Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1139343 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29936948_1.fastq.gz | Fastqsanger.gz | |||
| SRR29936948_2.fastq.gz | Fastqsanger.gz | |||
| SRR29936949_1.fastq.gz | Fastqsanger.gz | |||
| SRR29936949_2.fastq.gz | Fastqsanger.gz | |||
| SRR29936950_1.fastq.gz | Fastqsanger.gz |
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Project description:We did single cell RNA sequencing on cultured chlamydomonas cells. We used two strains, one with cell wall, one without cell wall. The cells were cultured under three different conditions, with iron, without iron and without nitrogen.
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Project description:The goals of this study are to compare transcriptome profiling (RNA-seq) on iron of hepatocytes and stellate cells. Methods: mRNA profiles of wild-type (WT) NCD hepatocytes treated with or without DFO (100 uM) (n=6) and WT chow diet stellate cells treated with or without iron were generated by deep sequencing,
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Project description:Endophytic fungi are fungi that live inside the roots of plants. They can promote plant growth through a variety of direct and indirect mechanisms. Direct mechanisms include the production of phytohormones, such as auxin and gibberellins, which can stimulate plant growth. Endophytic fungi can also fix nitrogen, solubilize phosphate, and produce siderophores, which are compounds that chelate iron and make it available to plants. In addition, some endophytic fungi produce antimicrobial metabolites that can protect plants from pests and pathogens. Indirect mechanisms include the induction of systemic resistance, which is a plant's ability to defend itself against pests and pathogens. Endophytic fungi can also help plants to tolerate abiotic stresses, such as drought, salinity, and heavy metals. In this study, we used a proteomic approach to identify the proteins that are expressed in rice plants after they are treated with endophytic fungi. We found that the treatment with endophytic fungi resulted in the expression of a number of proteins involved in plant growth, stress response, and defense. These results suggest that endophytic fungi can promote plant growth and improve plant resilience to stress.
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Project description:Regulation of iron acquisition genes is critical for microbial survival under both iron-limiting conditions (to acquire essential iron) and iron-replete conditions (to limit iron toxicity). In fungi, iron acquisition genes are repressed under iron-replete conditions by a conserved GATA transcriptional regulator. Here we investigate the role of this transcription factor, Sre1, in the cellular responses of the fungal pathogen Histoplasma capsulatum to iron. We showed that cells in which SRE1 levels were diminished by RNA interference were unable to repress siderophore biosynthesis and utilization genes in the presence of abundant iron, and thus produced siderophores even under iron-replete conditions. Mutation of a GATA-containing consensus site found in the promoters of these genes also resulted in inappropriate gene expression under iron-replete conditions. Microarray analysis comparing control and SRE1-depleted strains under conditions of iron limitation or abundance revealed both iron-responsive genes and Sre1-dependent genes, which comprised distinct but overlapping sets. Iron-responsive genes included putative oxidoreductases, metabolic and mitochondrial enzymes, superoxide dismutase, and nitrosative-stress response genes; Sre1-dependent genes were of diverse function. Genes regulated by iron levels and Sre1 included all of the siderophore biosynthetic genes, a gene involved in reductive iron acquisition, an iron-responsive transcription factor, and two catalases. Based on transcriptional profiling and phenotypic analyses, we conclude that Sre1 plays a critical role in the regulation of both traditional iron-responsive genes and iron-independent pathways such as regulation of cell morphology. These data highlight the evolving realization that the effect of Sre1 orthologs on fungal biology extends beyond the iron regulon. For microarray studies, initial cultures of HcLH120 (Control RNAi-1) or 123 (SRE1 RNAi-2) yeast cells were grown in 5 mL HMM, and then passaged 1:25 into 100 mL HMM. After 2 days of growth, the cultures were pelleted, washed in 100 mL of PBS, resuspended in 100 mL of mRPMI pH 6.5 and diluted to an OD600~2 in 1 L of mRPMI. After 24 hours of growth, 200 mL of culture was harvested for each of the three zero time points. Then the cultures were split into 2 X 400 mL, and 10 uM FeSO4 (final concentration) was added to one set of cultures. At each time point (.5, 1, 4, or 8 hours), 100 mL of culture was harvested for RNA extraction.
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Project description:Two Near Isogenic soybean (Glycine max) lines were grown in hydroponic conditions with either 50uM ferric nitrate or 100uM ferric nitrate. After 10 days, half the plants were harvested (total root tissue). At 12 days after planting, iron was added to plants grown in low iron conditions bringing them up to sufficient iron growth conditions. Root tissue was harvested for the remaining plants at 14 days after planting. Gene expression analysis from root tissue of two Near Isogenic Lines (NILs), Clark (PI548553) and IsoClark (PI547430), grown in iron stress or iron stress recovered conditions.
2010-09-06 | GSE22227 | GEO
Project description:The ferric uptake regulator (Fur) plays a critical role in the transcriptional regulation of iron metabolism in many bacteria. However, the full regulatory potential of Fur beyond iron metabolism remains undefined. Here, we comprehensively reconstructed the Fur transcriptional regulatory network in Escherichia coli K-12 MG1655 in response to iron availability using genome-wide measurements (ChIP-exo and RNA-seq). Polyomic data analysis revealed that a total of 81 genes in 42 transcription units (TUs) are directly regulated by three different modes of Fur regulation, including apo- and holo-Fur activation as well as holo-Fur repression. We showed that Fur connects iron transport and utilization enzymes with negative-feedback loop pairs for iron homeostasis. In addition, direct involvement of Fur in the regulation of DNA synthesis, energy metabolism, and biofilm development was found. These results indicate that Fur exhibits a comprehensive regulatory role affecting many fundamental cellular processes linked to iron metabolism in order to coordinate E. coli responses to the availability of iron. [ChIP-exo]: A total of twelve samples were analyzed. WT and Fur-8-myc tagged cells were cultured in the presense and absence of iron with biological duplicates. To analyze static RNAP binding, rifampicin was also added to the media with biological duplicates. DPD = iron chelator.
2014-09-09 | E-GEOD-54899 | biostudies-arrayexpress
Project description:Siderophores are specialized molecules with different chemical structures, produced by bacteria and fungi to scavenge iron from the environment, a crucial nutrient for their growth and metabolism. These iron-chelating compounds enable bacteria to overcome iron limitation, a key factor in microbial survival and pathogenesis. Catecholate-type siderophores are primarily produced by bacteria, while hydroxamates are predominantly produced by fungi. The capacity of nine hydroxamate-type siderophores produced by fungi to serve as siderophores for iron acquisition by Pseudomonas aeruginosa, a human pathogen, has been investigated. Growth assays under iron limitation and 55Fe incorporation tests clearly highlighted that all nine siderophores promoted bacterial growth and facilitated iron transport. Additionally, the study aimed to identify the TonB-dependent transporters (TBDTs) responsible for iron import mediated by the tested siderophores. Mutant strains lacking genes encoding TBDTs were employed, revealing that iron is imported into P. aeruginosa cells solely by FpvB for the siderophores coprogen, triacetylfusarinine C, fusigen, ferrirhodin, and ferrirubin siderophores. Iron complexed by desferioxamine G is imported by two TBDTs, FpvB and FoxA. Ferricrocin-Fe and ferrichrycin-Fe complexes are imported by FpvB and FiuA. Lastly, rhodotorulic acid-Fe complexes are imported by FpvB, FiuA, and another unidentified TBDT. In conclusion, the data illustrate the effectiveness of hydroxamate-type siderophores in transporting iron into P. aeruginosa cells and provide insights into the intricate molecular mechanisms involved in iron acquisition, which have implications for understanding bacterial pathogenesis and developing potential therapeutic strategies.
2024-08-26 | PXD052483 | Pride
Project description:Caco-2 cells (a human gastrointestinal epithelial cell line) grown to form confluent cell layers on permeable membrane supports were treated with variously (A) iron depleted medium, (B) iron depleted medium with 10 uM ferric nitrilotiracetate added to the apical medium or (C) iron depleted medium with 30 uM human holo-transferrin added to the basolateral medium for 7 days (days 14-21 after cell seeding). RNA was extract from the cells on day 21 for transcription profiling by array.
2015-04-27 | E-MTAB-3442 | biostudies-arrayexpress
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2023-01-17 | GSE221057 | GEO