Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Soil metagenome

ABSTRACT: Associative nitrogen fixation in nodules of the conifer Lepidothamnus fonkii Raw sequence reads

PROVIDER: PRJNA319299 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR3417612_1.fastq.gz	Fastqsanger.gz
	SRR3417612_2.fastq.gz	Fastqsanger.gz
	SRR3417613_1.fastq.gz	Fastqsanger.gz
	SRR3417613_2.fastq.gz	Fastqsanger.gz
	SRR3417614_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Biological nitrogen fixation maintains C/N balance and photosynthesis at elevated CO2

Project description:To investigate the effect that biological nitrogen fixation will have on plant responses to nitrogen dose at elevated CO2, alfalfa (Medicago sativa) lines were grown at three nitrogen doses and ambient or elevated CO2. Four lines were used in the study, two lines that can form nodules capable of fixing nitrogen (effective lines) and two lines that can not form nodules capable of nitrogen fixation (ineffective lines). The ineffective lines are the result of a complementary mutation in the same gene.

2024-02-26 | GSE244008 | GEO

The NAC transcription factors SNAP1/2/3/4 are central regulators mediating high nitrogen responses in mature nodules of soybean

Project description:Legumes can utilize atmospheric nitrogen via symbiotic nitrogen fixation, but this process is inhibited by high soil inorganic nitrogen. So far, how high nitrogen inhibits N2 fixation in mature nodules is still poorly understood. Here we construct a co-expression network in soybean nodule and find that a dynamic and reversible transcriptional network underlies the high N inhibition of N2 fixation. Intriguingly, several NAC transcription factors (TFs), designated as Soybean Nitrogen Associated NAPs (SNAPs), are amongst the most connected hub TFs. The nodules of snap1/2/3/4 quadruple mutants show less sensitivity to the high N inhibition of nitrogenase activity and acceleration of senescence. Integrative analysis shows that these SNAP TFs largely influence the high N transcriptional response through direct regulation of a subnetwork of senescence-associated genes and transcriptional regulators. We propose that the SNAP-mediated transcriptional network may trigger nodule senescence in response to high N.

2023-07-05 | GSE236557 | GEO

Proteome analysis of the soybean nodule phosphorus response mechanism and characterisation of stress-induced ribosome structural and protein expression changes

Project description:In agroecosystems, a plant-usable form of nitrogen is mainly generated by legume-based biological nitrogen fixation, a process that requires phosphorus (P) as an essential nutrient. To investigate the physiological mechanism whereby phosphorus influences soybean nodule nitrogen fixation, soybean root nodules were exposed to four phosphate levels: 1 mg/L (P stress), 11 mg/L (P stress), 31 mg/L (Normal P), 61 mg/L (High P) then proteome analysis of nodules was conducted to identify phosphorus-associated proteome changes. We found that phosphorus stress-induced ribosomal protein structural changes were associated with altered key root nodule protein synthesis profiles. Importantly, up-regulated expression of peroxidase was observed as an important phosphorus stress-induced nitrogen fixation-associated adaptation that supported two nodule-associated activities: scavenging of reactive oxygen species (ROS) and cell wall growth. In addition, phosphorus transporter (PT) and purple acid phosphatase (PAPs) were up-regulated that regulated phosphorus transport and utilisation to maintain phosphorus balance and nitrogen fixation function in phosphorus-stressed root nodules.

2022-08-11 | PXD033875 | Pride

soil metagenome

Project description:nitrogen fertilization Raw sequence reads

| PRJNA353163 | ENA

Morus alba Raw protein sequence reads

Project description:Morus alba L. Raw protein sequence reads and sequence

2024-02-08 | PXD049451 |

Gene expression analysis in developmentally arrested root nodules formed by Sinorhizobium meliloti and Medicago truncatula

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

Metabolomics and transcriptomics identify multiple downstream targets of Paraburkholderia phymatum σ54 during symbiosis with Phaseolus vulgaris

Project description:RpoN (σ54) is the key sigma factor for the regulation of transcription of nitrogen fixation genes in diazotrophic bacteria, which include alpha- and beta-rhizobia. Our previous studies showed that a rpoN mutant of the beta-rhizobial strain Paraburkholderia phymatum formed root nodules on Phaseolus vulgaris that were unable to reduce atmospheric nitrogen into ammonia. In an effort to further characterize the RpoN regulon of P. phymatum, transcriptomics was combined with a powerful metabolomics approach. The metabolome of P. vulgaris root nodules infected by the P. phymatum rpoN Fix- mutant revealed statistically significant metabolic changes compared to wild-type Fix+ nodules, including reduced amounts of chorismate and elevated levels of flavonoids. A transcriptome analysis on Fix+ and Fix- nodules – combined with a search for RpoN binding sequences in promoter regions of regulated genes – confirmed the expected control of σ54 on nitrogen fixation genes in nodules. The transcriptomic data also identified additional target genes, whose differential expression was able to explain the observed metabolite changes in a numerous cases. Moreover, the genes encoding the two-component regulatory system NtrBC were downregulated in root nodules induced by the rpoN mutant and contained a putative RpoN binding motif in their promoter region, suggesting direct regulation. The construction and characterization of an ntrB mutant strain revealed impaired nitrogen assimilation in free-living conditions, as well as a noticeable symbiotic phenotype by forming less but heavier nodules on P. vulgaris roots.

2018-06-06 | GSE111993 | GEO

soil metagenome

Project description:black soil nitrogen-fixation bacteria Metagenome

| PRJNA385763 | ENA

Proteomic analysis dissects the impact of nodulation and biological nitrogen fixation on Vicia faba root nodule physiology

Project description:Symbiotic nitroegn fixation in functional (Fix+) and non-functional (Fix-) nodules of Vicia faba infected with Rhizobium leguminosarum was investigated using label-free shotgun tandem MS. Proteins involved in symbiotic nitrogen fixation and maintenance of the symbiosis were identified.

2018-05-30 | PXD008548 | Pride

soil metagenome

Project description:Nitrogen-fixing microorganism ,nifH gene Raw sequence reads

| PRJNA506358 | ENA