Papers by Takashi Hirayama
Plant and Cell Physiology, Aug 15, 2004
Nuclear magnetic resonance (NMR) will become a key technology in plant metabolomics with the use ... more 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 ethanolhypersensitive mutant plants. Furthermore, we followed nitrogen fluxes in 15 N-labeled seeds during the initiation of germination in vivo. The future role of stable isotopelabeling combined with advanced hetero-nuclear NMR in plant metabolomics is discussed.
International Journal of Molecular Sciences, Oct 5, 2021
Mitochondria have their own double-stranded DNA genomes and systems to regulate transcription, mR... more Mitochondria have their own double-stranded DNA genomes and systems to regulate transcription, mRNA processing, and translation. These systems differ from those operating in the host cell, and among eukaryotes. In recent decades, studies have revealed several plant-specific features of mitochondrial gene regulation. The polyadenylation status of mRNA is critical for its stability and translation in mitochondria. In this short review, I focus on recent advances in understanding the mechanisms regulating mRNA polyadenylation in plant mitochondria, including the role of poly(A)-specific ribonuclease-like proteins (PARNs). Accumulating evidence suggests that plant mitochondria have unique regulatory systems for mRNA poly(A) status and that PARNs play pivotal roles in these systems.
Proceedings of the National Academy of Sciences of the United States of America, Apr 25, 1995
A cDNA corresponding to a putative phosphatidylinositol-specific phospholipase C (PI-PLC) in the ... more 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 cAtPLCl, 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-g3, -y, and -6. The overall structure of the putative AtPLCl protein is most similar to that of PLC-8, although the AtPLCl protein is much smaller than PLCs from other organisms. The recombinant AtPLCl 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 AtPLCI 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 AtPLCl might be involved in the signal-transduction pathways of environmental stresses and that an increase in the level of AtPLCl might amplify the signal, in a manner that contributes to the adaptation of the plant to these stresses. In animal cells, phosphatidylinositol-specific phospholipase C (PI-PLC) plays a key role in various signal-transduction pathways. Extracellular stimuli such as hormones and growth factors activate PI-PLCs. PI-PLC hydrolyzes phosphatidylinositol 4,5-bisphosphate (PIP2) and generates two second mes- sengers, inositol 1,4,5-trisphosphate (IP3), which induces the release of Ca2+ from intracellular stores, and 1,2-diacylglycerol (DG), which activates protein kinase C (1-3). These initial events in the transmembrane signal-transduction process are referred to as the PI turnover system. PI turnover in higher organisms is involved in a variety of cellular processes, includ- ing fertilization, development, the growth and differentiation of cells, and phototransduction, as well as in neural behavior, such as memory (1). In addition, PI, PIP2, and DG seem to be involved in the regulation of the organization of the cytoskeleton (4-6). In animal cells, PI-PLCs have been classified into three subgroups, f3, y, and S. Cloning and structural analysis of
Plant and Cell Physiology
Agriculture is particularly vulnerable to climate change. To cope with the risks posed by climate... more 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 its application to crop improvement. We present plant hormonomics as a key tool for deep physiological phenotyping, focusing on...
International Journal of Molecular Sciences, 2021
Climate resilience of crops is critical for global food security. Understanding the genetic basis... more 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-isoge...
The Plant Journal, 2020
SUMMARYRhizoctonia solani is a soil‐borne necrotrophic fungus that causes sheath blight in grasse... more SUMMARYRhizoctonia 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...
Plant, Cell & Environment, 2018
Plants closing stomata in the presence of harmful gases is believed to be a stress avoidance mech... more Plants closing stomata in the presence of harmful gases is believed to be a stress avoidance mechanism. SO 2 , 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 O 3. SLOW ANION CHANNEL-ASSOCIATED 1 (SLAC1) and OPEN STOMATA 1 (OST1) were identified as genes mediating O 3-induced closure. SLAC1 and OST1 are also known to mediate stomatal closure in response to CO 2 , together with RESPIRATORY BURST OXIDASE HOMOLOGs (RBOHs). The overlaying roles of these genes in response to O 3 and CO 2 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 SO 2 in Arabidopsis through molecular genetic approaches. O 3-and CO 2-insensitive stomata mutants did not show significant differences from the wild type in stomatal sensitivity, guard cell viability and chlorophyll content revealing that SO 2-induced closure is not regulated by the same molecular mechanisms as for O 3 and CO 2. Non-apoptotic cell death is shown as the reason for SO 2-induced closure, which proposed the closure as a physicochemical process resulted from SO 2 distress, instead of a biological protection mechanism.
BMC Plant Biology, 2018
Background: The ureides allantoin and allantoate are major metabolic intermediates of purine cata... more Background: The 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. Results: The 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-tonitrogen 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. Conclusions: This 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.
Nature communications, Jan 6, 2018
Abscisic acid (ABA) regulates abiotic stress and developmental responses including regulation of ... more 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 s...
F1000 - Post-publication peer review of the biomedical literature, 2002
Regulation of gene expression at the posttranscriptional level is mainly achieved by proteins con... more Regulation of gene expression at the posttranscriptional level is mainly achieved by proteins containing well-defined sequence motifs involved in RNA binding. The most widely spread motifs are the RNA recognition motif (RRM) and the K homology (KH) domain. In this article, we survey the complete Arabidopsis thaliana genome for proteins containing RRM and KH RNA-binding domains. The Arabidopsis genome encodes 196 RRM-containing proteins, a more complex set than found in Caenorhabditis elegans and Drosophila melanogaster. In addition, the Arabidopsis genome contains 26 KH domain proteins. Most of the Arabidopsis RRM-containing proteins can be classified into structural and/or functional groups, based on similarity with either known metazoan or Arabidopsis proteins. Approximately 50% of Arabidopsis RRM-containing proteins do not have obvious homologues in metazoa, and for most of those that are predicted to be orthologues of metazoan proteins, no experimental data exist to confirm this. Additionally, the function of most Arabidopsis RRM proteins and of all KH proteins is unknown. Based on the data presented here, it is evident that among all eukaryotes, only those RNA-binding proteins that are involved in the most essential processes of post-transcriptional gene regulation are preserved in structure and, most probably, in function. However, the higher complexity of RNA-binding proteins in Arabidopsis, as evident in groups of SR splicing factors and poly(A)-binding proteins, may account for the observed differences in mRNA maturation between plants and metazoa. This survey provides a first systematic analysis of plant RNAbinding proteins, which may serve as a basis for functional characterisation of this important protein group in plants.
F1000 - Post-publication peer review of the biomedical literature, 2006
Cells are organized into a complex network of subcellular compartments that are specialized for v... more Cells are organized into a complex network of subcellular compartments that are specialized for various biological functions. Subcellular location is an important attribute of protein function. To facilitate systematic elucidation of protein subcellular location, we analyzed experimentally verified protein localization data of 1,300 Arabidopsis (Arabidopsis thaliana) proteins. The 1,300 experimentally verified proteins are distributed among 40 different compartments, with most of the proteins localized to four compartments: mitochondria (36%), nucleus (28%), plastid (17%), and cytosol (13.3%). About 19% of the proteins are found in multiple compartments, in which a high proportion (36.4%) is localized to both cytosol and nucleus. Characterization of the overrepresented Gene Ontology molecular functions and biological processes suggests that the Golgi apparatus and peroxisome may play more diverse functions but are involved in more specialized processes than other compartments. To support systematic empirical determination of protein subcellular localization using a technology called fluorescent tagging of full-length proteins, we developed a database and Web application to provide preselected green fluorescent protein insertion position and primer sequences for all Arabidopsis proteins to study their subcellular localization and to store experimentally verified protein localization images, videos, and their annotations of proteins generated using the fluorescent tagging of full-length proteins technology. The database can be searched, browsed, and downloaded using a Web browser at http://aztec.stanford.edu/gfp/. The software can also be downloaded from the same Web site for local installation.
Botanica Marina, 2017
Emerging studies suggest that seaweeds contain phytohormones; however, their chemical entities, b... more 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),
Journal of Applied Phycology, 2015
Emerging work has suggested the existence of phytohormones in seaweeds, although chemical species... more 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-(∆ 2-isopentenyl)adenine (iP), abscisic acid (ABA) and salicylic acid, although trans-zeatin, dihydrozeatin, gibberellinA 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, and ABA, 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.
F1000 - Post-publication peer review of the biomedical literature, 2001
Oxidative stress, resulting from an imbalance in the accumulation and removal of reactive oxygen ... more Oxidative stress, resulting from an imbalance in the accumulation and removal of reactive oxygen species such as hydrogen peroxide (H 2 O 2), is a challenge faced by all aerobic organisms. In plants, exposure to various abiotic and biotic stresses results in accumulation of H 2 O 2 and oxidative stress. Increasing evidence indicates that H 2 O 2 functions as a stress signal in plants, mediating adaptive responses to various stresses. To analyze cellular responses to H 2 O 2 , we have undertaken a large-scale analysis of the Arabidopsis transcriptome during oxidative stress. Using cDNA microarray technology, we identified 175 non-redundant expressed sequence tags that are regulated by H 2 O 2. Of these, 113 are induced and 62 are repressed by H 2 O 2. A substantial proportion of these expressed sequence tags have predicted functions in cell rescue and defense processes. RNA-blot analyses of selected genes were used to verify the microarray data and extend them to demonstrate that other stresses such as wilting, UV irradiation, and elicitor challenge also induce the expression of many of these genes, both independently of, and, in some cases, via H 2 O 2 .
Plants closing stomata in the presence of harmful gases is believed to be a stress avoidance mech... more 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. O3and CO2-insensitive stomata mutants did not show significant differences from the wild type in stomatal sensitivity, guard cell via...
Nature, 2020
Genetic diversity is key to crop improvement. Owing to pervasive genomic structural variation, a ... more 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 (Hordeum vulgare 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 t...
Plant and Cell Physiology, 2020
F1000 - Post-publication peer review of the biomedical literature, 2003
Ethylene signaling in plants is mediated by a family of receptors related to bacterial two-compon... more Ethylene signaling in plants is mediated by a family of receptors related to bacterial two-component histidine kinases. Of the five members of the Arabidopsis ethylene receptor family, members of subfamily I (ETR1 and ERS1) contain completely conserved histidine kinase domains, whereas members of subfamily II (ETR2, EIN4, and ERS2) lack conserved residues thought to be necessary for kinase activity. To examine the role of the conserved histidine kinase domain in receptor signaling, ers1;etr1 loss-of-function double mutants were generated. The double mutants exhibited a severe constitutive ethylene response phenotype consistent with the negative regulator model for receptor function. The adult ers1-2;etr1-6 and ers1-2;etr1-7 phenotypes included miniature rosette size, delayed flowering, and both male and female sterility, whereas etiolated-seedling responses were less affected. Chimeric transgene constructs in which the ETR1 promoter was used to drive expression of cDNAs for each of the five receptor isoforms were transferred into the ers1-2;etr1-7 double-mutant plants. Subfamily I constructs restored normal growth, whereas subfamily II constructs failed to rescue the double mutant, providing evidence for a unique role for subfamily I in receptor signaling. However, transformation of either the ers1-2;etr1-6 or ers1-2;etr1-7 mutant with a kinase-inactivated ETR1 genomic clone also resulted in complete restoration of normal growth and ethylene responsiveness in the double-mutant background, leading to the conclusion that canonical histidine kinase activity by receptors is not required for ethylene receptor signaling.
PLOS ONE, 2019
Most deciduous fruit trees cultivated in the temperate zone require a genotype-dependent amounts ... more 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 chillingmediated 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 (Malus spp.). 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.
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Papers by Takashi Hirayama