Biology subjects

Hachiya, T.

Publications and source records attributed to Hachiya, T..

16 recordsLinked to original sources

bioRxiv2026

LBD-type transcription factors suppress local and systemic nitrogen responses through distinct regulatory pathways

Nitrogen (N) is a major determinant of plant growth and productivity. Because soil N availability and internal N demand fluctuate, plants have evolved sophisticated mechanisms to coordinate N acquisition and utilization at the whole-plant level. However, how this coordination is achieved remains poorly understood. Here, we show that N-inducible LATERAL ORGAN BOUNDARIES DOMAIN transcription factors LBD37, LBD38, and LBD39 (LBDs) function as repressors of local N uptake and assimilation and systemic N-demand signaling in Arabidopsis. Triple mutants lacking these three LBDs displayed enhanced nitrate influx and increased accumulation of nitrate, amino acids, and total N. Transcriptome analysis identified an array of N-starvation- and nitrate-inducible genes derepressed in shoots and roots, including C-TERMINALLY ENCODED PEPTIDE (CEP) and CEP DOWNSTREAM (CEPD) genes, as well as genes involved in N uptake and assimilation. Grafting and genetic analyses revealed that LBDs gate the systemic N-demand signaling relay by repressing CEP and CEPD expression organ-autonomously. We also found that LBDs locally repress genes involved in N uptake and assimilation through a distinct regulatory mechanism. We propose that LBDs are key transcriptional repressors in a regulatory framework for optimizing N acquisition and utilization under fluctuating N conditions at the whole-plant level.

plant biology↗

bioRxiv2025

Cytokinin receptor AHK3 modulates root-to-shoot transport of trans-zeatin type cytokinin

Trans-zeatin (tZ)-type cytokinins (CKs) are synthesized in roots in response to nitrate, transported to shoot via xylem, and coordinate diverse physiological processes in aerial organs. Within this mechanism, the regulation of CK biosynthesis by nitrate signaling via NIN-like protein 7 as well as the loading of tZ-type CKs into xylem by ATP-binding cassette transporter G14 have been well studied. However, the roles of other components remain unclear. Here, we show that CK perception and degradation in roots, as mediated by Arabidopsis histidine kinase 3 (AHK3) and CK oxidase/dehydrogenase 4 (CKX4), modulate xylem tZ-type CKs transport and leaf CK status. Grafting experiments demonstrated that root-specific AHK3 deficiency systemically increased leaf blade area through long-distance signals of root-derived tZ-type CK, perceived by shoot-expressed AHK3. Transcriptome and hormonome analyses revealed that root-specific AHK3 deficiency reduced CKX4 expression in roots, elevating tZ-type CK levels in roots and xylem sap and thereby enhancing leaf CK response. Transfer experiments manipulating root nitrate levels showed that root-specific AHK3 deficiency promoted leaf blade area in a manner dependent on both nitrate and root-derived tZ-type CK signaling. Moreover, both nitrate signals and root-expressed AHK3 are required for maximal CKX4 induction in roots, and root-specific CKX4 deficiency enhanced leaf blade area in a nitrate-dependent manner. These findings reveal a novel mechanism in which an AHK3-CKX4 module governs xylem transport of tZ-type CKs, fine-tuning leaf size according to nitrogen availability in roots. SIGNIFICANCE STATEMENTTo clarify a mechanism that attenuates trans-zeatin-type cytokinin transport from roots to shoots in response to nitrate signaling, this study examined the root-specific role of cytokinin receptors. Our results show that cytokinin perception and degradation, as mediated by Arabidopsis histidine kinase 3 and cytokinin oxidase/dehydrogenase 4, modulate xylem trans-zeatin-type cytokinin transport, thereby fine-tuning leaf cytokinin status and growth in a nitrate-dependent manner, providing new insights into long-distance cytokinin transport according to nitrogen availability.

plant biology↗

bioRxiv2025

Proto-MHC signatures in the lamprey genome

Jawless vertebrates, which diverged from jawed vertebrates approximately 550 million years ago, possess an adaptive immune system characterized by two distinct lineages of lymphocytes bearing unique antigen receptors. However, despite decades of research, the mechanism of antigen presentation in these organisms remains unclear. In this study, we report that chromosomes 22, 50, and 59 in the sea lamprey (Petromyzon marinus) exhibit synteny with the human major histocompatibility complex (MHC) region. The syntenic region spans from DHX16 to RING1 (chromosome 6: 30,517,301-33,034,069) in the human genome (T2T-CHM13v2.0). Similar to the human MHC region, P. marinus chromosome 59 harbors homologs of DDX39B, NOTCH, PBX, TNF, and BRD genes, yet notably lacks the core MHC class I, II, and III (complement) genes. Genotyping of three independent lampreys showed no signatures of balancing selection, a characteristic feature of the human MHC. Additionally, these lamprey chromosomes exhibit synteny with chromosome 9 in amphioxus (Branchiostoma lanceolatum), which contains conserved homologs that form its "proto-MHC." These findings suggest that chromosomes 22, 50, and 59 in P. marinus are a proto-MHC or its paralog.

evolutionary biology↗

bioRxiv2025

Arabidopsis root-type ferredoxin:NADP(H) oxidoreductases are crucial for root growth and ferredoxin-dependent processes

Root-type ferredoxin:NADP(H) oxidoreductase (RFNR) is believed to reduce ferredoxin using NADPH in nonphotosynthetic tissues, facilitating ferredoxin-dependent biological processes. However, the physiological functions of RFNR remain unclear due to the difficulty in obtaining mutants lacking redundant RFNR isoproteins. The present study successfully generated Arabidopsis homozygous rnfr1;2 double mutants by traditional crossing and selection. However, they displayed severely stunted roots, challenging subsequent growth and abundant seed recovery. Notably, grafted plants combining mutant scions with wild-type rootstocks exhibited normal growth and produced abundant mutant seeds. Growth analysis employing reciprocal grafts with the wild-type and mutant plants showed that primary root growth was inhibited only when the rootstock was derived from the mutants. Meanwhile, the absence of RFNR1 and 2 in the scion had no apparent impact on shoot and root growth. Root transcriptome analysis revealed that RFNR1 and 2 deficiency upregulated genes encoding ferredoxin-dependent enzymes and root-type ferredoxin, leading to genome-wide reprogramming associated with cell walls, lipids, photosynthesis, secondary metabolism, and biotic/abiotic stress responses. Thus, Arabidopsis RFNR1 and 2 are crucial for root growth and various ferredoxin-dependent biological processes.

plant biology↗

bioRxiv2024

Shoot nitrate status regulates Arabidopsis shoot growth and systemic transcriptional responses via shoot adenylate isopentenyltransferase 3

Plants systemically regulate growth and gene expression according to their internal nitrate status. Our previous study reported that shoot nitrate accumulation increases shoot expression of adenosine phosphate-ISOPENTENYLTRANSFERASE 3 (IPT3) and shoot levels of N6-({Delta}2-isopentenyl) adenine (iP)-type cytokinins (CKs). IPT3 expression is localized in the phloem, and iP-type CKs, which are synthesized by IPT3, are phloem-mobile. As CKs are a class of phytohormones that control growth and genome-wide gene expression, shoot-expressed IPT3 may mediate the systemic regulation of growth and transcriptomic responses to shoot nitrate status. To examine this, we developed a novel system to manipulate nitrate levels and IPT3 expression in a shoot-specific manner and performed growth analysis, CK determination, and RNA-sequencing. Our results demonstrated that shoot nitrate accumulation significantly promoted shoot growth and elevated shoot concentrations of iP ribotides, iP-7-N-glucoside, and iP-9-N-glucoside through the action of shoot IPT3. Transcriptomic responses to shoot nitrate accumulation were largely tuned by shoot IPT3, with opposite effects in shoots and roots. Shoot IPT3 amplified shoot responses of nitrate-inducible genes and immune response genes to shoot nitrate accumulation, while it dampened root responses of nitrate transport/assimilation genes. This transcriptomic modulation via shoot IPT3 was accompanied by coherent transcriptional changes in genes encoding mobile peptides and transcriptional repressors. Here we present a novel scheme integrating shoot nitrate status responses with CK signaling.

plant biology↗

bioRxiv2024

STOP1 dominates Arabidopsis tolerance to ammonium over NRT1.1/NPF6.3/CHL1

The Arabidopsis nitrate transceptor NITRATE TRANSPORTER 1.1 (NRT1.1/NPF6.3/CHL1) plays significant roles even in the absence of nitrate. The loss-of-function of NRT1.1 alleviates growth suppression and chlorosis under toxic levels of ammonium as the sole nitrogen source. Recently, we reported that acidic stress-inducible genes are downregulated by NRT1.1 deficiency under ammonium toxicity conditions, implying that NRT1.1 may exacerbate ammonium-dependent acidic stress. The transcription factor SENSITIVE TO PROTON RHIZOTOXICITY 1 (STOP1) enhances Arabidopsis tolerance to ammonium and acidic stresses. Furthermore, STOP1 directly activates NRT1.1 transcription. These previous findings prompted us to analyze the association between NRT1.1 and STOP1 on ammonium tolerance. Here, we show that ammonium-inducible STOP1 plays a dominant role over NRT1.1 in ammonium tolerance and expression of direct target genes of STOP1. We present a novel scheme in which NRT1.1 and STOP1 jointly regulate common target(s) associated with ammonium tolerance.

plant biology↗

bioRxiv2024

Time-course analysis of the transcriptome of Arabidopsis thaliana leaves under high-concentration ammonium sulfate treatment

Nitrogen is essential for plant growth and is sourced primarily from nitrate and ammonium in the soil. Even though plants can take ammonium up for nutrition, it often results in toxic effects such as growth suppression and chlorosis. To elucidate the mechanism of ammonium toxicity, a time-course analysis of the transcriptome was performed on A. thaliana leaves treated with high concentrations of ammonium sulfate in the presence of sufficient nitrate. The expression of nitrate-inducible genes tended to be downregulated by the treatment. The expression of genes relating to abscisic acid, jasmonic acid (JA), salicylic acid (SA), and membrane trafficking was upregulated, whereas that of photosynthesis-, auxin-, and cytokinin-related genes involved in growth and development was downregulated. The induction of many osmotic stress-responsive genes suggests the involvement of osmotic stress in ammonium toxicity. Furthermore, the upregulation of nitric oxide (NO)-inducible genes and the simultaneous upregulation of genes involved in JA biosynthesis, glutathione metabolism, and SA response suggested the involvement of endogenous NO and protein S-nitrosylation in response to high concentrations of ammonium sulfate. This study provides a novel and comprehensive overview of transcriptional changes occurring in response to high ammonium sulfate concentrations and proposes possible mechanisms of ammonium toxicity that can be explored in future research.

plant biology↗

bioRxiv2024

Alternative oxidase alleviates mitochondrial oxidative stress during limited nitrate reduction in Arabidopsis thaliana

The conversion of nitrate to ammonium, i.e., nitrate reduction, is a major consumer of reductants in plants. Previous studies have reported that the mitochondrial alternative oxidase (AOX) is upregulated under limited nitrate reduction conditions, including no/low nitrate or when ammonium is the sole nitrogen (N) source. Electron transfer from ubiquinone to AOX bypasses the proton-pumping complexes III and IV, thereby consuming reductants efficiently. Thus, upregulated AOX under limited nitrate reduction may dissipate excessive reductants and thereby attenuate oxidative stress. Nevertheless, so far there is no firm evidence for this hypothesis due to the lack of experimental systems to analyze the direct relationship between nitrate reduction and AOX. We therefore developed a novel culturing system for A. thaliana that manipulates activities of nitrate reduction and AOX separately without causing N starvation, ammonium toxicity, and lack of nitrate signal. Using this system we examined genome-wide gene expression and plant growth to better understand the relationship between AOX and nitrate reduction. Here we show that AOX alleviates mitochondrial oxidative stress and sustains plant growth under limited nitrate reduction.

plant biology↗

bioRxiv2023

Genetic and transcriptomic dissection of nitrate-independent function of Arabidopsis NRT1.1/NPF6.3/CHL1 under high ammonium condition

The Arabidopsis nitrate transceptor NRT1.1/NPF6.3/CHL1 regulates physiological responses to nitrate. Several studies have reported that Arabidopsis plants lacking NRT1.1 show enhanced shoot growth under toxic levels of ammonium without nitrate, suggesting a nitrate-independent function for NRT1.1. To further investigate this nitrate-independent function and its impact on ammonium tolerance, we conducted genetic analysis, tissue-specific expression analysis, and transcriptome analysis using various NRT1.1-related lines. Transgenic plants expressing either nonphosphomimic or phosphomimic mutants of NRT1.1 exhibited similar ammonium tolerance to the wild-type. The chl1-9 mutant, in which NRT1.1 with the P492L substitution is localized intracellularly rather than at the plasma membrane and fails to transport nitrate, showed significantly improved ammonium tolerance. Confocal imaging revealed that the NRT1.1-GFP signal was detected in the plasma membrane of various tissues, including cotyledon pavement cells, hypocotyl epidermal cells, mesophyll cells, root cap cells, and epidermal cells near root tips. In early seedlings, the absence of functional NRT1.1 altered the expression of genes associated with aliphatic glucosinolate biosynthesis, ethylene signaling, and low pH stress. Genes predicted to encode products localized to the extracellular space were enriched among those differentially expressed due to NRT1.1 deficiency. Our data suggest that in the absence of nitrate, plasma membrane-targeted NRT1.1 reduces ammonium tolerance irrespective of its phosphorylation state with alterations of gene expression associated with stress and senescence.

plant biology↗

bioRxiv2023

Dimension reduction of microbiome data linked Bifidobacterium to allergic rhinitis

Dimension reduction has been used to visualise the distribution of multidimensional microbiome data, but the composite variables calculated by the dimension reduction methods have not been widely used to investigate the relationship of the human gut microbiome with lifestyle and disease. In the present study, we applied several dimension reduction methods, including principal component analysis (PCA), principal coordinate analysis (PCoA), non-metric multidimensional scaling (NMDS), and non-negative matrix factorization (NMF), to a microbiome dataset from 186 subjects with symptoms of AR and 106 controls. All the dimension reduction methods supported that the enterotype clusters were overlapped in the dimension reduction plots, and that the distribution of microbial data points appeared to be continuous rather than discrete. Comparison of the composite variables calculated from the different dimension reduction methods showed that the characteristics of the composite variables differed between the dimension reduction methods. The second composite variable calculated from PCoA was significantly associated with the intake of several nutrients, including omega-3 polyunsaturated fatty acids, and the risk of AR. The composite variable was also correlated with the relative abundance of Bifidobacterium, and thus, Bifidobacterium was related to the risk of AR and intake of several nutrients through dimension reduction. Our results highlight the usefulness of the dimension reduction methods for investigating the association of microbial composition with lifestyle and disease in clinical research.

microbiology↗

bioRxiv2022

Root-specific activation of plasma membrane H+-ATPase 1 enhances plant growth and shoot accumulation of nutrient elements under nutrient-poor conditions in Arabidopsis thaliana

Plasma membrane (PM) H+-ATPase contributes to nutrient uptake and stomatal opening by creating proton gradient across the membrane. Previous studies report that a dominant mutation in the OPEN STOMATA2 locus (OST2-2D) constitutively activates Arabidopsis PM H+-ATPase 1 (AHA1), which enlarges proton motive force for root nutrient uptake. However, the stomatal opening is also constitutively enhanced in the ost2-2D, causing drought hypersensitivity. To develop plants with improved nutrient acquisition and normal stomatal movement, we generated grafted plants (scion/rootstock : Col-0 (WT)/ost2-2D), and compared their growth and nutrient element content with those of control plants (WT/WT) under two nutrient regimes. WT/ost2-2D shoots had larger weights, rosette diameter, leaf blade area, and content of C, N, K, Ca, S, P, Mg, Na, Mn, B, Co, and Mo under nutrient-poor conditions compared with WT/WT shoots. The root weights and primary root length were greater in WT/ost2-2D plants than in WT/WT plants under both nutrient conditions. These results suggest that root-specific activation of PM H+-ATPase enhances root nutrient uptake, which accelerates the plant growth under nutrient-poor condition. Our study presents a novel approach to improving nutrient uptake efficiency in crops and vegetable for the implementation of low-input sustainable agriculture.

plant biology↗

bioRxiv2021

Multiple nutritional and gut microbial factors associated with allergic rhinitis: the Hitachi Health Study

Several studies suggest the involvement of dietary habits and gut microbiome in allergic diseases. However, little is known about the nutritional and gut microbial factors associated with the risk of allergic rhinitis (AR). We recruited 186 apparently healthy workers with symptoms of AR and 106 controls at the Hitachi Health Care Center, Japan. The habitual consumption of 42 selected nutrients were examined using the brief-type self-administered diet history questionnaire. Faecal samples were collected and subjected to amplicon sequencing of the 16S ribosomal RNA gene hypervariable regions. Association analysis revealed that four nutrients (retinol, vitamin A, cryptoxanthin, and copper) were negatively associated with AR. Among 40 genera examined, relative abundance of Prevotella and Escherichia were associated with AR. Furthermore, significant statistical interactions were observed between retinol and Prevotella. The age- and sex-adjusted odds of AR were 25-fold lower in subjects with high retinol intake and high Prevotella abundance compared to subjects with low retinol intake and low Prevotella abundance. Our data provide insights into complex interplay between dietary nutrients, gut microbiome, and the development of AR.

microbiology↗

bioRxiv2021

Root-specific reduction of cytokinin perception enhances shoot growth with an alteration of trans-zeatin distribution in Arabidopsis thaliana

Compelling evidence demonstrates that root-derived cytokinins (CKs) contribute to shoot growth via long-distance transport; therefore, we hypothesized that an increase in root-derived CKs enhances shoot growth. To demonstrate this, we grafted Arabidopsis Col-0 (WT) scion onto rootstock originated from WT or a double-knockout line of CK receptors AHK2 and AHK3 (ahk23) because the knockout line over accumulates CKs in the body due to feedback homeostasis regulation. The grafted plants (scion/rootstock: WT/WT and WT/ahk23) were grown in vermiculite pots or solid media under high and low nitrogen regimes for vegetative growth and biochemical analysis. The root-specific deficiency of AHK2 and AHK3 increased root concentrations of trans-zeatin (tZ)-type and N6-({Delta}2-isopentenyl) adenine (iP)-type CKs, induced CK biosynthesis genes, and repressed CK degradation genes in the root. Shoot growth, shoot concentrations of tZ-type CKs, and shoot expression of CK-inducible marker genes were consistently larger in the WT/ahk23 plants than in the WT/WT plants. Moreover, the root-specific deficiency of AHK2 and AHK3 enhanced shoot growth in the WT scion more strongly than in the ahk23 scion. Given that tZ-type CKs are predominantly produced from iP-type CKs in the root and xylem-mobile, it is concluded that the root-specific reduction of CK perception would enhance shoot growth by increasing the amount of root-derived tZ-type CKs and their perception by the shoot. This study will present a novel approach to improve plant growth and productivity.

plant biology↗

bioRxiv2021

Systemic regulation of nitrogen acquisition and use in Oryza longistaminata ramets under nitrogen heterogeneity

Oryza longistaminata, a wild rice, vegetatively reproduces and forms a networked clonal colony consisting of ramets connected by rhizomes. Although water, nutrients, and other molecules can be transferred between ramets via the rhizomes, inter-ramet communication in response to spatially heterogeneous nitrogen availability is not well understood. We studied the response of ramet pairs to heterogeneous nitrogen availability by using a split hydroponic system that allowed each ramet root to be exposed to different conditions. Ammonium uptake was compensatively enhanced in the sufficient-side root when roots of the ramet pairs were exposed to ammonium-sufficient and deficient conditions. Comparative transcriptome analysis revealed that a gene regulatory network for effective ammonium assimilation and amino acid biosynthesis was activated in the sufficient-side roots. Allocation of absorbed nitrogen from the nitrogen-sufficient to the deficient ramets was rather limited. Nitrogen was preferentially used for newly growing axillary buds on the sufficient-side ramets. Biosynthesis of trans-zeatin, a cytokinin, was up-regulated in response to the nitrogen supply, but trans-zeatin appears not to target the compensatory regulation. Our results also implied that the O. longistaminata ortholog of OsCEP1 plays a role as a nitrogen-deficient signal in inter-ramet communication, providing compensatory up-regulation of nitrogen assimilatory genes. These results provide insights into the molecular basis for efficient growth strategies of asexually proliferating plants growing in areas where the distribution of ammonium ions is spatially heterogeneous. One sentence summaryOryza longistaminata, a rhizomatous wild rice, systemically regulates ammonium acquisition and use in response to spatially heterogeneous nitrogen availability via inter-ramet communication.

plant biology↗

bioRxiv2020

Requirement for proper mitochondrial RNA processing in the restrictive control of cell proliferation during early lateral root morphogenesis

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, root redifferentiation defective 1 (rrd1), rrd2, and root initiation defective 4 (rid4), 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 excessive 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.

plant biology↗

bioRxiv2019

Excessive assimilation of ammonium by plastidic glutamine synthetase is a major cause of ammonium toxicity in Arabidopsis thaliana

Plants use nitrate and ammonium in the soil as their main nitrogen sources. Recently, ammonium has attracted attention due to evidence suggesting that, in C3 species, an elevated CO2 environment inhibits nitrate assimilation. However, high concentrations of ammonium as the sole nitrogen source for plants causes impaired growth, i.e. ammonium toxicity. Although ammonium toxicity has been studied for a long time, the primary cause remains to be elucidated. Here, we show that ammonium assimilation in plastids rather than ammonium accumulation is a primary cause for toxicity. Our genetic screen of ammonium-tolerant Arabidopsis lines with enhanced shoot growth identified plastidic GLUTAMINE SYNTHETASE 2 (GLN2) as the causal gene. Our reciprocal grafting of wild-type and GLN2 or GLN1;2-deficient lines suggested that shoot GLN2 activity results in ammonium toxicity, whilst root GLN1;2 activity prevents it. With exposure to toxic levels of ammonium, the shoot GLN2 reaction produced an abundance of protons within cells, thereby elevating shoot acidity and stimulating expression of acidic stress-responsive genes. Application of an alkaline ammonia solution to the toxic ammonium medium efficiently alleviated the ammonium toxicity with a concomitant reduction in shoot acidity. Consequently, we conclude that a primary cause of ammonium toxicity is acidic stress in the shoot. This fundamental insight provides a framework for enhanced understanding of ammonium toxicity in plants.

plant biology↗