how much the metabolite network is affected by chloroplast function in plants and shows the effectiveness of NMR-based metabolic analysis for metabolite profiling. On the basis of these findings, we propose that future investigations of plant systems biology combine transcriptomic, metabolomic, and phenomic analyses of gene disruptant lines.

DOI： 10.1074/jbc.M700549200

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Acid soil syndrome causes severe yield losses in various crop plants because of the rhizotoxicities of ions, such as aluminum (Al3+). Although protons (H+) could be also major rhizotoxicants in some soil types, molecular mechanisms of their tolerance have not been identified yet. One mutant that was hypersensitive to H+ rhizo-toxicity was isolated from ethyl methanesulfonate mutagenized seeds, and a single recessive mutation was found on chromosome 1. Positional cloning followed by genomic sequence analysis revealed that a missense mutation in the zinc finger domain in a predicted CY5(2)His(2)-type zinc finger protein, namely sensitive to proton rhizotoxicity (STOP)1, is the cause of hypersensitivity to H+ rhizotoxicity. The STOP1 protein belongs to a functionally unidentified subfamily of zinc finger proteins, which consists of two members in Arabidopsis based on a Blast search. The stop1 mutation resulted in no effects on cadmium, copper, lanthanum, manganese and sodium chloride sensitivitities, whereas it caused hypersensitivity to Al3+ rhizotoxicity. This stop1 mutant lacked the induction of the AtALMT1 gene encoding a malate transporter, which is concomitant with Al-indluced malate exudation. There was no induction of AtALMT1 by Al3+ treatment in the stop1 mutant. These results indicate that STOP1 plays a critical role in Arabidopsis tolerance to major stress factors in acid soils.

DOI： 10.1073/pnas.0700117104

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We isolated a lesion mimic mutant, n ecrotic potted lesions 1 (nsl1), from Ds-tagged Arabidopsis thaliana accession No-0. The nsl1 mutant exhibits a growth retardation phenotype and develops spotted necrotic lesions on its rosette and cauline leaves. These phenotypes occur in the absence of pathogens indicating that nsl1 mutants may constitutively express defense responses. Consistent with this idea, nsl1 accumulates high levels of callose and autofluorescent phenolic compounds localized to the necrotic lesions. Furthermore RNA gel blot analysis revealed that genes associated with disease resistance activation are upregulated in the nsl1 mutants and these plants contain elevated levels of salicylic acid (SA). Crossing nsl1 with an SA deficient mutant, eds16-1, revealed that the nsl1 lesions and growth retardation are dependent upon SA. The nsl1 phenotypes are not suppressed under either the rar1-10 or sgt1b-1 genetic background. NSL1 encodes a novel 612aa protein which contains a membrane-attack complex/perforin (MACPF) domain, which is conserved in bacteria, fungi, mammals and plants. The possible modes of action of NSL1 protein in negative regulation of cell death programs and defense responses are discussed.

DOI： 10.1007/s11103-006-9001-6

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Mutant lines covering all Arabidopsis genes allow us to pursue systematic functional genomics. A comprehensive phenotype description, called a phenome, is highly sought after in the profiling of -omics data. We selected 4000 transposon-insertional lines with transposon insertions in their gene-coding regions, and systematically observed the visible phenotype of each line. For the first 3 weeks after germination, plants were grown on agar plates and the juvenile phenotypes were recorded. Then the plants were transferred to soil and their phenotypes were recorded at each growth stage. About 140 lines showed clear and reproducible visible phenotypes, including novel phenotypic mutants as well as previously reported ones. All descriptions of the mutants showing visible phenotypes were classified into eight primary categories (seedling, leaves, flowering and growth, stems, branching, flowers, siliques and seed yield) and 43 secondary categories of morphological phenotypes. Phenotypic images have been entered into a searchable database (http://rarge.gsc.riken.jp/phenome/). One example investigated through the use of plural alleles was a mutant of a novel gene related to glycerolipid biosynthesis, with a unique visible phenotype of sepal opening. Our results suggest that we can find more novel visible phenotypes and their corresponding genes, and that phenotypic mutants of gene knockouts are not exhausted yet. This study provides basic data on large-scale phenotyping of gene knockout lines in plants, and will contribute to the completion of an international effort to develop a phenome database of all the functional genes in Arabidopsis.

DOI： 10.1111/j.1365-313X.2006.02808.x

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER SOC PLANT BIOLOGISTS  

The phytohormone abscisic acid (ABA) regulates physiologically important developmental processes and stress responses. Previously, we reported on Arabidopsis (Arabidopsis thaliana) L. Heynh. ahg mutants, which are hypersensitive to ABA during germination and early growth. Among them, ABA-hypersensitive germination3 (ahg3) showed the strongest ABA hypersensitivity. In this study, we found that the AHG3 gene is identical to AtPP2CA, which encodes a protein phosphatase 2C (PP2C). Although AtPP2CA has been reported to be involved in the ABA response on the basis of results obtained by reverse-genetics approaches, its physiological relevance in the ABA response has not been clarified yet. We demonstrate in vitro and in vivo that the ahg3-1 missense mutation causes the loss of PP2C activity, providing concrete confirmation that this PP2C functions as a negative regulator in ABA signaling. Furthermore, we compared the effects of disruption mutations of eight structurally related PP2C genes of Arabidopsis, including ABI1, ABI2, HAB1, and HAB2, and found that the disruptant mutant of AHG3/AtPP2CA had the strongest ABA hypersensitivity during germination, but it did not display any significant phenotypes in adult plants. Northern-blot analysis clearly showed that AHG3/AtPP2CA is the most active among those PP2C genes in seeds. These results suggest that AHG3/AtPP2CA plays a major role among PP2Cs in the ABA response in seeds and that the functions of those PP2Cs overlap, but their unique tissue- or development-specific expression confers distinct and indispensable physiological functions in the ABA response.

DOI： 10.1104/pp.105.070128

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

Accumulating evidence suggests that mRNA degradation systems are crucial for various biological processes in eukaryotes. Here we provide evidence that an mRNA degradation system is associated with some plant hormones and stress responses in plants. We analysed a novel Arabidopsis abscisic acid (ABA)-hypersensitive mutant, ahg2-1, that showed ABA hypersensitivity not only in germination, but also at later developmental stages, and that displayed pleiotropic phenotypes. We found that ahg2-1 accumulated more endogenous ABA in seeds and mannitol-treated plants than did the wild type. Microarray experiments showed that the expressions of ABA-, salicylic acid- and stress-inducible genes were increased in normally grown ahg2-1 plants, suggesting that the ahg2-1 mutation somehow affects various stress responses as well as ABA responses. Map-based cloning of AHG2 revealed that this gene encodes a poly(A)-specific ribonuclease (AtPARN) that is presumed to function in mRNA degradation. Detailed analysis of the ahg2-1 mutation suggests that the mutation reduces AtPARN production. Interestingly, expression of AtPARN was induced by treatment with ABA, high salinity and osmotic stress. 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.

DOI： 10.1111/j.1365-313X.2005.02589.x

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：OXFORD UNIV PRESS  

To gain more insight into ABA signaling mechanisms, we conducted genetic screens searching for mutants with altered ABA response in germination and post-germination growth. We isolated seven putative ABA-hypersensitive Arabidopsis mutants and named them ABA-hypersensitive germination (ahg). These mutants exhibited diminished germination or growth ability on medium supplemented with ABA. We further studied four of them: ahg1, ahg2, ahg3 and ahg4. Mapping suggested that they were new ABA-hypersensitive loci. Characterization showed that all of them had enhanced sensitivity to salinity and high osmotic stress in germinating seeds, whereas they each had distinct sugar responses. RT-PCR experiments showed that the expression patterns of the ABA-inducible genes RAB18, AtEm1, AtEm6 and ABI5 in germinating seeds were affected by these four ahg mutations, whereas those of ABI3 and ABI4 were not. ahg4 displayed slightly increased mRNA levels of several ABA-inducible genes upon ABA treatment. By contrast, ahg1 had no clear ABA-hypersensitive phenotypes in adult plants despite its strong phenotype in germination. These results suggest that ahg1, ahg2, ahg3 and ahg4 are novel ABA-hypersensitive mutants representing distinct components in the ABA response.

DOI： 10.1093/pcp/pch171

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：OXFORD UNIV PRESS  

Storage of excess nitrate in the vacuole and its subsequent remobilization is an important aspect of a plant's nitrogen economy, but the genes controlling the underlying processes have not all been identified and characterized. Cape Verdi Island (Cvi)/Landsberg erecta (Ler) and Columbia (Col)/Landsberg erecta recombinant inbred line (RIL) populations of Arabidopsis thaliana were used to identify quantitative trait loci (QTL) controlling natural variation in nitrate concentrations. One major and two minor QTLs were found for the Cvi/Ler population and one minor QTL for the Col/Ler RIL. These were designated NA1 to NA4. The major Cvi/Ler QTL (NA3) was located at the bottom of chromosome 5. No interaction among the QTLs was found by two-way ANOVA. By comparing in silico the locations of the QTLs with a physical map of the Arabidopsis genome, candidate genes for each QTL were identified. Several of these were anion channels of the AtCLC family. One of these, AtCLC-c, coincided with NA3 and its role was investigated using a mutant with a transposon insertion in AtCLC-c. Mutant plants homozygous for the insertion (designated clcc-1) had less than 5% of AtCLC-c mRNA compared with wild-type (WT) shoots. They also had significantly lower nitrate concentrations when grown at a range of external nitrate concentrations. The concentrations of chloride, malate, and citrate were also affected in the mutant. In wild-type plants, expression of AtCLC-c was down-regulated in the presence of nitrate, but ammonium had a much smaller effect while chloride and sulphate did not affect expression. These and published results suggest that multiple genes affect nitrate concentrations in plants and that AtCLC-c and other members of the AtCLC gene family play some role in this.

DOI： 10.1093/jxb/erh224

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：OXFORD UNIV PRESS  

We analyzed the spatial expression pattern of Arabidopsis thaliana adenosine phosphates-isopentenyltransferase genes (AtIPT1, AtIPT3 to AtIPT8) and the effect of inorganic nitrogen sources on their regulation. In mature plants, the AtIPTs were differentially expressed in various tissues including the roots, leaves, stems, flowers and siliques. In transgenic seedlings expressing a gene for green fluorescent protein (GFP) driven by the AtIPT promoters, AtIPT1::GFP was predominantly expressed in the vascular stele of the roots, AtIPT3::GFP was in the phloem companion cells, AtIPT5::GFP was in the lateral root primordium and pericycle, and AtIPT7::GFP was in both the vascular stele and the phloem companion cells of the roots. In a long-term treatment, the accumulation level of AtIPT5 transcript was correlated with the concentrations of NO3- and NH4+ in the growth medium. However, under nitrogen-limited conditions, AtIPT3 expression was rapidly induced by NO3- in the seedlings accompanying the accumulation of cytokinins, whereas AtIPT5 expression was little affected. The NO3--dependent accumulation of both the AtIPT3 transcript and the cytokinins was markedly reduced in a Ds transposon-insertion mutant of AtIPT3. These results suggest that nitrogen availability differentially regulates expression of AtIPT3 and AtIPT5, and that AtIPT3 is a key determinant of cytokinin biosynthesis in response to rapid changes in the availability of NO3-.

DOI： 10.1093/pcp/pch119

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：OXFORD UNIV PRESS  

Nuclear magnetic resonance (NMR) will become a key technology in plant metabolomics with the use of stable isotope labeling and advanced hetero-nuclear NMR methodologies. To demonstrate the power of this approach, we performed multi-dimensional hetero-nuclear NMR analysis of metabolic movement of carbon and nitrogen nuclei in Arabidopsis thaliana. First, distinct ethanol-stress response was investigated using (13)C-labeled wild type and an ethanol-hypersensitive mutant plants. Furthermore, we followed nitrogen fluxes in (15)N-labeled seeds during the initiation of germination in vivo. The future role of stable isotope-labeling combined with advanced hetero-nuclear NMR in plant metabolomics is discussed.

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER PHYTOPATHOLOGICAL SOC  

When challenged with the crucifer pathogen Colletotrichum higginsianum, Arabidopsis thaliana ecotype Columbia (Col-0) was colonized by the fungus within 2 to 3 days, developing brown necrotic lesions surrounded by a yellow halo. Lesions spread from the inoculation site within 3 to 4 days, and subsequently continued to expand until they covered the entire leaf. Electron microscopy confirmed that C. higginsianum is a hemibiotroph on Arabidopsis, feeding initially on living cells as a biotroph before switching to a necrotrophic mode of growth. A collection of 37 ecotypes of Arabidopsis varied in their responses to infection by C. higginsianum. The ecotype Eil-0 was highly resistant, with symptoms limited to necrotic flecking and with only very limited fungal colonization. Analyses suggested that the hypersensitive response and reactive oxygen species may be important in this defense response. Expression analyses with cDNA microarrays indicated that the defense reaction depends primarily on the jasmonic acid- and ethylene-dependent signaling pathways and, to a lesser extent, on the salicylate-dependent pathway. Crosses between the Eil-0 and Col-0 ecotypes suggested that the resistance in Eil-0 was dominant and was conferred by a single locus, which we named RCH1. RCH1 is the first resistance locus to be identified from Arabidopsis against the hemibiotrophic fungus genus Colletotrichum.

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Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：OXFORD UNIV PRESS  

A novel ethanol-hypersensitive mutant, gek1, of Arabidopsis shows 10-100 times greater sensitivity to ethanol compared to the wild type, while it grows normally in the absence of ethanol, and responds normally to other alcohols and to environmental stresses such as heat shock and high salinity. Mapping of the gek1 locus indicated it is a previously unreported locus. In order to address the GEK1 function, we identified the GEK1 gene by means of map-based cloning. The GEK1 gene encodes a novel protein without any known functional motifs. Transgenic Arabidopsis plants overexpressing GEK1 displayed an enhanced tolerance to ethanol and acetaldehyde, suggesting that GEK1 is directly involved in the tolerance to those chemicals. By contrast, expression of GEK1 in E. coli and yeasts did not increase their tolerance to ethanol or acetaldehyde. Interestingly, a similarity search revealed that GEK1-related genes are conserved only in plants and archaea. These results might suggest that plants, and presumably archaea, have a novel mechanism for protection from acetaldehyde toxicity.

DOI： 10.1093/pcp/pch086

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：OXFORD UNIV PRESS  

A novel ethanol-hypersensitive mutant, geko1 (gek1), was isolated from Arabidopsis thaliana. The gek1 mutant displays an enhanced sensitivity (10-100 times greater than the wild type) to ethanol in growth medium, while it grows normally in the absence of ethanol, and responds normally to other alcohols and to environmental stresses such as heat shock and high salinity. The ethanol-hypersensitive phenotype of gek1 requires alcohol dehydrogenase activity, indicating that gek1 is sensitive not to ethanol itself but to the metabolites of ethanol. Consistent with this, gek1 shows enhanced sensitivity to acetaldehyde in the medium. The endogenous acetaldehyde levels were not different between gek1-2 and wild-type seedlings treated with ethanol. These results indicate that the ethanol hypersensitivity of gek1 is due to an enhanced sensitivity to acetaldehyde toxicity, instead of abnormally elevated accumulation of toxic acetaldehyde, which has been thought to be the major cause of ethanol toxicity in mammal cells.

DOI： 10.1093/pcp/pch078

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：BLACKWELL PUBLISHING LTD  

More than 10 000 transposon-tagged lines were constructed by using the Activator (Ac)/Dissociation (Ds) system in order to collect insertional mutants as a useful resource for functional genomics of Arabidopsis. The flanking sequences of the Ds element in the 11 800 independent lines were determined by high-throughput analysis using a semi-automated method. The sequence data allowed us to map the unique insertion site on the Arabidopsis genome in each line. The Ds element of 7566 lines is inserted in or close to coding regions, potentially affecting the function of 5031 of 25 000 Arabidopsis genes. Half of the lines have Ds insertions on chromosome 1 (Chr. 1), in which donor lines have a donor site. In the other half, the Ds insertions are distributed throughout the other four chromosomes. The intrachromosomal distribution of Ds insertions varies with the donor lines. We found that there are hot spots for Ds transposition near the ends of every chromosome, and we found some statistical preference for Ds insertion targets at the nucleotide level. On the basis of systematic analysis of the Ds insertion sites in the 11 800 lines, we propose the use of Ds-tagged lines with a single insertion in annotated genes for systematic analysis of phenotypes (phenome analysis) in functional genomics. We have opened a searchable database of the insertion-site sequences and mutated genes (http://rarge.gsc.riken.go.jp/) and are depositing these lines in the RIKEN BioResource Center as available resources (http://www.brc.riken.go.jp/Eng/).

DOI： 10.1111/j.1365-313X.2003.02009.x

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DOI： 10.1093/pcp/pch009

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DOI： 10.1093/pcp/pch117

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：OXFORD UNIV PRESS  

Phospholipid metabolism is involved in hyperosmotic-stress responses in plants. To investigate the role of phosphoinositide-specific phospholipase C (PI-PLC)-a key enzyme in phosphoinositide turnover-in hyperosmotic-stress signaling, we analyzed changes in inositol 1,4,5-trisphosphate (Ins(1,4,5)P-3) content in response to hyperosmotic shock or salinity in Arabidopsis thaliana T87 cultured cells. Within a few s, a hyperosmotic shock, caused by mannitol, NaCl, or dehydration, induced a rapid and transient increase in Ins(1,4,5)P-3. However, no transient increase was detected in cells treated with ABA, Neomycin and U73122, inhibitors of PI-PLC, inhibited the increase in Ins(1,4,5)P-3 caused by the hyperosmotic shock. A rapid increase in phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P-2) in response to the hyperosmotic shock also occurred, but the rate of increase was much slower than that of Ins(1,4,5)P-3. These findings indicate that the transient Ins(1,4,5)P-3 production was due to the activation of PI-PLC in response to hyperosmotic stress. PI-PLC inhibitors also inhibited hyperosmotic stress-responsive expression of some dehydration-inducible genes, such as rd29A (lti78/cor78) and rd17 (cor47), that are controlled by the DRE/CRT cis-acting element but did not inhibit hyperosmotic stress-responsive expression of ABA-inducible genes, such as rd20. Taken together, these results suggest the involvement of PI-PLC and Ins(1,4,5)P-3 in an ABA-independent hyperosmotic-stress signal transduction pathway in higher plants.

DOI： 10.1093/pcp/pce028

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Authorship：Lead author,　Corresponding author   Language：English   Publisher：JAPANESE SOC PLANT PHYSIOLOGISTS  

More than three decades ago, transition metal such as copper or zinc were postulated to be required for the ethylene perception. However, there was no direct evidence for this metal requirement until very recently. Two studies using arabidopsis thaliana, one genetic and the other biochemical, have provided complementary evidence for the role of copper in ethylene perception, closing this argument. Additional evidence for the importance of the metal in the ethylene-signaling pathway came with the recent discovery that EIN2, a central signal transducer in the ethylene-signaling pathway, has significant homology to the Nramp divalent cation transporters. These studies suggest that metal metabolism may have a critical role not only in ethylene perception but also in ethylene signaling.

DOI： 10.1093/pcp/41.5.548

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER SOC PLANT PHYSIOLOGISTS  

Water deficit and the resulting osmotic stress affect plant growth. To understand how plant cells monitor and respond to osmotic change from water stress, we isolated a cDNA from dehydrated Arabidopsis plants, This cDNA encodes a novel hybrid-type histidine kinase, ATHK1. Restriction fragment length polymorphism mapping showed that the ATHK1 gene is on chromosome 2. The predicted ATHK1 protein has two putative transmembrane regions in the N-terminal half and has structural similarity to the yeast osmosensor synthetic lethal of N-end rule 1 (SLN1), The ATHK1 transcript was more abundant in roots than other tissues under normal growth conditions and accumulated under conditions of high or low osmolarity. Histochemical analysis of beta-glucuronidase activities driven by the ATHK1 promoter further indicates that the ATHK1 gene is transcriptionally upregulated in response to changes in external osmolarity, Overexpression of the ATHK1 cDNA suppressed the lethality of the temperature-sensitive osmosensing-defective yeast mutant sin I-ts. By contrast, ATHK1 cDNAs in which conserved His or Asp residues had been substituted failed to complement the sin1-ts mutant, indicating that ATHK1 functions as a histidine kinase. Introduction of the ATHK1 cDNA into the yeast double mutant sin1 Delta sho1 Delta which lacks two osmosensors, suppressed lethality in high-salinity media and activated the high-osmolarity glycerol response 1 (HOG1) mitogen-activated protein kinase (MAPK). These results imply that ATHK1 functions as an osmosensor and transmits the stress signal to a downstream MAPK cascade.

DOI： 10.1105/tpc.11.9.1743

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER ASSOC ADVANCEMENT SCIENCE  

Ethylene regulates plant growth, development, and responsiveness to a variety of stresses. Cloning of the Arabidopsis EIN2 gene identifies a central component: of the ethylene signaling pathway. The amino-terminal integral membrane domain of EIN2 shows similarity to the disease-related Nramp family of metal-ion transporters. Expression of the EIN2 CEND is sufficient to constitutively activate ethylene responses and restores responsiveness to jasmonic acid and paraquat-induced oxygen radicals to mutant plants. EIN2 is thus recognized as a molecular link between previously distinct hormone response pathways. plants may use a combinatorial mechanism for assessing various stresses by enlisting a common set of signaling molecules.

DOI： 10.1126/science.284.5423.2148

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：CELL PRESS  

Ethylene is an important regulator of plant growth. We identified an Arabidopsis mutant, responsive-to-antagonist1 (ran1), that shows ethylene phenotypes in response to treatment with trans-cyclooctene, a potent receptor antagonist. Genetic epistasis studies revealed an early requirement for RAN1 in the ethylene pathway. RAN1 was cloned and found to encode a protein with similarity to copper-transporting P-type ATPases, including the human Menkes/Wilson proteins and yeast Ccc2p. Expression of RAN1 complemented the defects of a ccc2 Delta mutant, demonstrating its function as a copper transporter. Transgenic CaMV 35S::RAN1 plants showed constitutive expression of ethylene responses, due to cosuppression of RAN1. These results provide an in planta demonstration that ethylene signaling requires copper and reveal that RAN1 acts by delivering copper to create functional hormone receptors.

DOI： 10.1016/S0092-8674(00)80747-3

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Language：English  

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

To isolate Arabidopsis cDNAs that encode signal transducers and components involved in the regulation of meiosis, a trans-complementation analysis was performed using a Schizosaccharomyces pombe meiosis-defective mutant in which the genes for pheromone receptors were disabled, One cDNA obtained in this screening encodes a polypeptide, named AML1, that shows significant similarity to S, pombe Mei2 protein and has three putative RNA-recognition motifs like as Mei2, Mei2 is involved in the regulation of meiosis in fission yeast, Northern blot analysis showed that the AML1 gene is expressed in each organ, The possible functions of AML1 are discussed, (C) 1997 Federation of European Biochemical Societies.

DOI： 10.1016/S0014-5793(97)00871-5

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：KLUWER ACADEMIC PUBL  

A cDNA encoding a phosphoinositide-specific phospholipase C (PI-PLC) from the higher plant Arabidopsis thaliana was cloned and characterized.
The gene corresponding to this cDNA is designated AtPLC2. The overall structure of the predicted AtPLC2 protein is similar to those of plant PI-PLCs and mammalian delta-type PI-PLCs. Northern blot analysis revealed that AtPLC2 is expressed constitutively whereas AtPLC1S, another gene for PI-PLC of Arabidopsis, is induced by environmental stresses such as dehydration and salinity, indicating that the function of AtPLC2 is distinct from that of AtPLC1S. The AtPLC2 mRNA was detected in vegetative and floral tissues. We determined the positions of these two PI-PLCs genes on Arabidopsis chromosomes by RFLP mapping using P1 genomic clones.

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We cloned and characterized a cDNA corresponding to a cdc5(+) homolog of the higher plant, Arabidopsis thaliana. The cDNA, named AtCDC5 cDNA, encodes a polypeptide of 844 amino acid residues. The amino acid sequence of N-terminal one-fourth region of the predicted protein bears significant similarity to that of Schizosaccharomyces pombe Cdc5 and Myb-related proteins. Overexpression of the AtCDC5 cDNA in S. pombe cells is able to complement the growth defective phenotype of a cdc5 temperature-sensitive mutant. These results indicate that the AtCDC5 gene is a plant counterpart of S. pombe cdc5(+). This is the first report of a cdc5(+)-like gene in a multicellular organism. We also demonstrated that a recombinant AtCDC5 protein possesses a sequence specific DNA binding activity (CTCAGCG) and the AtCDC5 gene is expressed extensively in shoot and root meristems. In addition, we cloned a PCR fragment corresponding to the DNA binding domain of human Cdc5-like protein. These results strongly suggest that Cdc5-like protein exists in all eukaryotes and may function in cell cycle regulation.

DOI： 10.1073/pnas.93.23.13371

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We describe here the cloning and characterization of a cDNA encoding a protein kinase that has high sequence homology to members of the mitogen-activated protein kinase (MAPK) kinase kinase (MAPKKK or MEKK) family; this cDNA is named cATMEKK1 (Arabidopsis thaliana MAP kinase or ERK kinase kinase 1), The catalytic domain of the putative ATMEKK1 protein shows approximate to 40% identity with the amino acid sequences of the catalytic domains of MAPKKKs (such as Byr2 from Schizosaccharomyces pombe, Ste11 from Saccharomyces cerevisiae, Bck1 from S. cerevisiae, MEKK from mouse, and NPK1 from tobacco), In yeast cells that overexpress ATMEKK1, the protein kinase replaces Ste11 in responding to mating pheromone, In this study, the expression of three protein kinases was examined by Northern blot analyses: ATMEKK1 (structurally related to MAPKKK), ATMPK3 (structurally related to MAPK), and ATPK19 (structurally related to ribosomal S6 kinase), The mRNA levels of these three protein kinases increased markedly and simultaneously in response to touch, cold, and salinity stress. These results suggest that MAP kinase cascades, which are thought to respond to a variety of extracellular signals, are regulated not only at the posttranslational level but also at the transcriptional level in plants and that MAP kinase cascades in plants may function in transducing signals in the presence of environmental stress.

DOI： 10.1073/pnas.93.2.765

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATL ACAD SCIENCES  

A cDNA corresponding to a putative phosphatidylinositol-specific phospholipase C (PI-PLC) in the higher plant Arabidopsis thaliana was cloned by use of the polymerase chain reaction, The cDNA, designated cAtPLC1, encodes a putative polypeptide of 561 aa with a calculated molecular mass of 64 kDa. The putative product includes so-called X and Y domains found in all PI-PLCs identified to date. In mammalian cells, there are three types of PI-PLC, PLC-beta, -gamma, and -delta. The overall structure of the putative AtPLC1 protein is most similar to that of PLC-delta, although the AtPLC1 protein is much smaller than PLCs from other organisms. The recombinant AtPLC1 protein synthesized in Escherichia coli was able to hydrolyze phosphatidylinositol 4,5-bisphosphate and this activity was completely dependent on Ca2+, as observed also for mammalian PI-PLCs. These results suggest that the AtPLC1 gene encodes a genuine PI-PLC of a higher plant. Northern blot analysis showed that the AtPLC1 gene is expressed at very low levels in the plant under normal conditions but is induced to a significant extent under various environmental stresses, such as dehydration, salinity, and low temperature, These observations suggest that AtPLC1 might be involved in the signal-transduction pathways of environmental stresses and that an increase in the level of AtPLC1 might amplify the signal, in a manner that contributes to the adaptation of the plant to these stresses.

DOI： 10.1073/pnas.92.9.3903

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Language：English   Publishing type：Research paper (international conference proceedings)   Publisher：KLUWER ACADEMIC PUBL  

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DOI： 10.1007/BF00290358

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During the course of characterizing polymerase chain reaction products corresponding to protein kinases of a higher plant, Arabidopsis thaliana, we found a DNA fragment that potentially codes for a polypeptide with mosaic sequences of two classes of protein kinases, a tyrosine-specific and a serine/threonine-specific one. Overlapping complementary-DNA (cDNA) clones coinciding with this fragment were isolated from an A. thaliana cDNA library. From their sequence analyses a protein kinase was predicted composed of 410 amino acid residues (APK1, Arabidopsis protein kinase 1), in which the kinase domain was flanked by short non-kinase domains. Upon expression of APK1 in Escherichia coli cells, several bacterial proteins became reactive with anti-phosphotyrosine antibody but not with the same antibody preincubated with phosphotyrosine, convincing us that APK1 phosphorylated tyrosine residues. APK1 purified from an over-producing E. coli strain showed serine/threonine kinase activity, and no tyrosine kinase activity, towards APK1 itself, casein, enolase, and myosin light chains. APK1 was thus concluded to be a novel type of protein kinase, which could phosphorylate tyrosine, serine, and threonine residues, though tyrosine phosphorylation seemed to occur only on limited substrates. Since the structure of the APK1 N-terminal portion was indicative of N-myristoylation, APK1 might associate with membranes and thereby contribute to signal transduction. The A. thaliana genome contained two APK1 genes close to each other (APK1a and APK1b).

DOI： 10.1007/BF00046450

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We have previously shown by cDNA cloning that a higher plant, Arabidopsis thaliana, possesses at least two CDC2 genes (CDC2a and CDC2b) similar to the cell-cycle-controlling cdc2 gene of Schizosaccharomyces pombe. To understand the exon-intron organization of these genes, genomic clones were isolated and their nucleotide sequences determined. The coding and 5'-untranslated regions of CDC2a were interrupted by seven and one introns, respectively, whilst CDC2h contained three introns within the coding portion. These intron positions partly overlapped with each other and with those of the yeast cdc2 gene, nevertheless the lengths and sequences of the corresponding introns were diverse.

DOI： 10.1016/0014-5793(92)80592-5

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Other Link： http://orcid.org/0000-0002-3868-2380

Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

The cdc2 gene product (p34cdc2) has been thought to play a central role in control of the mitotic cell cycle of yeasts and animals. To approach an understanding of the cell-cycle-control system in higher plants, we isolated, from an Arabidopsis thaliana cDNA library, two clones (CDC2a and CDC2b) similar to the Schizosaccharomyces pombe cdc2 gene. Genomic Southern-blot analysis with the CDC2a and CDC2b cDNA probes suggested that the A. thaliana genome contains several additional cdc2-like genes, which together with the CDC2a and CDC2b genes may constitute at CDC2 gene family. The CDC2a cDNA expressed in Sc. pombe corrected the elongated morphology, caused by the temperature-sensitive cdc2-33 mutation, to the normal shapes, indicating that the A. thaliana CDC2a gene product resembles Sc. pombe p34cdc2 functionally as well as structurally. These results support the view that the cell cycle of higher plants is controlled by an analogue of a p34cdc2 -centered regulatory system like that of yeasts and animals.

DOI： 10.1016/0378-1119(91)90146-3

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Other Link： http://orcid.org/0000-0002-3868-2380

Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

DOI： 10.1016/0014-5793(90)80364-O

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Other Link： http://orcid.org/0000-0002-3868-2380

Language：English   Publisher：ELSEVIER SCIENCE BV  

DOI： 10.1016/0378-1119(89)90325-9

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Other Link： http://orcid.org/0000-0002-3868-2380

Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER VERLAG  

DOI： 10.1007/BF00339586

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Other Link： http://orcid.org/0000-0002-3868-2380

Language：Japanese   Publisher：公益社団法人 日本農芸化学会  

DOI： 10.1271/kagakutoseibutsu.48.555

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Language：English   Publisher：(一社)日本生物物理学会  

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DOI： 10.14841/jspp.2007.0.S039.0

J-GLOBAL

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Publisher：日本植物生理学会  

When challenged with the fungus &lt;i&gt;Colletotrichum higginsianum&lt;/i&gt;, &lt;i&gt;Arabidopsis&lt;/i&gt; accession Columbia plant (Col-0) developed brown necrotic lesions, including a yellow halo around the lesion. The &lt;i&gt;Arabidopsis&lt;/i&gt; accessions showed variation in response to &lt;i&gt;C. higginsianum&lt;/i&gt;. &lt;i&gt;Arabidopsis&lt;/i&gt; accession Eil-0 was highly resistant to &lt;i&gt;C. higginsianum&lt;/i&gt;. In the Eil-0 plant inoculated with the fungus, cell death did not appear as a rapid response, and the level of camalexin accumulated was low. Analyses using RNA gel blotting and cDNA microarray suggested that the defense responses against &lt;i&gt;C. higginsianum&lt;/i&gt; occur mainly through the JA/ET-dependent pathway. Segregation analysis of progeny from crosses between Eil-0 and Col-0 plants was performed to determine the genetic basis of resistance. The resistance was dominant and seemed to be conferred by a single locus. &lt;i&gt;Arabidopsis&lt;/i&gt; and &lt;i&gt;C. higginsianum&lt;/i&gt; provide an excellent pathosystem for studying the molecular and cellular bases of plant-pathogen interactions

DOI： 10.14841/jspp.2004.0.454.0

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Language：Japanese   Publisher：植物化学調節学会  

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Language：Japanese   Publisher：東京化学同人  

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Language：Japanese   Publisher：The Japanese Society for Chemical Regulation of Plants  

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Event date： 2011.6.14 - 2011.6.18

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Event date： 2007.3.15

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Event date： 2006.3

Language：Japanese  

In these days of post genome era, metabolome studies attract more attention because the information on metabolites is the key data for so-called systems biology. To analyze the metabolites, mass spectrometry (MS) has been used mainly. However, the MS analysis is not always suitable to detect chemically-diversed metabolites. Therefore, we have been trying to establish NMR-based metabolomics approach. We have conducted the stable isotope labeling of plants, insects and mice, optimization of the extraction solvent for metabolites, building a chemical shift database, and constructing a semi-automtic signal assignment system, SpinAssign. In this talk, we will review these methodologic developments. We will also show the in vivo NMR measurements of Arabidopsis T87 cultured cells treated with ABA coupled with transcriptome analysis, and our attempt to detect metabolite changes in Ds insertion mutants. In addition, the future perspective and the potential of NMR metabolomics will be discussed.

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Event date： 2004.3.20

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Event date： 2004.3.20

When challenged with the fungus &lt;i&gt;Colletotrichum higginsianum&lt;/i&gt;, &lt;i&gt;Arabidopsis&lt;/i&gt; accession Columbia plant (Col-0) developed brown necrotic lesions, including a yellow halo around the lesion. The &lt;i&gt;Arabidopsis&lt;/i&gt; accessions showed variation in response to &lt;i&gt;C. higginsianum&lt;/i&gt;. &lt;i&gt;Arabidopsis&lt;/i&gt; accession Eil-0 was highly resistant to &lt;i&gt;C. higginsianum&lt;/i&gt;. In the Eil-0 plant inoculated with the fungus, cell death did not appear as a rapid response, and the level of camalexin accumulated was low. Analyses using RNA gel blotting and cDNA microarray suggested that the defense responses against &lt;i&gt;C. higginsianum&lt;/i&gt; occur mainly through the JA/ET-dependent pathway. Segregation analysis of progeny from crosses between Eil-0 and Col-0 plants was performed to determine the genetic basis of resistance. The resistance was dominant and seemed to be conferred by a single locus. &lt;i&gt;Arabidopsis&lt;/i&gt; and &lt;i&gt;C. higginsianum&lt;/i&gt; provide an excellent pathosystem for studying the molecular and cellular bases of plant-pathogen interactions

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