Ontology highlight
ABSTRACT:
PROVIDER: PRJNA578767 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10325503.fastq.gz | Fastqsanger.gz | |||
| SRR10325903.fastq.gz | Fastqsanger.gz | |||
| SRR10325504.fastq.gz | Fastqsanger.gz | |||
| SRR10325505.fastq.gz | Fastqsanger.gz | |||
| SRR10325914.fastq.gz | Fastqsanger.gz |
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Project description:Many plants associate with arbuscular mycorrhizal fungi for nutrient acquisition, while legumes also associate with nitrogen-fixing rhizobial bacteria. Both associations rely on symbiosis signaling and here we show that cereals can perceive lipochitooligosaccharides (LCOs) for activation of symbiosis signaling, surprisingly including Nod factors produced by nitrogen-fixing bacteria. However, legumes show stringent perception of specifically decorated LCOs, that is absent in cereals. LCO perception in plants is activated by nutrient starvation, through transcriptional regulation of Nodulation Signaling Pathway (NSP)1 and NSP2. These transcription factors induce expression of an LCO receptor and act through the control of strigolactone biosynthesis and the karrikin-like receptor DWARF14-LIKE. We conclude that LCO production and perception is coordinately regulated by nutrient starvation to promote engagement with mycorrhizal fungi. Our work has implications for the use of both mycorrhizal and rhizobial associations for sustainable productivity in cereals.
2022-10-06 | GSE214698 | GEO
Project description:Several studies have shown that plant hormones play key roles during legume-rhizobia symbiosis. For instance, auxins can induce formation of nodule-like structures (NLS) on legume roots in the absence of rhizobia. Furthermore, these NLS can be colonized by nitrogen-fixing bacteria, which favor nitrogen fixation compared to regular roots and subsequently increase plant yield. Interestingly, auxin also induces similar NLS in cereal roots. While several genetic studies have identified plant genes controlling NLS formation in legumes, no studies have investigated the genes involved in NLS formation in cereals. In this study, we performed a comprehensive RNA sequencing experiment to identify genes differentially expressed during NLS formation in rice at different stages and identified several promising genes for control of NLS based on their biological and molecular functions.
2019-01-01 | GSE92835 | GEO
Project description:We designed a new specific mRNA microarray targeting a subset of genes (956) of the diazotrophs Richelia intracellularis and Calothrix rhizosoleniae (genomes RintRC01, RintHH01, RintHM01 and CalSC01) which associate with diatom hosts. The aim was to be able to describe the gene expressions of genes related to several metabolic pathways, specifically nitrogen fixation and how they possibly differed between the closely related strains based on environment and host association. In this study we focused on the RintRC01 and RintHH01. To better understand how the gene expression of nitrogen fixation genes relates to nitrogen fixation rates both gene expression and rate measurements were done in parallell.
2019-10-31 | GSE139589 | GEO
Project description:Resendis-Antonio2007 - Genome-scale metabolic
network of Rhizobium etli (iOR363)
This model is described in the article:
Metabolic reconstruction and
modeling of nitrogen fixation in Rhizobium etli.
Resendis-Antonio O, Reed JL,
Encarnación S, Collado-Vides J, Palsson BØ.
PLoS Comput. Biol. 2007 Oct; 3(10):
1887-1895
Abstract:
Rhizobiaceas are bacteria that fix nitrogen during symbiosis
with plants. This symbiotic relationship is crucial for the
nitrogen cycle, and understanding symbiotic mechanisms is a
scientific challenge with direct applications in agronomy and
plant development. Rhizobium etli is a bacteria which provides
legumes with ammonia (among other chemical compounds), thereby
stimulating plant growth. A genome-scale approach, integrating
the biochemical information available for R. etli, constitutes
an important step toward understanding the symbiotic
relationship and its possible improvement. In this work we
present a genome-scale metabolic reconstruction (iOR363) for R.
etli CFN42, which includes 387 metabolic and transport
reactions across 26 metabolic pathways. This model was used to
analyze the physiological capabilities of R. etli during stages
of nitrogen fixation. To study the physiological capacities in
silico, an objective function was formulated to simulate
symbiotic nitrogen fixation. Flux balance analysis (FBA) was
performed, and the predicted active metabolic pathways agreed
qualitatively with experimental observations. In addition,
predictions for the effects of gene deletions during nitrogen
fixation in Rhizobia in silico also agreed with reported
experimental data. Overall, we present some evidence supporting
that FBA of the reconstructed metabolic network for R. etli
provides results that are in agreement with physiological
observations. Thus, as for other organisms, the reconstructed
genome-scale metabolic network provides an important framework
which allows us to compare model predictions with experimental
measurements and eventually generate hypotheses on ways to
improve nitrogen fixation.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180006.
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quantitative kinetic models.
To the extent possible under law, all copyright and related or
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2015-07-30 | MODEL1507180006 | BioModels
Project description:Rhizobium etli is a bacteria that fix nitrogen in symbiotic activity with Phaseolus vulgaris, the common bean plant. In order to accomplish this nitrogen reduction a especial environment is induced in nodules such that gene expression of bacteroid suffer a significant change with respect to its wild type life style. With the purpose to identify genetic alterations between these physiological states, replicates of microarray data were accomplished in similar conditions between bacteria cultivated in free-life (succinate-ammonia) and those carrying on nitrogen fixation inside nodule.
2014-02-03 | GSE21638 | GEO
Project description:Rhizobia are soil bacteria that can associate with some legumes and participate in symbiotic nitrogen fixation. Bacterial CspA family members are small, single stranded nucleic acid binding proteins. Differentiation of rhizobial bacteria from a free-living to symbiotic state within legume root nodules follows a massive re-programming of bacterial gene expression. Here, the role of Sinorhizobium meliloti CspA family members in symbiotic development with Medicago sativa (alfalfa) was investigated. We defined expression patterns of CspA family members, identified CspA interacting RNAs, and investigated phenotypes and transcriptional defects associated with cspA deletion strains. We propose that these proteins affect rhizobial physiology through their global control of the cellular RNA secondary structure strength environment and through specific modulation of small non-coding RNA (sRNA) structures involved in cis-regulation of stress responsive sigma factor expression. This work describes an RNA structure mediated mechanism important for bacterial stress adaptation and symbiotic development within a plant host.
2018-08-01 | GSE102800 | GEO
Project description:Rhizobia are soil bacteria that can associate with some legumes and participate in symbiotic nitrogen fixation. Bacterial CspA family members are small, single stranded nucleic acid binding proteins. Differentiation of rhizobial bacteria from a free-living to symbiotic state within legume root nodules follows a massive re-programming of bacterial gene expression. Here, the role of Sinorhizobium meliloti CspA family members in symbiotic development with Medicago sativa (alfalfa) was investigated. We defined expression patterns of CspA family members, identified CspA interacting RNAs, and investigated phenotypes and transcriptional defects associated with cspA deletion strains. We propose that these proteins affect rhizobial physiology through their global control of the cellular RNA secondary structure strength environment and through specific modulation of small non-coding RNA (sRNA) structures involved in cis-regulation of stress responsive sigma factor expression. This work describes an RNA structure mediated mechanism important for bacterial stress adaptation and symbiotic development within a plant host.
2018-08-01 | GSE102799 | GEO
Project description:black soil nitrogen-fixation bacteria Metagenome
| PRJNA385763 | ENA
Project description:The bacterium, Sinorhizobium meliloti, interacts symbiotically with leguminous plants such as Medicago truncatula to form nitrogen-fixing root nodules. During symbiosis, plant and bacterial cells differentiate in a coordinated manner, resulting in specialized plant cells that contain nitrogen-fixing bacteroids. Medicago nodules are organized in structurally distinct tissue zones, representing different stages of bacterial and plant differentiation. We used laser-capture microdissection (LCM) to analyze bacterial and plant gene expression in four root nodule regions. In parallel, we analyzed gene expression in nodules formed by wild type bacteria on six plant mutants with nitrogen fixation deficiencies (dnf). We found that bacteroid metabolism is drastically remodeled during bacteroid differentiation. Many processes required for bacterial growth are down-regulated in the nitrogen fixation zone. The overall transcriptional changes are similar to those occurring during nutrient limitation by the stringent response. We also observed differential expression of bacterial genes involved in nitrogen fixation, cell envelope homeostasis, cell division, stress response and polyamine biosynthesis at distinct stages of nodule development. In M. truncatula we observed the differential regulation of several host processes that may trigger bacteroid differentiation and control bacterial infection. We analyzed plant and bacterial gene expression simultaneously, which allowed us to correlate processes in both organisms.
2015-06-01 | GSE53705 | GEO
Project description:Our study revealed a synergistic effect between biological nitrogen fixation and current generation by G. sulfurreducens, providing a green nitrogen fixation alternative through shifting the nitrogen fixation field from energy consumption to energy production and having implications for N-deficient wastewater treatment.
2021-10-09 | GSE185414 | GEO