Biology subjects

Takemoto, D.

Publications and source records attributed to Takemoto, D..

15 recordsLinked to original sources

bioRxiv2026

Crop-associated differences in soil chemical properties and root-associated bacterial communities between Welsh onion and sweet potato

Crop species may shape soil chemical properties and root-associated microbiota, but direct comparisons between contrasting crops remain limited. We compared soils and root-associated bacterial communities of Welsh onion (Allium fistulosum) and sweet potato (Ipomoea batatas) under the same field context. Sweet potato soil showed significantly lower electrical conductivity, inorganic nitrogen, and Mg saturation than control soil. Root-associated communities differed between crops, whereas alpha diversity did not. Proteobacteria-related taxa were more represented in Welsh onion roots, whereas Actinomycetia-related taxa were more represented in sweet potato roots, providing a basis for future studies on crop-specific soil microbial management.

microbiology↗

bioRxiv2026

2'-Deoxyuridine-promoted infection in Pyricularia oryzae is counteracted by bacterial thymidine phosphorylase

Successful infection by the rice blast fungus Pyricularia oryzae depends on precise developmental transitions on the plant surface, yet the extracellular metabolites that regulate these events remain poorly understood. One such metabolite, 2'-deoxyuridine (dU), has been identified as a self-produced infection-promoting factor, but its mode of action has remained unclear. Exogenous dU did not significantly affect conidial germination but accelerated early appressorium initiation and promoted appressorium maturation, as indicated by increased glycogen mobilization and elevated intracellular turgor. Extracellular dU was detected during early infection-related development, indicating that dU accumulates under conditions conducive to appressorium formation. To test whether microbial turnover of dU influences pathogenicity, dU-degrading bacteria were isolated from rice field environments, and Enterobacter sp. strain C3 was identified as the most active isolate. Biochemical and structural analyses identified the responsible enzyme as the thymidine phosphorylase DeoA, which converts dU to uracil in a phosphate-dependent reaction. Recombinant DeoA reproduced this activity in vitro, and enzymatic depletion of dU attenuated invasive hyphal growth and lesion development. Appressorium-specific expression of deoA in P. oryzae likewise reduced pathogenicity. Together, these results identify extracellular dU as a factor promoting infection-related development in P. oryzae and suggest that dU degradation provides a potential approach for the biological control of rice blast disease. IMPORTANCESuccessful infection by the rice blast fungus Pyricularia oryzae depends on tightly regulated developmental changes on the plant surface. This study identifies 2'-deoxyuridine as an extracellular molecule that helps drive these early infection events. The fungus-derived nucleoside promoted appressorium formation and maturation, accumulated during early infection-related development, and could be targeted for disease suppression. A rice field bacterium, Enterobacter sp. strain C3, and its enzyme DeoA efficiently degraded 2'-deoxyuridine, and this depletion reduced fungal invasion and disease development. These findings uncover a previously unrecognized extracellular signal associated with infection-related development in the rice blast fungus and point to metabolite degradation by environmental microbes as a promising route for biological control.

microbiology↗

bioRxiv2025

Horizontally acquired IbACS gene modulates rhizosphere microbiota and contributes to sweet potato growth

Ipomoea batatas (sweet potato) exhibits tolerance to nutrient-poor environments and has historically been utilized as a staple crop during periods of food scarcity. Previously, genomic studies have identified Agrobacterium-derived sequences in the sweet potato genome. Among these, the IbACS (Agrocinopine Synthase) gene encodes an enzyme responsible for the biosynthesis of agrocinopine A, a sugar-phosphodiester opine that can be metabolized and utilized by specific microorganisms harboring the corresponding catabolic enzymes. Because IbACS has been conserved in cultivated sweet potato varieties, it is suggested that endogenous agrocinopine production by sweet potato contributes to interactions with environmental microbes, thereby supporting plant growth under nutrient-limited conditions. To test this hypothesis, we generated IbACS-disrupted lines using genome editing. Growth of the knockout plants was markedly reduced in non-sterile soil, while no difference was observed in sterile conditions. These results suggest that the role of IbACS is linked to interactions with the microbial community rather than to intrinsic plant development. Metagenomic analyses of rhizosphere communities revealed that IbACS disruption caused extensive remodeling of microbial composition, including strong reductions in Proteobacteria taxa such as Oxalobacteraceae and decreases in key genera like Massilia and Ensifer, along with lower community evenness and the expansion of opportunistic minor taxa. Together, these microbial shifts indicate that IbACS is required for the assembly of a functionally supportive rhizosphere microbiome that promotes sweet potato growth in soil environments.

plant biology↗

bioRxiv2025

Foliar application of mixed DAMP- and MAMP-oligosaccharides enhances root growth and fruit yield in okra and tomato in greenhouse experiments

Plants perceive diverse endogenous and microbial molecular patterns that shape their defense, growth, and productivity. Damage-associated molecular patterns (DAMPs) such as cello- and xylo-oligosaccharides, and microbe-associated molecular patterns (MAMPs) such as chitin-oligosaccharides, are known to promote both development and immunity. Here, we evaluated the combined application of these three oligosaccharides (Oligo-Mix) in okra and cherry tomato under greenhouse conditions. Regular foliar treatment with Oligo-Mix enhanced root elongation and biomass accumulation, and increased fruit number and yield in both crops. RNA-seq analysis of Oligo-Mix-treated tomato leaves showed coordinated induction of photosynthetic genes, components of the translational machinery, cell-wall remodeling factors, and enzymes involved in flavonoid/anthocyanin biosynthesis, indicating broad enhancement of metabolic capacity and protective secondary pathways. Together, these results demonstrate that Oligo-Mix functions as a biostimulant that supports both vegetative growth and fruit production, offering a sustainable approach to improving crop performance.

plant biology↗

bioRxiv2025

Cdc25-mediated activation of the small GTPase RasB is essential for hyphal fusion and symbiotic infection of Epichloë festucae

Epichloe festucae is a filamentous endophytic fungus that symbiotically colonizes the intercellular spaces of aerial tissues in perennial ryegrass (Lolium perenne) without causing disease symptoms. This mutualistic association enhances host resistance to both biotic and abiotic stresses. Balanced and coordinated growth of E. festucae with its host is essential for the establishment and long-term maintenance of the symbiotic relationship. Various E. festucae mutants defective in symbiosis with host plants have been isolated, and notably, many of these symbiosis-defective mutants also lack hyphal fusion ability under culture conditions, supporting a close functional connection between signal transduction required for hyphal fusion and symbiosis establishment. Using a plasmid insertional mutagenesis approach, we identified Cdc25 as an essential regulator of hyphal fusion in E. festucae. Cdc25 encodes a guanine nucleotide exchange factor (GEF) that activates the small GTPase Ras. The{Delta} cdc25 strain lost both hyphal fusion ability and the capacity to infect host plants. Furthermore, yeast two-hybrid assays revealed that Cdc25 specifically interacts with RasB, one of the five Ras proteins in E. festucae. Expression of constitutively active (CA) RasB in the{Delta} cdc25 strain restored both hyphal fusion and host infection, whereas expression of CA-RasB in the{Delta} mpkB deletion strain failed to rescue its defect in hyphal fusion, suggesting that the Cdc25-RasB signaling module acts upstream of the MAPK cascade. In pathogenic fungi, this signaling module is known to regulate infection-related morphogenesis. These findings indicate that E. festucae has evolutionarily repurposed the conserved Cdc25-RasB module to coordinate hyphal fusion and maintain a stable mutualistic interaction with its host.

microbiology↗

bioRxiv2025

STT3A is required for recognition of pathogen-derived sphingolipids in Arabidopsis

Plants recognize pathogen-associated molecular patterns (PAMPs) via pattern recognition receptors, leading to the activation of pattern-triggered immunity in response to pathogen attack. Phytophthora infestans ceramide D (Pi-Cer D) is a sphingolipid from the oomycete pathogen P. infestans. Pi-Cer D is cleaved by the plant extracellular ceramidase NEUTRAL CERAMIDASE 2 (NCER2), and the resulting 9-methyl-branched sphingoid base is recognized by the plant receptor RESISTANT TO DFPM-INHIBITION OF ABSCISIC ACID SIGNALING 2 (RDA2) at the plasma membrane to transduce a defense signal. However, additional components are likely involved in sphingolipid recognition, which remain to be identified. Here, we employed a screen based on Lumi-Map technology to look for Arabidopsis (Arabidopsis thaliana) mutants with altered defense responses to Pi-Cer D. We identified three mutants showing diminished responses to Pi-Cer D and elf18, each carrying mutations in STAUROSPORIN AND TEMPERATURE SENSITIVE 3-LIKE A (STT3A), which encodes an oligosaccharyltransferase. The stt3a mutants exhibited higher susceptibility to the pathogen Colletotrichum higginsianum than the wild type and displayed alterations in NCER2 protein modifications. These findings suggest that STT3A contributes to plant immunity via post-translational modification of proteins including NCER2.

plant biology↗

bioRxiv2024

Mixed DAMP/MAMP oligosaccharides promote both growth and defense against fungal pathogens of cucumber

Plants recognize a variety of environmental molecules, thereby triggering appropriate responses to biotic or abiotic stresses. Substances containing microbes-associated molecular patterns (MAMPs) and damage-associated molecular patterns (DAMPs) are representative inducers of pathogen resistance and damage repair, thus treatment of healthy plants with such substances can pre-activate plant immunity and cell repair functions. In this study, the effects of DAMP/MAMP oligosaccharides mixture (Oligo-Mix) derived from plant cell wall (cello-oligosaccharide and xylo-oligosaccharide), and fungal cell wall (chitin-oligosaccharide) were examined in cucumber. Treatment of cucumber with Oligo-Mix promoted root germination and plant growth, along with increased chlorophyll contents in the leaves. Oligo-Mix treatment also induced typical defense responses such as MAP kinase activation and callose deposition in leaves. Pretreatment of Oligo-Mix enhanced disease resistance of cucumber leaves against pathogenic fungi Podosphaera xanthii (powdery mildew) and Colletotrichum orbiculare (anthracnose). Oligo-Mix treatment increased the induction of hypersensitive cell death around the infection site of pathogens, which inhibited further infection and the conidial formation of pathogens on the cucumber leaves. RNA-seq analysis revealed that Oligo-Mix treatment upregulated genes associated with plant structural reinforcement, responses to abiotic stresses and plant defense. These results suggested that Oligo-Mix has beneficial effects on growth and disease resistance in cucumber, making it a promising biostimulant for agricultural application.

plant biology↗

bioRxiv2024

Botrytis cinerea detoxifies the sesquiterpenoid phytoalexin rishitin through multiple metabolizing pathways

Botrytis cinerea is a necrotrophic pathogen that infects across a broad range of plant hosts, including high-impact crop species. Its generalist necrotrophic behavior stems from its ability to detoxify structurally diverse phytoalexins. The current study aims to provide evidence of the ability of B. cinerea to tolerate the sesquiterpenoid phytoalexin rishitin, which is produced by potato and tomato. While the growth of potato pathogens Phytophthora infestans (late blight) and Alternaria solani (early blight) was severely inhibited by rishitin, B. cinerea was tolerant to rishitin. After incubation of rishitin with the mycelia of B. cinerea, it was metabolized to at least six oxidized forms. Structural analysis of these purified rishitin metabolites revealed a variety of oxidative metabolism including hydroxylation at C7 or C12, ketone formation at C5, and dihydroxylation at the 10,11-olefin. Six rishitin metabolites showed reduced toxicity to P. infestans and A. solani, indicating that B. cinerea has at least 5 distinct enzymatic reactions to detoxify rishitin. Four host-specialized phytopathogenic Botrytis species, namely B. elliptica, B. allii, B. squamosa, and B. tulipae also had at least a partial ability to metabolize rishitin as B. cinerea, but their metabolic capacity was significantly weaker than that of B. cinerea. These results suggest that the ability of B. cinerea to rapidly metabolize rishitin through multiple detoxification mechanisms could be critical for its pathogenicity in potato and tomato.

microbiology↗

bioRxiv2023

Skin coat color-dependent risks and risk factors of squamous cell carcinoma and deafness of domestic cats inferred via RNA-seq data

The transcriptome data of skin cells from domestic cats with brown, orange, and white coats were analyzed using a public database to investigate the possible relationship between coat color-related gene expression and squamous cell carcinoma risk, as well as the mechanism of deafness in white cats. We found that the ratio of the expression level of genes suppressing squamous cell carcinoma to that of genes promoting squamous cell carcinoma might be considerably lower than the theoretical estimation in skin cells with orange and white coats in white-spotted cat. We also found the possibility of the frequent production of KIT lacking the first exon (d1KIT) in skin cells with white coats, and d1KIT production exhibited a substantial negative correlation with the expression of SOX10, which is essential for melanocyte formation and adjustment of hearing function. Additionally, the production of d1KIT was expected to be due to the insulating activity of the feline endogenous retrovirus 1 (FERV1) LTR in the 1st intron of KIT and its CTCF binding sequence repeat. These results contribute to basic veterinary research to understand the relationship between cat skin coat and disease risk, as well as the underlying mechanism.

zoology↗

bioRxiv2023

Induction of plant disease resistance by mixed oligosaccharide elicitors prepared from plant cell wall and crustacean shells

Basal plant immune responses are activated by the recognition of the conserved pathogen-associated molecular patterns (PAMPs), or breakdown molecules released from plants after damage by pathogen infection, so-called danger-associated molecular patterns (DAMPs). While chitin-oligosaccharide (CHOS), a primary component of the fungal cell wall, is most known as PAMP, plant cell wall-derived oligosaccharides, cello-oligosaccharides (COS) from cellulose and xylo-oligosaccharide (XOS) from hemicellulose, are representative DAMPs, which activate signaling steps similar to PAMP-induced immunity to elicit defenses and provide protection against pathogens. In this study, elicitor activities of COS prepared from cotton linters, XOS prepared from corn cobs as well as chitin-oligosaccharide (CHOS) from crustacean shells were comparatively investigated. In Arabidopsis, treatment of COS, XOS or CHOS triggered typical defense responses such as reactive oxygen species (ROS) production, activation of MAP kinases phosphorylation, callose depositions, and activation of the promoter for defense-related transcription factor WRKY33. When COS, XOS and CHOS were used at concentrations with similar activity in inducing ROS production and callose depositions, CHOS was particularly highly potent in activating the MAPK kinases and WRKY33 promoters. Among the COS and XOS with different degrees of polymerization (DP), cellotriose (DP3) and xylotetraose (DP4) showed the highest activity for the activation of WRKY33 promoter. Simultaneous treatment of COS, XOS and CHOS leads to a strong transcriptional change for defense-related genes, and gene ontology (GO) enrichment analysis of RNAseq data revealed that a mixture of three oligosaccharide (oligo-mix) effectively activate the plants disease resistance. In practice, treatment of the oligo-mix enhanced the resistance of tomato to powdery mildew, but plant growth was not inhibited but rather tended to be promoted, providing evidence that mixed oligosaccharides have beneficial effects on improving disease resistance in plants, making them a promising class of compounds for practical application.

plant biology↗

bioRxiv2022

Functional characterization of Botrytis cinerea ABC transporter gene BcatrB in response to phytoalexins produced in plants belonging to families Solanaceae, Brassicaceae and Fabaceae

Botrytis cinerea, a generalist fungal pathogen of economically important crop species, has been shown to exhibit reduced sensitivity to fungicides and plant toxins. Specifically, previous reports indicate B. cinereas efficacy in tolerating a wide array of phytoalexins, toxic plant metabolites that play key role in plant immune defense strategies. Previously, we have shown that a distinct set of genes was induced in B. cinerea when treated with phytoalexins derived from different plant species such as rishitin (tomato and potato), capsidiol (tobacco and bell pepper) or resveratrol (grape and blueberry). In this study, we focused on the functional analyses of B. cinerea genes induced by rishitin treatment. B. cinerea can metabolize rishitin to at least 4 oxidized forms. Heterologous expression of rishitin-induced B. cinerea genes in the plant symbiotic fungus, Epichloe festucae, revealed that oxidoreductase (Bcin08g04910) and cytochrome P450 (Bcin16g01490) genes are involved in the oxidation of rishitin. BcatrB is an exporter of structurally unrelated anti-microbial compounds such as resveratrol, camalexin and fungicide fenpicionil. Expression of BcatrB is upregulated by rishitin, but not by structurally resembling capsidiol. BcatrB knock out transformants ({Delta}bcatrB) showed enhanced sensitivity to rishitin, but not to capsidiol. Likewise,{Delta} bcatrB showed reduced virulence on tomato fruits (which produce rishitin), but showed full virulence on Nicotiana benthamiana (which mainly produces capsidiol), suggesting that B. cinerea distinguishes phytoalexins and activates expression of appropriate transporter genes during the infection. Activation of BcatrB promoter was detected using P_BcatrB:GFP transformant during the B. cinerea infection in plant tissues. Surveying of 26 plant species across 13 families revealed that the BcatrB promoter is mainly activated during the infection of plants belonging to the Solanaceae, Fabaceae and Brassicaceae families. The BcatrB promoter is activated by the treatment with Fabaceae phytoalexins medicarpin and glyceollin, and{Delta} bcatrB showed reduced virulence on red clover, which produces medicarpin. These results suggest that BcatrB plays a critical role in the strategy employed by B. cinerea to bypass the plant innate immune responses in a wide variety of important crops belonging to the Solanaceae, Brassicaceae and Fabaceae families.

microbiology↗

bioRxiv2022

Botrytis cinerea identifies host plants via the recognition of antifungal capsidiol to induce expression of a specific detoxification gene

The gray mold pathogen Botrytis cinerea has a broad host range, causing disease in over 400 plant species, but it is not known how this pathogen evolved this polyxenous nature. B. cinerea can metabolize a wide range of phytoalexins, including the stilbenoid, resveratrol, and the sesquiterpenoids capsidiol in tobacco, and rishitin in potato and tomato. In this study, we analyzed the metabolism of sesquiterpenoid phytoalexins by B. cinerea. Capsidiol was dehydrogenated to capsenone which was then further oxidized, while rishitin was directly oxidized to epoxy-or hydroxy-rishitins indicating that B. cinerea has separate mechanisms to detoxify structurally similar sesquiterpenoid phytoalexins. RNAseq analysis revealed that a distinct set of genes were induced in B. cinerea when treated with capsidiol or rishitin, suggesting that B. cinerea can distinguish structurally similar phytoalexins to activate appropriate detoxification mechanisms. The gene most highly upregulated by capsidiol treatment encoded a dehydrogenase, designated Bccpdh. Heterologous expression of Bccpdh in a capsidiol-sensitive plant symbiotic fungus, Epichloe festucae, resulted in an acquired tolerance of capsidiol and the ability to metabolize capsidiol to capsenone, while B. cinerea {Delta}bccpdh mutants became relatively sensitive to capsidiol. The{Delta} bccpdh mutant showed reduced virulence on the capsidiol producing Nicotiana and Capsicum species but remained fully pathogenic on potato and tomato. Homologs of Bccpdh are not found in taxonomically distant Ascomycota fungi but not in related Leotiomycete species, suggesting that B. cinerea acquired the ancestral Bccpdh by horizontal gene transfer, thereby extending the pathogenic host range of this polyxenous pathogen to capsidiol-producing plant species. Significance StatementB. cinerea can metabolize a wide range of phytoalexins, however, the extent to which phytoalexin detoxification contributes to pathogenicity is largely unknown. In this study, we have shown that B. cinerea recognizes structurally resembling sesquiterpenoid phytoalexins, rishitin and capsidiol, to activate appropriate detoxification mechanisms. We identify Bccpdh, encoding a dehydrogenase for capsidiol detoxification, which is upregulated in B. cinerea exclusively during the infection of capsidiol producing plant species, and is required to exert full virulence. Analysis of the Bccpdh locus implicates that the gene was acquired via horizontal gene transfer. This work highlights that the polyxenous plant pathogen B. cinerea can distinguish its host plants by its anti-microbial compounds, to activate appropriate mechanisms for enhanced virulence.

microbiology↗

bioRxiv2021

AP2/ERF transcription factor NbERF-IX-33 is involved in the regulation of phytoalexin production for the resistance of Nicotiana benthamiana to Phytophthora infestans.

Plants recognize molecular patterns unique to a certain group of microbes to induce effective resistance mechanisms. Elicitins are secretory proteins produced by plant pathogenic oomycete genera including Phytophthora and Pythium. Treatment of INF1 (an elicitin produced by P. infestans) induces a series of defense responses in Nicotiana species, including reactive oxygen species (ROS) production, transient induction of ethylene production, hypersensitive cell death and accumulation of the sesquiterpenoid phytoalexin capsidiol. In this study, we analyzed the expression profiles of N. benthamiana genes after INF1 treatment by RNAseq analysis. Based on their expression patterns, N. benthamiana genes were categorized into 20 clusters and 4,761 (8.3%) out of 57,140 genes were assigned to the clusters for INF1-induced genes. All genes encoding enzymes dedicated to capsidiol production, 5-epi-aristolochene (EA) synthase (NbEAS, 10 copies) and EA dehydrogenase (NbEAH, 6 copies), and some genes for ethylene production, such as 1-aminocyclopropane 1-carboxylate (ACC) synthase (NbACS) and ACC oxidase (NbACO), were significantly upregulated by INF1 treatment. Analysis of NbEAS1 and NbEAS4 promoters revealed that AGACGCC (GCC box-like motif) is the essential cis-element required for INF1-induced expression of NbEAS genes. Given that the GCC box is known to be targeted by ERF (ethylene-responsive factor) transcription factors, we created a complete list of N. benthamiana genes encoding AP2/ERF family transcription factors, and identified 45 out of 337 AP2/ERF genes in the clusters for INF1-induced genes. Among INF1-induced NbERF genes, silencing of NbERF-IX-33 compromised resistance against P. infestans and INF1-induced production of capsidiol. Recombinant NbERF-IX-33 protein can bind to the promoter sequence of NbEAS4, suggesting that NbERF-IX-33 is a transcription factor directly regulating the expression of genes for phytoalexin production.

plant biology↗

bioRxiv2021

Two structurally different oomycete MAMPs induce distinctive plant immune responses.

Plants recognize a variety of external signals and induce appropriate mechanisms to increase their tolerance to biotic and abiotic stresses. Precise recognition of attacking pathogens and induction of effective resistance mechanisms are critical functions for plant survival. Some molecular patterns unique to a certain group of microbes, microbe-associated molecular patterns (MAMPs), are sensed by plant cells as non-self molecules via pattern recognition receptors. While MAMPs of bacterial and fungal origin have been identified, reports on oomycete MAMPs are relatively limited. This study aimed to identify MAMPs from an oomycete pathogen Phytophthora infestans, the causal agent of potato late blight. Using reactive oxygen species (ROS) production and phytoalexin production in potato as markers, two structurally different groups of elicitors, namely ceramides and diacylglycerols were identified. P. infestans ceramides (Pi-Cer A, B and D) induced ROS production, while diacylglycerol (Pi-DAG A and B), containing eicosapentaenoic acid (EPA) as a substructure, induced phytoalexins production in potato. The molecular patterns in Pi-Cers and Pi-DAGs essential for defense induction were identified as 9-methyl-4,8-sphingadienine (9Me-Spd) and 5,8,11,14-tetraene-type fatty acid (5,8,11,14-TEFA), respectively. These structures are not found in plants, but in oomycetes and fungi, indicating that they are microbe molecular patterns recognized by plants. When Arabidopsis was treated with Pi-Cer D and EPA, partially overlapping but different sets of genes were induced. Furthermore, expression of some genes is upregulated only after the simultaneous treatment with Pi-Cer D and EPA, indicating that plants combine the signals from simultaneously recognized MAMPs to adapt the defense response to pathogens.

plant biology↗

bioRxiv2021

Pathogen-derived 9-methyl sphingoid base is perceived by a lectin receptor kinase in Arabidopsis

In plants, many invading microbial pathogens are recognized by cell-surface pattern recognition receptors (PRRs), inducing defense responses; yet how PRRs perceive pathogen sphingolipids remains unclear. Here, we show that the ceramide Pi-Cer D from a plant pathogenic oomycete Phytophthora infestans triggers defense responses in Arabidopsis. Pi-Cer D is cleaved by an Arabidopsis apoplastic ceramidase, NCER2, and the resulting 9-methyl-branched sphingoid base is recognized by a plasma membrane lectin receptor-like kinase, RDA2. Importantly, 9-methyl-branched sphingoid base, which is unique to microbes, induces plant immune responses by interacting with RDA2. Loss of RDA2 or NCER2 function compromised Arabidopsis resistance against an oomycete pathogen, indicating that these are crucial for defense. We provide new insights that help elucidate the recognition mechanisms of pathogen-derived lipid molecules in plants. One Sentence SummaryOomycete-derived ceramide is cleaved into sphingoid base by ceramidase and recognized by an Arabidopsis receptor kinase.

plant biology↗