Ontology highlight
ABSTRACT:
PROVIDER: PRJNA961329 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24313745_1.fastq.gz | Fastqsanger.gz | |||
| SRR24313745_2.fastq.gz | Fastqsanger.gz | |||
| SRR24313746_1.fastq.gz | Fastqsanger.gz | |||
| SRR24313746_2.fastq.gz | Fastqsanger.gz | |||
| SRR24313747_1.fastq.gz | Fastqsanger.gz |
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Project description:Drought is one of the major environmental factors limiting biomass and seed yield production in agriculture. In this research we focused on plants from Fabaceae family, which have a unique ability for establishment of symbiosis with nitrogen-fixing bacteria, and are relatively susceptible to water limitation. We present the changes in nitrogenase activity and global gene expression occurring in Medicago truncatula and Lotus japonicus root nodules during water deficit. Our results prove a decrease in the efficiency of nitrogen fixation as well as extensive changes in plant and bacterial transcriptomes shortly after watering cessation. We show for the first time that not only symbiotic plant component, but also Sinorhizobium meliloti and Mesorhizobium loti bacteria residing in the root nodules of M. truncatula and L. japonicus, respectively, adjust their gene expression in response to water shortage. Although our results demonstrate that both M. truncatula and L. japonicus root nodules are susceptible to water deprivation, they indicate significant differences in plant and bacterial response to drought between tested species, which may be related to various type of root nodules formed by these species.
2019-02-26 | GSE126986 | GEO
Project description:H. seropedicae is a diazotrophic and endophytic bacterium that associates with economically important grasses promoting plant growth and increasing productivity. To identify genes related to bacterial ability to colonize and promote plant growth wheat seedlings growing hydroponically in Hoaglandâs medium were inoculated with H. seropedicae the bacteria and incubated for 3 days. mRNA from the bacteria present in the root surface and in the plant medium were purified, depleted from rRNA and used for RNA-seq profiling. RT-qPCR analyses were conducted to confirm regulation of selected genes. Comparison of RNA profile of bacteria attached to the root and planktonic revealed an extensive metabolic adaptation to the epiphytic life style.
2016-07-03 | E-MTAB-3646 | biostudies-arrayexpress
Project description:We studied potentially amyloidogenic proteins (e.g. protein forming polymers and complexes that are resistant to treatment with ionic detergents) in root nodules formed by two lines of garden pea (P. sativum L.): Sprint-2 (Fix+ phenotype) and Sprint-2Fix- (sym31) (Fix- phenotype) inoculated with the Rhizobium leguminosarum bv. viciae RCAM1026 root nodule bacteria. The Fix+ phenotype is characterized by effective (ability to fix nitrogen) root nodules formation. The Fix- line is a descendant of the Fix+ line and forms ineffective root nodules (unable to fix nitrogen) with undifferentiated bacteroids. We demonstrated the presence of both plant and bacterial proteins in detergent resistant fractions, including previously identified amyloid proteins RopA and RopB of R. leguminosarum and vicilin of P. sativum L.
2022-10-25 | PXD035724 | Pride
Project description:Endophytic bacteria influence plant growth and development and therefore are an attractive resource for applications in agriculture. However, little is known about the impact of these microorganisms on secondary metabolite (SM) production by medicinal plants. Here we assessed, for the first time, the effects of root endophytic bacteria on the modulation of SMs in the medicinal plant Lithospermum officinale (Boraginaceae family), with a focus on the naphthoquinones alkannin/shikonin (A/S). The study was conducted using a newly developed in vitro system as well as in the greenhouse. Targeted and non-targeted metabolomics approaches were used and supported by expression analysis of the gene PGT, encoding a key enzyme in the A/S biosynthesis pathway. Three bacterial strains, Chitinophaga sp. R-73072, Xanthomonas sp. R-73098 and Pseudomonas sp. R-71838 induced a significant increase of diverse SMs, including A/S, in L. officinale in both systems, demonstrating the strength of our approach for screening A/S derivative-inducing bacteria. Our results highlight the impact of root-endophytic bacteria on secondary metabolism in plants and indicate that production of A/S derivatives in planta likely involves cross-modulation of different metabolic pathways that can be manipulated by bacterial endophytes.
2021-08-11 | ST002062 | MetabolomicsWorkbench
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
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.
2012-06-01 | GSE36558 | GEO
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
Project description:The transformation of Sinorhizobium bacteria into nitrogen-fixing bacteroids located in the root-nodules of the Medicago plants is controlled by specific peptides released by the plants. In our study root nodules, and differently purified bacteroid mixtures were studied. Detailed description about sample preparation and data interpretation can be found in "Identification of Nodule-Specific Cysteine-Rich Plant Peptides in Endosymbiotic Bacteria" by H. Durgo et al., Proteomics (2015). CID spectra supporting all NCR identifications can be viewed using MS-Viewer on the public Protein Prospector website (prospector.ucsf.edu), search key: h7swi0wcik.
2015-02-17 | MSV000079037 | MassIVE
Project description:Distribution characteristics of endophytic bacteria and endophytic nitrogen-fixing bacteria in Vicia faba root nodules in rocky desertification areas of Southwest China
| PRJNA1184945 | ENA