Biology subjects

Okuma, N.

Publications and source records attributed to Okuma, N..

4 recordsLinked to original sources

bioRxiv2026

Lotus japonicus CLV1-Like Receptor HAR1 Promotes Nitrogen Utilization and Growth Under Non-Symbiotic Conditions.

Legumes establish mutualistic symbiosis with nitrogen (N)-fixing bacteria, which allows them to utilize atmospheric N2. Because the maintenance of symbiosis requires abundant carbon (C) sources, legumes regulate the balance between carbon consumption and nitrogen acquisition by systemically controlling the nodule number through CLAVATA1 (CLV1)-like receptors. In Lotus japonicus, the CLV1-like receptor HYPERNODULATION ABERRANT ROOT FORMATION1 (HAR1) acts in shoots to regulate root nodulation and contributes to symbiotic C/N coordination. This raises the possibility that HAR1 may also influence plant growth and nitrogen utilization beyond symbiotic nodulation. In this study, we showed that HAR1 plays a critical role in regulating nitrogen use to enhance growth under conditions of high nitrate availability, even in non-symbiotic environments. Unlike the wild-type, the har1 mutant failed to increase its growth in response to higher nitrate availability. This lack of growth response was associated with a lower rate of net biomass production per unit leaf area and a reduced capacity for biomass production per unit plant nitrogen. We further found that nitrate-responsive TCA cycle-related organic acids were higher in har1 leaves than in wild-type leaves even under low nitrate conditions. Because the HAR1 mutation did not affect photosynthetic traits, we propose that HAR1 promotes growth under non-symbiotic conditions by coordinating nitrogen utilization with primary metabolism. One-sentence summaryLotus japonicus CLV1-like receptor HAR1 improves nitrogen utilization and growth at high nitrate conditions by regulating organic acid metabolism, independent of root nodule symbiosis.

plant biology↗

bioRxiv2026

Chromid-like secondary replicons as key sites of biosynthetic gene clusters in Ktedonobacteria

Soils harbour immense biosynthetic gene cluster (BGC) diversity that can mediate microbial interactions, yet this potential is still mapped unevenly across the tree of life. Ktedonobacteria--a class of actinomycete-like bacteria within phylum Chloroflexota--are widespread in terrestrial environments and repeatedly dominate pioneer communities in extremely oligotrophic volcanic bare-ground soils; however, their secondary metabolism and genome architecture remain poorly characterised. Here, we integrate targeted cultivation using volcanic soils from Mount Zao with genome-resolved metagenomics and public genomes to analyse 183 ktedonobacterial genomes. Using antiSMASH and BiG-SLiCE, we identified 1,546 BGCs comprising 1,162 non-redundant gene-cluster families (GCFs). In our dataset, nearly one quarter of genomes encode [≥]10 distinct GCFs, and several family-level clades show mean GCF counts comparable to those in genus Streptomyces. Most ktedonobacterial BGCs are highly divergent from reference collections and exhibit unusually low intra-genomic redundancy, suggesting broad, underexplored chemotypes. Long-read assemblies from ten strains reveal recurrent 1.6-3.5 Mb chromid-like secondary replicons with chromosome-like composition but distinct maintenance signatures. These replicons are consistently enriched in BGCs and mobility-associated genes, with mobility loci concentrated near BGC boundaries. Collectively, our results expand the current knowledge of the phylogenetic landscape of soil biosynthetic diversity and highlight chromid-like secondary replicons as major genomic reservoirs for specialised metabolism in Ktedonobacteria.

microbiology↗

bioRxiv2018

Cell type-specific regulation of nutrient absorption, metabolism and transfer in arbuscular mycorrhizal fungi

Arbuscular mycorrhizal fungi (AMF) establish symbiotic relationships with most land plants, mainly for the purpose of nutrient exchange. Many studies have revealed the regulation of absorption, metabolism, and transfer of nutrients in AMF and the genes involved in these processes. However, the spatial regulation of the genes among the structures comprising each developmental stage are not well understood. Here, we demonstrate the structure-specific transcriptome of the model AMF species, Rhizophagus irregularis. We performed an ultra-low input RNA-seq analysis, SMART-seq2, comparing five extraradical structures, germ tubes, runner hyphae, branched absorbing structures, immature spores, and mature spores. In addition, we reanalyzed the recently reported RNA-seq data comparing intraradical hyphae and arbuscules. Our analyses captured the distinct features of each structure and revealed the structure-specific expression patterns of genes related to absorption, metabolism, and transfer of nutrients. Of note, the transcriptional profiles suggest the distinct functions of branched absorbing structures in nutrient absorption. These findings provide a comprehensive dataset to advance our understanding of the transcriptional dynamics of fungal nutrition in this symbiotic system.

plant biology↗

bioRxiv2017

Evidence of non-tandemly repeated rDNAs and their intragenomic heterogeneity in Rhizophagus irregularis

Arbuscular mycorrhizal fungus (AMF) species are one of the most widespread symbionts of land plants. Our substantially improved reference genome assembly of a model AMF, Rhizophagus irregularis DAOM-181602 (total contigs = 210), facilitated discovery of repetitive elements with unusual characteristics. R. irregularis has only ten or eleven copies of complete 45S rDNAs, whereas the general eukaryotic genome has tens to thousands of rDNA copies. R. irregularis rDNAs are highly heterogeneous and lack a tandem repeat structure. These findings provide evidence for the hypothesis that rDNA heterogeneity depends on the lack of tandem repeat structures. RNA-Seq analysis confirmed that all rDNA variants are actively transcribed. Observed rDNA/rRNA polymorphisms may modulate translation by using different ribosomes depending on biotic and abiotic interactions. The non-tandem repeat structure and intragenomic heterogeneity of AMF rDNA/rRNA may facilitate adaptation to a various environmental condition including the broad host range.

genomics↗