Ontology highlight
ABSTRACT:
PROVIDER: PRJNA759113 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We present the draft genome of Nitrospirae bacterium Nbg-4 as a representative of this clade and couple this to in situ protein expression under sulfate-enriched and sulfate-depleted conditions in rice paddy soil. The proteins were extracted from the soil and analysed via LC-MS/MS measurements.
2018-01-08 | PXD007817 | Pride
Project description:Iron (Fe) is an essential element to plants, but can be harmful if accumulated to toxic concentrations. Fe toxicity can be a major nutritional disorder in rice (Oryza sativa) when cultivated under waterlogged conditions, as a result of excessive Fe solubilization of in the soil. However, little is known about the basis of Fe toxicity and tolerance at both physiological and molecular level. Here we aim at understand the genotypic differences in two rice cultivars with contrasting phenotypes under Fe toxicity.
2019-05-16 | GSE131287 | GEO
Project description:Iron (Fe) is an essential plant micronutrient, and its deficiency limits plant growth and development on alkaline soils. Under Fe deficiency, plant responses include upregulation of genes involved in Fe uptake from the soil. However, little is known about shoot responses to Fe deficiency. Using microarrays to probe gene expression in Kas-1 and Tsu-1 ecotypes of Arabidopsis thaliana revealed conserved rosette gene expression responses to Fe deficiency. Fe regulated genes included known metal homeostasis-related genes, and a number of genes of unknown function.
2012-09-30 | GSE39268 | GEO
Project description:Previous studies have demonstrated that the iron content in marine heterotrophic bacteria is comparatively higher than that of phytoplankton. Therefore, they have been indicated to play a major role in the biogeochemical cycling of iron. In this study, we aimed to investigate the potential of viral lysis as a source of iron for marine heterotrophic bacteria. Viral lysates were derived from the marine heterotrophic bacterium, Vibrio natriegens PWH3a (A.K.A Vibrio alginolyticus). The bioavailability of Fe in the lysates was determined using a model heterotrophic bacterium, namely, Dokdonia sp. strain Dokd-P16, isolated from Fe-limited waters along Line P transect in the Northeastern Pacific Ocean. The bacteria were grown under Fe-deplete or Fe-replete conditions before being exposed to the viral lysate. Differential gene expression following exposure to the viral lysate was analyzed via RNA sequencing to identify differentially expressed genes under iron-replete and iron-deplete conditions. This study would provide novel insights into the role of viral lysis in heterotrophic bacteria in supplying bioavailable iron to other marine microorganisms under iron-limiting and non-limiting conditions. First, the marine heterotrophic bacterium genome, Dokdonia sp. strain Dokd-P16, was sequenced to provide a genomic context for the expression studies. Subsequently, the relative gene expression in Dokdonia sp. strain Dokd-P16 grown under Fe limiting and non-limiting conditions were analyzed. This transcriptomic approach would be utilized to elucidate genes regulated by Fe availability in Dokdonia sp. strain Dokd-P16, which indicate its Fe-related response viral lysate exposure. Taken together, in this study, the transcriptomic responses of Fe-limited and non-limited marine heterotrophic bacteria were analyzed, which provided novel insights into the biological availability of Fe from the viral lysates.
2021-11-01 | GSE166618 | GEO
Project description:<p>High-affinity iron (Fe) scavenging compounds, or siderophores, are widely employed by soil bacteria to survive scarcity in bioavailable Fe. Siderophore biosynthesis relies on cellular carbon metabolism, despite reported decrease in both carbon uptake and Fe-containing metabolic proteins in Fe-deficient cells. Given this paradox, the metabolic network required to sustain the Fe-scavenging strategy is poorly understood. Here, through multiple <sup>13</sup>C-metabolomics experiments with Fe-replete and Fe-limited cells, we uncover how soil <em>Pseudomonas</em> species reprogram their metabolic pathways to prioritize siderophore biosynthesis. Across the three species investigated (<em>Pseudomonas putida</em> KT2440, <em>Pseudomonas protegens</em> Pf-5, and <em>Pseudomonas putida</em> S12), siderophore secretion is higher during growth on gluconeogenic substrates than during growth on glycolytic substrates. In response to Fe limitation, we capture decreased flux toward the tricarboxylic acid (TCA) cycle during the metabolism of glycolytic substrates but, due to carbon recycling to the TCA cycle via enhanced anaplerosis, the metabolism of gluconeogenic substrates results in an increase in both siderophore secretion (up to threefold) and Fe extraction (up to sixfold) from soil minerals. During simultaneous feeding on the different substrate types, Fe deficiency triggers a hierarchy in substrate utilization, which is facilitated by changes in protein abundances for substrate uptake and initial catabolism. Rerouted metabolism further promotes favorable fluxes in the TCA cycle and the gluconeogenesis-anaplerosis nodes, despite decrease in several proteins in these pathways, to meet carbon and energy demands for siderophore precursors in accordance with increased proteins for siderophore biosynthesis. Hierarchical carbon metabolism thus serves as a critical survival strategy during the metal nutrient deficiency.</p><p><br></p><p><strong>Data availability:</strong></p><p>The proteomics data have been deposited into the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier <a href='https://www.ebi.ac.uk/pride/archive/projects/PXD013605' rel='noopener noreferrer' target='_blank'>PXD013605</a>.</p>
2020-12-05 | MTBLS1715 | MetaboLights
Project description:Four Fe(II) concentrations (0.03, 0.09, 0.12 & 0.75 mM) were tested to investigate the stimulation and inhibition effects of ferrous iron on anammox bacterial activity. RNAs were extracted from the cultures, and the synthesized cDNAs by reverse transcription were used to carry out GeoChip analysis, by which the functional communities and expression level differences in functional genes under different Fe(II) concentrations conditions were obtained, and the response of anammox bacteria to Fe(II) stimulation and inhibition are speculated.
2020-08-28 | GSE120704 | GEO
Project description:Iron (Fe) is an essential plant micronutrient, and its deficiency limits plant growth and development on alkaline soils. Under Fe deficiency, plant responses include upregulation of genes involved in Fe uptake from the soil. However, little is known about shoot responses to Fe deficiency. Using microarrays to probe gene expression in Kas-1 and Tsu-1 ecotypes of Arabidopsis thaliana revealed conserved rosette gene expression responses to Fe deficiency. Fe regulated genes included known metal homeostasis-related genes, and a number of genes of unknown function. Kas and Tsu Arabidopsis seedlings were grown on complete media for 24 d, and then put on complete or -Fe media and collected after 24 and 48 h.
2012-09-30 | E-GEOD-39268 | biostudies-arrayexpress
Project description:Iron (Fe) deficiency is a yield-limiting factor for a variety of field crops across the world and generally results from the interaction of limited soil Fe bioavailability and susceptible genotype cultivation. Tomato, a Strategy I, model plant for Fe deficiency, is an important economical crop. Tomato responses in order to improve Fe uptake are based on acidification of rhizosphere, reduction of Fe3+ to Fe2+ and transport of Fe2+ into the cells.
2012-03-22 | GSE31112 | GEO