Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1022778 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26290351_1.fastq.gz | Fastqsanger.gz | |||
| SRR26290351_2.fastq.gz | Fastqsanger.gz | |||
| SRR26290352_1.fastq.gz | Fastqsanger.gz | |||
| SRR26290352_2.fastq.gz | Fastqsanger.gz | |||
| SRR26290353_1.fastq.gz | Fastqsanger.gz |
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Project description:Legume plants can establish symbiotic nitrogen fixation (SNF) with rhizobia mostly in root nodules, where rhizobia-infected cells are accompanied with uninfected cells in a mosaic pattern. Inside the mature nodules of legume, carbon and nitrogen nutrients between host plant cells and their resident bacteria are actively exchanged. To elucidate the metabolite dynamics relevant for SNF in nodules, three cell-types from nodule tissues of a model legume, Lotus japonicus, were isolated using laser microdissesction, and transcriptome analysis was done by an oligoarray with 60-mer length representing 21,495 genes. In our cell-type-specific profiling, many genes were identified as being expressed in nodules with spatial-specific manners. Among them, genes coding for metabolic enzymes were classified according to their function, and detailed data analysis figured out that secondary metabolic pathway was highly activated in nodule cortex. In particular, a number of metabolic genes for phenyl propanoid pathway were found as highly expressed genes accompanied with those encoding putative transporters of secondary metabolites. These data suggest the involvement of novel physiological function of phenylpropanoids in SNF. Gene expression in three different cell-types of Lotus japonicus nodule was measured. Three independent experiments were performed at each cell-types.
2011-12-29 | E-GEOD-34753 | biostudies-arrayexpress
Project description:RNA-seq analysis was performed to know the expression profiles of Lotus japonicus genes during nodule development and nitrogen fixation.
2019-12-31 | GSE129778 | GEO
Project description:Legumes establish endosymbiotic associations with nitrogen-fixing rhizobia, which they host inside root nodules. Here, specific physiological and morphological adaptations, such as the production of oxygen-binding leghemoglobin proteins and the formation of an oxygen diffusion barrier in the nodule periphery, are essential to protect the oxygen-labile bacterial nitrogenase enzyme. The molecular basis of the latter process remains elusive, as the identification of required genes is limited by the epistatic effect of nodule organogenesis over nodule infection and rhizobia accommodation. We overcame this by exploring the phenotypic diversity of Lotus japonicus accessions that uncouple nodule organogenesis from nodule infection when inoculated with a sub-compatible Rhizobium strain. Using comparative transcriptomics, we identified genes with functions associated with oxygen homeostasis and deposition of lipid polyesters on cell walls to be specifically upregulated in infected compared to uninfected nodules. As such hydrophobic modifications on cell walls are pivotal for creating diffusion barriers like the root endodermis, we focused on two Fatty acyl-CoA reductase genes that were specifically activated in the nodule or in the root endodermis. Mutant lines in a Fatty acyl-CoA reductase gene expressed exclusively in the nodule endodermis showed had decreased suberization of this cell layer and increased nodule permeability compared to wild type plants. Oxygen concentrations were significantly increased in the inner cortex of mutant nodules, which correlated with reduced nitrogen fixation rates, and impaired shoot growth. These results provide the first genetic evidence for the formation of the nodule oxygen diffusion barrier, a key adaptation enabling nitrogen fixation in legume nodules.
2022-11-01 | GSE216502 | GEO
Project description:Legume plants can establish symbiotic nitrogen fixation (SNF) with rhizobia mostly in root nodules, where rhizobia-infected cells are accompanied with uninfected cells in a mosaic pattern. Inside the mature nodules of legume, carbon and nitrogen nutrients between host plant cells and their resident bacteria are actively exchanged. To elucidate the metabolite dynamics relevant for SNF in nodules, three cell-types from nodule tissues of a model legume, Lotus japonicus, were isolated using laser microdissesction, and transcriptome analysis was done by an oligoarray with 60-mer length representing 21,495 genes. In our cell-type-specific profiling, many genes were identified as being expressed in nodules with spatial-specific manners. Among them, genes coding for metabolic enzymes were classified according to their function, and detailed data analysis figured out that secondary metabolic pathway was highly activated in nodule cortex. In particular, a number of metabolic genes for phenyl propanoid pathway were found as highly expressed genes accompanied with those encoding putative transporters of secondary metabolites. These data suggest the involvement of novel physiological function of phenylpropanoids in SNF.
2011-12-29 | GSE34753 | GEO
Project description:Acting in a partially redundant manner, NF-Ys were shown previously to regulate bacterial infection, including selection of a superior rhizobial strain, and to participate in mediating nodule structure formation. However, the exact mechanism(s) by which these transcriptional factors exert their symbiotic functions has remained elusive. Gene expression profiling for wild-type and Nuclear Factor YA (nf-ya)-A mutants in roots of Lotus japonicus were conducted 4 days after inoculation with Mesorhizobium loti in order to understand the interaction of NF-Ys and other genes in Lotus japonicus.
2017-05-03 | E-MTAB-4970 | biostudies-arrayexpress
Project description:Heme is utilized as the cofactor of diverse proteins and plays critical roles in different redox reactions. The fixation active nodules of legumes are abundant with heme-containing leghemoglobin to buffer the oxygen concentration. Symbiotic rhizobia could also synthesize heme, and employ heme for efficient respiration and iron uptake regulation. However, the role and regulation of host-controlled heme production during symbiotic nitrogen fixation have not been directly investigated and experimentally proved. Here, we identified the coproporphyrinogen III oxidase plastid related 1 (CPOP1) as a key regulator of symbiotic heme synthesis enzyme in Lotus japonicus. CPOP1 is specifically highly expressed in nitrogen-fixing nodules, and knocking out CPOP1 alone causes leaf etiolation and dwarfism which could be fully recovered by the exogenous application of nitrogen source, indicating nitrogen fixation defect. The cpop1 mutant shows significantly increased nodule oxygen level and decreased nitrogen fixation activity compared to the wild type (WT). Moreover, cell division and related gene expression of bacteroids are also affected upon CPOP1 knockout. We conclude that CPOP1 is essential for the microaerophilic environment control of infected cells and the activation of rhizobial nitrogenase required for symbiotic nitrogen fixation, through host-regulated nodule heme synthesis.
2025-09-01 | GSE262662 | GEO
Project description:The casparian strip serves as a crucial diffusion barrier in the endodermis, playing a vital role in controlling the flow of substances between the root and its external environment. Here, we observed that when the casparian strip is absent, bacteria can accumulate abundantly on the roots. To investigate the impact of this bacterial accumulation on the root indued by casparian strip deficiency , we inoculated Col-0 and sgn3 myb36 roots with CHA0 in a hydroponic system. Ultimately, we found that the bacterial accumulation on the roots, resulting from the absence of the Casparian strip, strongly induces the immune response of the roots. This indicates that the casparian strip plays an important role in regulating the interaction between the root and microorganisms.
2024-11-06 | GSE280679 | GEO
Project description:A time-course transcriptomic study was performed on mature nodules of Lotus japonicus MG-20 at 4 weeks post-inoculation (wpi) with Mesorhizobium loti MAFF303099. Plants were exposed to 10 mM KNO3 for six days and then nitrate was removed for five more days.
2023-03-23 | GSE197362 | GEO