R. sphaeroides Δirr -Fe vs. R. sphaeroides Δirr +Fe under microaerobic conditions
Ontology highlight
ABSTRACT:
ORGANISM(S): Rhodobacter sphaeroides 2.4.1
SUBMITTER: Verena Peuser
PROVIDER: E-GEOD-33533 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE33533: R. sphaeroides Δirr -Fe vs. R. sphaeroides Δirr +Fe under microaerobic conditions GSE33534: R. sphaeroides Δirr vs. R. sphaeroides 2.4.1 under microaerobic conditions Refer to individual Series
2011-11-09 | E-GEOD-33535 | biostudies-arrayexpress
Project description:Transcriptional profiling of R. sphaeroides Δirr under iron limitation (-Fe) compared to control R. sphaeroides Δirr under normal growth conditions (+Fe).
2011-11-09 | GSE33533 | GEO
Project description:High intracellular levels of unbound iron can contribute to the production of reactive oxygen species (ROS) in the Fenton reaction, while depletion of iron limits the availability of iron containing proteins, some of which have important functions in the oxidative stress defense. Vice versa increased ROS levels lead to damage of proteins with iron sulfur centers. Thus organisms have to coordinate and balance their responses to oxidative stress and iron availability. Our knowledge on the molecular mechanisms underlying the coregulation of these responses is still limited. To discriminate between a direct cellular response to iron limitation and indirect responses, which are the consequence of increased levels of ROS, we compared the response of the alpha proteobacterium Rhodobacter sphaeroides to iron limitation in presence or absence of oxygen. While some genes respond to iron limitation exclusively or much stronger in presence of oxygen, other genes show much stronger response in anaerobic conditions. Remarkably few genes show even opposite response to iron depletion in presence or absence of iron. RNA samples collected from anaerobically grown cultures in presence or absence of iron were analyzed by two-color microarrays
2013-05-23 | E-GEOD-47182 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in a Nitrosomonas europaea (ATCC 19718) wildtype and pFur::Kan mutant [kanamycin resistance cassette insertion in the promoter region of the fur gene (NE0616)] strains grown in Fe-replete and Fe-limited media. The Nitrosomonas europaea (ATCC 19718) wiltype cells grown in Fe-limited media were compared to cells grown in Fe-replete media to gain a better understanding of the metabolic changes occurring in response to iron stress. The Nitrosomonas europaea (ATCC 19718) pFur::Kan mutant strain grown in Fe-replete & Fe-limited media were compared to wildtype cells grown in Fe=replete & Fe-limited media to gain a better understanding of the role Fur (NE0616) plays in iron homeostasis control. A 4-plex 3 chip study using total RNA recovered from three separate wild-type cultures each of N. europaea grown in Fe-replete media and Fe-limited media and three seperate cultures each of N. europaea pFur::Kan mutant strain grown in Fe-replete and Fe-limited media. Each chip measures the expression level of 2368 genes from Nitrosomonas europaea (ATCC19718) with 4 X 72,000 60-mer 14 probe pairs per gene, with two-fold technical redundancy.
2010-06-20 | E-GEOD-18709 | biostudies-arrayexpress
Project description:High intracellular levels of unbound iron can contribute to the production of reactive oxygen species (ROS) in the Fenton reaction, while depletion of iron limits the availability of iron containing proteins, some of which have important functions in the oxidative stress defense. Vice versa increased ROS levels lead to damage of proteins with iron sulfur centers. Thus organisms have to coordinate and balance their responses to oxidative stress and iron availability. Our knowledge on the molecular mechanisms underlying the coregulation of these responses is still limited. To discriminate between a direct cellular response to iron limitation and indirect responses, which are the consequence of increased levels of ROS, we compared the response of the alpha proteobacterium Rhodobacter sphaeroides to iron limitation in presence or absence of oxygen. While some genes respond to iron limitation exclusively or much stronger in presence of oxygen, other genes show much stronger response in anaerobic conditions. Remarkably few genes show even opposite response to iron depletion in presence or absence of iron. RNA samples collected from anaerobically or microaerobically grown cultures in presence or absence of iron were analyzed by RNA_sequencing
2013-05-30 | E-GEOD-47449 | biostudies-arrayexpress
Project description:Diatoms, which are responsible for up to 40% of the 45 to 50 billion metric tons of organic carbon production each year in the sea, are particularly sensitive to Fe stress. Here we describe the transcriptional response of the pennate diatom Phaeodactylum tricornutum to Fe limitation using a partial genome microarray based on EST and genome sequence data. Processes carried out by components rich in Fe, such as photosynthesis, mitochondrial electron transport and nitrate assimilation are down-regulated to cope with the reduced cellular iron quota. This retrenchment is compensated by nitrogen (N) and carbon (C) reallocation from protein and storage carbohydrate degradation, adaptations to chlorophyll biosynthesis and pigment metabolism, removal of excess electron s by mitochondrial alternative oxidase (AOX), augmented Fe-independent oxidative stress responses, and sensitized iron capture mechanisms. Keywords: Marine phytoplankton, pinnate diatom Wild-type Phaeodactylum tricornutum was grown under Fe replete (10,000 nM) and Fe limiting (5nM) conditions. Partial genome gene expression analysis of iron-inducible genes was conducted using a two-color competitive hybridization microarray.
2010-05-27 | E-GEOD-8675 | biostudies-arrayexpress
Project description:Iron-sulphur (Fe-S) clusters are ensembles of iron and sulphide centres. They are found in all life forms and are important components of many enzymes involved in diverse cellular processes, including respiration, DNA synthesis or gene regulation. However, the increase in oxygen after the emergence of oxygenic photosynthesis created a threat to FeM-bM-^@M-^SS proteins and, consequently, to the organisms relying on them. Therefore, bacteria have evolved mechanisms to maintain a precise intracellular iron concentration. A major role of IscR in R. sphaeroides iron dependent regulation was suggested in a bioinformatic study , which predicted a binding site in the upstream regions of several iron uptake genes. Most known IscR proteins have Fe-S clusters featuring (Cys)3(His)1 ligation. However, IscR proteins from Rhodobacteraceae harbour only one Cys residue and it was considered unlikely that they can ligate an Fe-S cluster. In this study, the role of R. sphaeroides IscR as transcriptional regulator and sensor of the Fe-S cluster status of the cell was analysed. The results provide evidence that R. sphaeroides IscR functions as transcriptional repressor of genes involved in iron metabolism by binding to the predicted DNA binding motif. Furthermore, IscR possesses a unique Fe-S cluster ligation scheme with only a single cysteine involved. RNA samples collected from a control strain (wild type 2.4.1) and of the iscR deletion strain (2.4.1M-bM-^HM-^FiscR) were analyzed by two-color microarrays
2015-02-03 | E-GEOD-65537 | biostudies-arrayexpress
Project description:Iron-sulfur (Fe-S) clusters are ubiquitous metallocofactors involved in redox chemistry, radical generation, and gene regulation. Common methods to monitor Fe-S clusters include spectroscopic analysis of purified proteins, and auto-radiographic visualization of radiolabeled iron distribution in proteomes. Here, we report a chemoproteomic strategy that monitors changes in the reactivity of Fe-S cysteine ligands to inform on Fe-S cluster occupancy. We highlight the utility of this platform in E. coli by: (1) demonstrating global disruptions in Fe-S incorporation in cells cultured under iron-depleted conditions; (2) determining Fe-S client proteins reliant on three scaffold/carrier proteins within the Isc Fe-S biogenesis pathway; and, (3) identifying two previously unannotated Fe-S proteins, TrhP and DppD. In summary, the chemoproteomic strategy described herein is a powerful tool that reports on Fe-S cluster incorporation directly within a native proteome, and enables the interrogation of Fe-S biogenesis pathways, and the identification of previously uncharacterized Fe-S proteins.
2024-05-22 | PXD026488 | Pride
Project description:We used RNA-Seq to compare the transcriptomes of Fe-replete vs. Fe-deficient vs. Fe-limited Chlamydomonas wild-type cells. Our RNA-Seq data revealed 90 and 49 genes to be specifically expressed under hetero-phototrophic and phototrophic conditions, respectively. Around 30 genes represent putative Fe-deficiency targets, independent of the carbon source used. Many of these Fe-specific responses are conserved between Chlamydomonas and land plants. We identified several transporters (NRAMP4, a CCC1-like proteins and a ferroportin homologue) all of them most likely being involved in intracellular Fe redistribution. RNA-seq of Chlamydomonas Fe-deficient and limited cells indicated that about 40% of differentially expressed genes represent proteins of unknown functions. Whereas Fe-deficiency gave us insides into putative Fe-specific responses, Fe-limitation revealed responses related to increased oxidative stress. Quantitative proteomics on the soluble Chlamydomonas extracts indicated a fair correlation between changes we detected at mRNA levels compared to changes in protein levels in Fe-deficient and Fe-limited Chlamydomonas. We found that Fe-deficient and Fe-limited cells have increased ascorbate levels, a major antioxidant molecule in plants. Ascorbate levels appear to be elevated by de novo synthesis via the L-Galactose pathway and recycling by monodehydroascorbate reductase. Fe-limited cells showed increased transcript and protein levels of enzymatic antioxidant components of the ascorbate-glutathione scavenging system (MSD3, MDAR1 or GSH1). Fe-limited cells showed the increase of several proteases indicative of elevated proteolitic activity under these severe nutrient limitation conditions. Sampling of Chlamydomonas CC-1021 (2137) cells cultivated photoheterotrophically (TAP) or phototrophically (minimal) under Fe-replete (20mM), Fe-deficient (1 mM) and Fe-limited (0.25 mM) conditions.
2012-06-18 | E-GEOD-35305 | biostudies-arrayexpress
Project description:Transcription profiling of citrus rootstock Poncirus trifoliata (L.) Raf. Keywords: Abiotic stress (Iron chlorosis) Total RNA from four replicates for each sample category (Poncirus trifoliata (L.) Raf watered for 60 days with 18 uM Fe-EDDHA or without Fe-EDDHA) were generated and compared.
2010-05-19 | E-GEOD-17255 | biostudies-arrayexpress