Biology subjects

Izumi, M.

Publications and source records attributed to Izumi, M..

7 recordsLinked to original sources

bioRxiv2026

Genome-wide conservation and locus-specific coding variation in Teratoramularia rumicicola, a candidate microbial herbicide for Rumex weeds

The Rumex pathogen Teratoramularia rumicicola is a candidate microbial herbicide, but its functional genomic repertoire and variation among isolates remain poorly characterised. We generated a PacBio HiFi reference and evidence-supported gene annotation for TR4 and a short-read assembly for GR1, then compared the isolates using assembly- and read-based analyses. The TR4 and GR1 nuclear assemblies comprised 22.34 Mb (13 contigs; N50, 2.90 Mb) and 21.23 Mb (486 contigs; N50, 0.350 Mb), respectively. The TR4 annotation predicted 8,898 protein-coding genes, and the representative protein set was 96.7% complete in the Benchmarking Universal Single-Copy Orthologues assessment. Functional annotation identified 593 putatively secreted proteins, 258 candidate effectors, 355 carbohydrate-active enzyme (CAZyme) candidates and 20 predicted secondary-metabolite biosynthetic regions. Seven secreted CAZymes were prioritised as potential host-barrier-associated factors based on predicted activities and homology to virulence-related entries in the Pathogen-Host Interactions database. Despite 99.81% average nucleotide identity across aligned regions, read-based comparison identified 28,040 high-confidence isolate-fixed differences. Of 158 reconstructed candidate GR1 alleles, 147 showed strong assembly support. Notable differences included predicted truncations of two Zn(II)2Cys6 transcription factors, one adjacent to an intact nonribosomal peptide synthetase-like core gene, and a separate gene showing a localised repeat-induced point mutation (RIP)-like substitution pattern and predicted premature termination. Together, these resources and candidate loci provide a foundation for investigating pathogenicity and strain variation relevant to microbial herbicide development.

genomics↗

bioRxiv2025

Early occurrence of Teratoramularia rumicicola in Japan: re-identification of historic strain GR1 and its pathogenic effects on Rumex species

Teratoramularia rumicicola is a plant pathogenic fungus infecting Rumex species. Although it was described as a new species in 2016, its fundamental characteristics, including historical occurrence, geographic distribution, and host range, remain poorly resolved. In this study, we re-identified strain GR1, which was originally isolated from a diseased Rumex plant in the Bonin (Ogasawara) Islands in 1996 and deposited in a public bioresource center, together with the plant voucher specimen, and evaluated its host range. Colony and conidial morphology and a phylogenetic analysis based on concatenated internal transcribed spacer (ITS) and large subunit (LSU) rDNA sequences identified GR1 as T. rumicicola. Morphological examination of the host plant voucher specimen confirmed Rumex japonicus as the natural host. Pathogenicity assays demonstrated that GR1 infected R. japonicus, reproduced the original disease symptoms, and was successfully re-isolated from diseased tissues, consistent with Kochs postulates. In addition, GR1 caused significant disease and shoot biomass reduction in R. japonicus, R. crispus and R. obtusifolius. The identification of GR1 reveals the presence of T. rumicicola in Japan approximately two decades prior to its formal description, representing the earliest known record of this species. Furthermore, this finding extends its known distribution from temperate regions to the subtropical Bonin Islands, a well-preserved and isolated ecosystem. This study documents for the first time R. japonicus as a natural host of T. rumicicola.

microbiology↗

bioRxiv2025

Bioherbicidal activity and host range of Teratoramularia rumicicola strain TR4 isolated from Rumex crispus in Japan

Rumex species, including R. crispus, R. obtusifolius, and R. japonicus, are problematic weeds that reduce forage production and hinder effective land use in Japanese pasture systems. This study aimed to identify a bioherbicide candidate that selectively targets Rumex weeds while remaining safe for forage crops. To this end, we isolated a fungal pathogen from a naturally infected R. crispus leaf collected in Japan and conducted morphological and molecular identification and host range evaluations. The isolate, designated TR4, was identified as Teratoramularia rumicicola based on its morphological characteristics and phylogenetic analysis of concatenated internal transcribed spacer (ITS) and large subunit (LSU) rDNA sequences. Host range studies revealed that TR4 caused visible symptoms and significantly reduced shoot biomass in all three Rumex species, while no disease symptoms were observed in any of the five forage crops tested. This study reports T. rumicicola for the first time in Japan, extending its known distribution beyond South Korea. The host specificity and liquid culture compatibility of TR4 suggest its potential as a locally adapted microbial herbicide for selective Rumex control in pasture systems.

plant biology↗

bioRxiv2023

Integration of shoot-derived polypeptide signals by root TGA transcription factors is essential for survival under fluctuating nitrogen environments

Unlike plants in the field, which experience significant temporal fluctuations in environmental conditions, plants in the laboratory are typically grown in controlled, stable environments. Therefore, signaling pathways evolved for survival in continuously fluctuating environments often remain functionally latent in laboratory settings. Here, we show that TGA1 and TGA4 act as hub transcription factors through which the expression of genes involved in high-affinity nitrate uptake are regulated in response to shoot-derived phloem mobile polypeptides, CEP DOWNSTREAM 1 (CEPD1), CEPD2 and CEPD-like 2 (CEPDL2) as nitrogen (N) deficiency signals, and Glutaredoxin S1 (GrxS1) to GrxS8 as N sufficiency signals. CEPD1/2/CEPDL2 and GrxS1-S8 competitively bind to TGA1/4 in roots, with the former acting as transcription coactivators that enhance the uptake of nitrate, while the latter function as corepressor complexes together with TOPLESS to limit nitrate uptake. Arabidopsis plants deficient in TGA1/4 maintain basal nitrate uptake and exhibit growth similar to wild-type plants in a stable N environment, but were impaired in regulation of nitrate acquisition in response to shoot N demand, leading to defective growth under continuously fluctuating N environments where rhizosphere nitrate ions switch periodically between deficient and sufficient states. TGA1/4 are crucial transcription factors that enable plants to survive under fluctuating and challenging N environmental conditions.

plant biology↗

bioRxiv2023

Autophagosome development and chloroplast segmentation occur synchronously for piecemeal degradation of chloroplasts

Plants distribute many nutrients to chloroplasts during leaf development and maturation. When leaves senesce or experience sugar starvation, the autophagy machinery degrades chloroplast proteins to facilitate efficient nutrient reuse. Here, we report on the intracellular dynamics of an autophagy pathway responsible for piecemeal degradation of chloroplast components. Through live-cell monitoring of chloroplast morphology, we observed the formation of chloroplast budding structures in sugar-starved leaves. These buds were then released and incorporated into the vacuolar lumen as an autophagic cargo termed a Rubisco-containing body. The budding structures did not accumulate in mutants of core autophagy machinery, suggesting that autophagosome creation is required for forming chloroplast buds. Simultaneous tracking of chloroplast morphology and autophagosome development revealed that the isolation membranes of autophagosomes interact closely with part of the chloroplast surface before forming chloroplast buds. Chloroplasts then protrude at the site associated with the isolation membranes, which divide synchronously with autophagosome maturation. This autophagy-related division does not require DYNAMIN-RELATED PROTEIN 5B, which constitutes the division ring for chloroplast proliferation in growing leaves. An unidentified division machinery may thus fragment chloroplasts for degradation in coordination with the development of the chloroplast-associated isolation membrane.

plant biology↗

bioRxiv2019

Biosynthesis of β-(1->5)-Galactofuranosyl Chains of Fungal-Type and O-Mannose-Type Galactomannans within the Invasive Pathogen Aspergillus fumigatus

The pathogenic fungus Aspergillus fumigatus contains galactomannans localized on the surface layer of its cell walls, which are involved in various biological processes. Galactomannans comprise -(1[->]2)-/-(1[->]6)-mannan and {beta}-(1[->]5)-/{beta}-(1[->]6)-galactofuranosyl chains. We previously revealed that GfsA is a {beta}-galactofuranoside {beta}-(1[->]5)-galactofuranosyltransferase involved in the biosynthesis of {beta}-(1[->]5)-galactofuranosyl chains. Here, we clarified the entire biosynthesis of {beta}-(1[->]5)-galactofuranosyl chains in A. fumigatgus. Two paralogs exist within A. fumigatus: GfsB and GfsC. We show that GfsB and GfsC, in addition to GfsA, are {beta}-galactofuranoside {beta}-(1[->]5)-galactofuranosyltransferases by biochemical and genetic analyses. GfsA, GfsB, and GfsC can synthesize {beta}-(1[->]5)-galactofuranosyl oligomers up to lengths of 7, 3, and 5 galactofuranoses within an established in vitro highly efficient assay of galactofuranosyltransferase activity. Structural analyses of galactomannans extracted from the strains {Delta}gfsB, {Delta}gfsC, {Delta}gfsAC, and {Delta}gfsABC revealed that GfsA and GfsC synthesized all {beta}-(1[->]5)-galactofuranosyl residues of fungal-type and O-mannose-type galactomannans, and GfsB exhibited limited function in A. fumigatus. The loss of {beta}-(1[->]5)-galactofuranosyl residues decreased the hyphal growth rate and conidia formation ability as well as increased the abnormal hyphal branching structure and cell surface hydrophobicity, but this loss is dispensable for sensitivity to antifungal agents and virulence toward immune-compromised mice.\n\nIMPORTANCE{beta}-(1[->]5)-galactofuranosyl residues are widely distributed in the subphylum Pezisomycotina of the phylum Ascomycota. Pezizomycotina includes many plant and animal pathogens. Although the structure of {beta}-(1[->]5)-galactofuranosyl residues of galactomannans in filamentous fungi was discovered long ago, it remains unclear which enzyme is responsible for biosynthesis of this glycan. Fungal cell wall formation processes are complicated, and information concerning glycosyltransferases is essential for their understanding. In this study, we show that GfsA and GfsC are responsible for the biosynthesis of all {beta}-(1[->]5)-galactofuranosyl residues of fungal-type and O-mannose-type galactomannans. The data presented here indicates that {beta}-(1[->]5)-galactofuranosyl residues are involved in cell growth, conidiation, polarity, and cell surface hydrophobicity. Our new understanding of {beta}-(1[->]5)-galactofuranosyl residue biosynthesis provides important novel insights into the formation of the complex cell wall structure and the virulence of the subphylum Pezisomycotina.

microbiology↗

bioRxiv2016

Autophagy mitigates high-temperature injury during microsporogenesis in Arabidopsis thaliana

Autophagy is one of the cellular processes that break down cellular components during senescence, starvation, and stress. The susceptibility of plant pollen development to high-temperature (HT) stress is well known, but the involvement of autophagy in HT injury is yet to be clarified. Here, we found that following transfer to 30 {degrees}C, all autophagy-deficient (atg) mutants (atg2-1, 5-1, 7-2, and 10-1) of Arabidopsis thaliana tested displayed visibly impaired pollen development and anther dehiscence. HT-induced male sterility significantly increased in the atg mutants, but the degree of HT-induced obstacles did not change between the wild type (WT) and mutants from the seedling stage to the bolting stage. Cytological analyses showed that 30 {degrees}C promoted autophagy and autolysosome formation in both anther wall cells and microspores in developing anthers of WT, but the atg5-1 mutant did not show completion of tapetum degeneration and microspore maturation. HT upregulated hydrogen peroxide and dehydroascorbate reductase 1 production in both WT and atg5-1 anthers, but the basal levels were already higher in the mutant. HT repressed expression of UNDEAD and its regulator MYB80, which are required for tapetal programmed cell death (PCD) for proper pollen development. Taken together, our results suggest that autophagy functions in tapetum degeneration and pollen development during HT-caused tapetal PCD abortion.\n\nHighlightsO_LIIn Arabidopsis, autophagy is not essential for completion of the life cycle under normal temperatures.\nC_LIO_LIHigh temperature (HT) stress induces autophagy in developing anther wall cells and microspores.\nC_LIO_LIAutophagy deficient atg mutants become almost completely male-sterile at moderate HT.\nC_LIO_LIAutophagy plays a role in tapetum degeneration and pollen development during HT-caused abortion of tapetal program cell death.\nC_LI

plant biology↗