Expression of Frankia inefficax EuI1c under selenite stress
Ontology highlight
ABSTRACT:
ORGANISM(S): Pseudofrankia inefficax
PROVIDER: GSE176380 | GEO | 2024/12/31
REPOSITORIES: GEO
Similar Datasets
Project description:Purpose: To compare RNASeq data of Frankia inefficax EuI1c in normal growth conditions to biphenyl-stressed Frankia inefficax EuI1c. Frankia cultures were grown for 3 days under one of three conditions before harvesting: 1.) 1 mM biphenyl stress with glucose as an alternative carbon and energy source, 2.) 1mM biphenyl with no alternative carbon or energy source, or 3.) media with glucose as a carbon and energy source (Control). RNA-seq analysis provided insight into how the the bacteria responds to biphenyl stress and exhibits biphenyl tolerance.
2024-12-31 | GSE178353 | GEO
Project description:Purpose: To compare RNASeq data of Frankia CcI3 in plants under salt stress. Casuarina glauca root nodules infected with Frankia CcI3 were exposed to either no salt or 100 mM NaCl for 21 days. RNA-seq analysis provided insight into how the sybiont responds to salt stress.
2019-12-02 | GSE60938 | GEO
Project description:Purpose: To compare RNASeq data of Frankia strains (EAN1pec, EuIC and EUN1f) under nitrogen stress. Frankia cultures were grown for 2 days under nitrogen replete (+NH4) or nitrogen- deficient (N2) conditions. RNA-seq analysis provided insight into how the the bacteria responds to nitrogen stress.
2018-04-18 | GSE64517 | GEO
Project description:Purpose:to identify the response of Frankia sp.strain CcI6 to salt and osmotic stress. Frankia sp.strain CcI6 was exposed to salt and osmotic stress for seven days. RNAseq analysis was carried out to ge an insight into the response of the bacterium under salt and osmotic stress conditons
2017-09-22 | GSE95217 | GEO
Project description:Background: Frankia sp. strains are actinobacteria that form N2-fixing root nodules on angiosperms. Several reference genome sequences are available enabling transcriptome studies in Frankia sp. Genomes from Frankia sp. strains differ markedly in size, a consequence proposed to be associated with a high number of indigenous transposases, more than 200 of which are found in Frankia sp. strain CcI3 used in this study. Because Frankia exhibits a high degree of cell heterogeneity as a consequence of its mycelial growth pattern, its transcriptome is likely to be quite sensitive to culture age. This study focuses on the behavior of the Frankia sp. strain CcI3 transcriptome as a function of nitrogen source and culture age. Results: To study global transcription in Frankia sp. CcI3 grown under different conditions, complete transcriptomes were determined using high throughput RNA deep sequencing. Samples varied by time (five days vs. three days) and by culture conditions (NH4+ added vs. N2 fixing). Assembly of millions of reads revealed more diversity of gene expression between five-day and three-day old cultures than between three day old cultures differing in nitrogen sources. Heat map analysis organized genes into groups that were expressed or repressed under the various conditions compared to median expression values. Twenty-one SNPs common to all three transcriptome samples were detected indicating culture heterogeneity in this slow-growing organism. Significantly higher expression of transposase ORFs was found in the five-day and N2-fixing cultures, suggesting that N starvation and culture aging provide conditions for on-going genome modification. Transposases have previously been proposed to participate in the creating the large number of gene duplication or deletion in host strains. Subsequent RT-qPCR experiments confirmed predicted elevated transposase expression levels indicated by the mRNA-seq data. Conclusions: The overall pattern of gene expression in aging cultures of CcI3 suggests significant cell heterogeneity even during normal growth on ammonia. The detection of abundant transcription of nif (nitrogen fixation) genes likely reflects the presence of anaerobic, N-depleted microsites in the growing mycelium of the culture, and the presence of significantly elevated transposase transcription during starvation indicates the continuing evolution of the Frankia sp. strain CcI3 genome, even in culture, especially under stressed conditions. These studies also sound a cautionary note when comparing the transcriptomes of Frankia grown in root nodules, where cell heterogeneity would be expected to be quite high.
2011-07-15 | GSE30680 | GEO
Project description:Background: Frankia sp. strains are actinobacteria that form N2-fixing root nodules on angiosperms. Several reference genome sequences are available enabling transcriptome studies in Frankia sp. Genomes from Frankia sp. strains differ markedly in size, a consequence proposed to be associated with a high number of indigenous transposases, more than 200 of which are found in Frankia sp. strain CcI3 used in this study. Because Frankia exhibits a high degree of cell heterogeneity as a consequence of its mycelial growth pattern, its transcriptome is likely to be quite sensitive to culture age. This study focuses on the behavior of the Frankia sp. strain CcI3 transcriptome as a function of nitrogen source and culture age. Results: To study global transcription in Frankia sp. CcI3 grown under different conditions, complete transcriptomes were determined using high throughput RNA deep sequencing. Samples varied by time (five days vs. three days) and by culture conditions (NH4+ added vs. N2 fixing). Assembly of millions of reads revealed more diversity of gene expression between five-day and three-day old cultures than between three day old cultures differing in nitrogen sources. Heat map analysis organized genes into groups that were expressed or repressed under the various conditions compared to median expression values. Twenty-one SNPs common to all three transcriptome samples were detected indicating culture heterogeneity in this slow-growing organism. Significantly higher expression of transposase ORFs was found in the five-day and N2-fixing cultures, suggesting that N starvation and culture aging provide conditions for on-going genome modification. Transposases have previously been proposed to participate in the creating the large number of gene duplication or deletion in host strains. Subsequent RT-qPCR experiments confirmed predicted elevated transposase expression levels indicated by the mRNA-seq data. Conclusions: The overall pattern of gene expression in aging cultures of CcI3 suggests significant cell heterogeneity even during normal growth on ammonia. The detection of abundant transcription of nif (nitrogen fixation) genes likely reflects the presence of anaerobic, N-depleted microsites in the growing mycelium of the culture, and the presence of significantly elevated transposase transcription during starvation indicates the continuing evolution of the Frankia sp. strain CcI3 genome, even in culture, especially under stressed conditions. These studies also sound a cautionary note when comparing the transcriptomes of Frankia grown in root nodules, where cell heterogeneity would be expected to be quite high. Detection of gene expression variance among Frankia HfpCci3 (Cci3) cells grown in ammonium chloride for three days, five days and HfpCci3 cells grown in nitrogen fixing conditions for three days using mRNA-seq
2011-07-15 | E-GEOD-30680 | biostudies-arrayexpress
Project description:Expression data of Frankia CcI3 in plant root nodules under salt stress
| PRJNA259867 | ENA
Project description:The yeast S. cerevisiae does not require selenium for growth, so it is an excellent model to investigate the toxicity of this element without interference from its requirement as growth factor as occurs in animal cells. Exposure to selenite interferes with the yeast iron metabolism. Aft2 is a transcription factor related (with Aft1) to maintenance of iron homeostasis. We have found that aft2 cells are highly sensitive to selenite (a common environmental source for selenium). In these experiments we investigate the transcriptional response to a sub-lethal dose of selenite in wild type and aft2 cells. Our results show that the aft2 mutation strongly potentiates the transcriptional response to selenite, showing induction of many genes related to the responses to oxidative stress and DNA damage. Wild type (W303-1A) background and its MML1086 derivative (Daft2) were exposed to 1 mm selenite and samples taken at time 0, 1, 3 and 5 h of selenite treatment. Two biological replicates were prepared for each time-point. Therefore, there are 8 samples per replicate (4 samples for WT and 4 samples for aft2 cells). The WT strain is used here as reference.
2015-12-31 | E-GEOD-70835 | biostudies-arrayexpress
Project description:The bacterium Pseudomonas putida KT2440 has the ability to reduce selenite forming nanoparticles of elemental selenium. This is the transcriptome of the organism when cultured in the presence of selenite.
2022-10-01 | GSE214391 | GEO
Project description:The yeast S. cerevisiae does not require selenium for growth, so it is an excellent model to investigate the toxicity of this element without interference from its requirement as growth factor as occurs in animal cells. Exposure to selenite interferes with the yeast iron metabolism. Aft2 is a transcription factor related (with Aft1) to maintenance of iron homeostasis. We have found that aft2 cells are highly sensitive to selenite (a common environmental source for selenium). In these experiments we investigate the transcriptional response to a sub-lethal dose of selenite in wild type and aft2 cells. Our results show that the aft2 mutation strongly potentiates the transcriptional response to selenite, showing induction of many genes related to the responses to oxidative stress and DNA damage.
2015-12-31 | GSE70835 | GEO