Ontology highlight
ABSTRACT:
PROVIDER: PRJNA717099 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR20215132_1.fastq.gz | Fastqsanger.gz | |||
| SRR20215132_2.fastq.gz | Fastqsanger.gz |
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Project description:We characterized transcriptomes of Sinorhizobium meliloti root nodule bacteria with mutations in sigma factor genes.
2018-09-05 | GSE116664 | GEO
Project description:Root nodule microbial communities of legume samples collected from Mexico - Siratro Mexico nodule mix metagenome
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Project description:Expression profile of bacteria during nodule development
2006-02-01 | E-TABM-74 | biostudies-arrayexpress
Project description:During the legume-rhizobium symbiosis, free-living soil bacteria known as rhizobia trigger the formation of root nodules. The rhizobia infect these organs and adopt an intracellular lifestyle within the symbiotic nodule cells where they become nitrogen-fixing bacteroids. Several legume lineages enforce their symbionts into an extreme cellular differentiation, comprising cell enlargement and genome endoreduplication. The antimicrobial peptide transporter BclA is a major determinant of this differentiation process in Bradyrhizobium sp. ORS285, a symbiont of Aeschynomene spp.. In the absence of BclA, Bradyrhizobium sp. ORS285 proceeds until the intracellular infection of nodule cells but the bacteria cannot differentiate into enlarged polyploid bacteroids and fix nitrogen. The nodule bacteria of the bclA mutant constitute thus an intermediate stage between the free-living soil bacteria and the intracellular nitrogen-fixing bacteroids. Metabolomics on whole nodules of Aeschynomene afraspera and Aeschynomene indica infected with the ORS285 wild type or the bclA mutant revealed 47 metabolites that differentially accumulated concomitantly with bacteroid differentiation. Bacterial transcriptome analysis of these nodules discriminated nodule-induced genes that are specific to differentiated and nitrogen-fixing bacteroids and others that are activated in the host microenvironment irrespective of bacterial differentiation and nitrogen fixation. These analyses demonstrated that the intracellular settling of the rhizobia in the symbiotic nodule cells is accompanied with a first transcriptome switch involving several hundreds of upregulated and downregulated genes and a second switch accompanying the bacteroid differentiation, involving less genes but that are expressed to extremely elevated levels. The transcriptomes further highlighted the dynamics of oxygen and redox regulation of gene expression during nodule formation and we discovered that bclA represses the expression of non-ribosomal peptide synthetase gene clusters suggesting a non-symbiotic function of BclA. Together, our data uncover the metabolic and gene expression changes that accompany the transition from intracellular bacteria into differentiated nitrogen-fixing bacteroids.
2019-06-01 | GSE126971 | GEO
Project description:Root nodule microbial communities of legume samples collected from Mexico - Turtle bean Mexico white nodule metagenome
| PRJNA375142 | ENA
Project description:Root nodule microbial communities of legume samples collected from Mexico - Turtle bean Mexico pink nodule metagenome
| PRJNA375141 | ENA
Project description:The actinobacteria Frankia alni is able to induce the formation of nodules on the root of a large spectrum of actinorhizal plants, where it converts dinitrogen to ammonia in exchange for plant photosynthates. In the present study, transcriptional analyses were performed on nitrogen-replete free-living cells and on Alnus glutinosa nodule bacteria, using whole genome microarrays. Distribution of nodule-induced genes on the genome was found to be mostly over regions with high synteny between three Frankia genomes, while nodule-repressed genes, which were mostly hypothetical and not conserved, were spread around the genome. Genes known to be related to symbiosis were highly induced: nif (nitrogenase), hup2 (hydrogenase uptake), suf (sulfur-iron cluster) and shc (hopanoids synthesis). The expression of genes involved in ammonium assimilation and transport was strongly modified suggesting that bacteria ammonium assimilation was limited. Genes involved in particular in transcriptional regulation, signalling processes, protein drug export, protein secretion, lipopolysaccharide and peptidoglycan biosynthesis that may play a role in symbiosis were also identified. We showed that this nodule transcriptome of Frankia was highly similar among phylogenetically distant plant families.
2010-09-12 | GSE18190 | GEO
Project description:Bathymodiolin mussels are a group of bivalves associated with deep-sea reducing habitats, such as hydrothermal vents and cold seeps. These mussels usually engage in an obligatory symbiosis with sulfur and/or methane oxidizing Gammaproteobacteria. In addition to these bacteria, Bathymodiolus heckerae that inhabit gas and oil seeps in Campeche Bay, the southern Gulf of Mexico, host bacteria phylogenetically with the Cycloclasticus genus. We recently discovered the capability for short-chain alkane degradation in draft genomes of symbiotic Cycloclasticus. With proteomics, we investigated whether the genes required for this process are expressed by the symbionts.
2016-12-05 | PXD005351 | Pride
Project description:affy_med_2011_06 - affy_med_2011_06 - Legume plants establish a symbiotic interaction with soil bacteria called rhizobia. A complex molecular dialogue between the two partners is necessary for the successful infection and organogenesis processes that will ultimately result in the formation of a nitrogen fixing nodule. During a M. truncatula Tnt1 mutant screen, a new class of symbiotic mutant called noot (nodule root) was identified. This original single recessive mutant develops a root in apical position of nodules that are colonized by bacteria and functional for nitrogen fixation. This conversion suggests that the legume nodule morphogenetic pathway may be derived from a root program. We cloned the NOOT gene and showed that it corresponds to Pisum sativum COCH (Ferguson and Reid, 2005, Plant Cell Physiol 46, 1583-1589). The goal of this project is to compare the transcriptomes from wild type nodules and roots to the noot nodule one. This will allow us to unravel the similarity and differences between the wild type and mutant nodule transcriptomes but also to know which developmental pathway is under the control of the NOOT gene. --Seeds of the WT and noot mutant lines (two mutant alleles: Tnk507 and NF2717) were surface sterilized and placed at 4°C for three days on a minimal BNM medium square plate (12cm X 12cm). Seeds were germinated at room temperature and 10 seeds were placed in a row on nitrogen poor (BNM) plate. Seedlings were inoculated using Sinorhizobium meliloti Rm41 for nodule production. Some WT plants were not infected by the bacteria in order to collect roots. Nodules and roots were harvested 18 to 21 days post inoculation. Each experimental repetition (3 WT nodules, 3 WT roots and 2 mutant nodules of each allele) was harvested at a separated day. RNA preparations were done using a Quiagen Kit. 10 arrays - Medicago; gene knock out,organ comparison
2012-05-31 | E-GEOD-36558 | biostudies-arrayexpress