Low-oxygen stress responses of Brassicaceae Species
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana Rorippa islandica Arabis stelleri Eutrema salsugineum
PROVIDER: GSE129468 | GEO | 2019/05/15
REPOSITORIES: GEO
Similar Datasets
Project description:Low-oxygen stress responses of Brassicaceae Species
| PRJNA531462 | ENA
Project description:We have investigated the response of the cyanobacterium Synechocystis sp. PCC 6803 during growth at very low O2 concentration (bubbled with 99.9% N2/0.1% CO2). Significant transcriptional changes upon low O2 incubation included up-regulation of a cluster of genes that contained psbA1 and an operon that includes a gene encoding the two-component regulatory histidine kinase, Hik31. This regulatory cluster is of particular interest, since there are virtually identical copies on both the chromosome and on plasmid pSYSX. We used a knockout mutant lacking the chromosomal copy of hik31 and studied differential transcription during the aerobic- low O2 transition in this ΔHik31 strain and the wild type. We observed two distinct responses to this transition, one Hik31 dependent, the other Hik31 independent. The Hik31 independent responses included the psbA1 induction and genes involved in chlorophyll biosynthesis. In addition, there were changes in a number of genes that may be in involved in assembling or stabilizing Photosystem II (PSII), and the hox operon and the LexA-like protein (Sll1626) were up-regulated during low O2 growth. This family of responses mostly focused on PSII and overall redox control. There was also a large set of genes that responded differently in the absence of the chromosomal Hik31. In the vast majority of these cases, Hik31 functioned as a repressor and transcription was enhanced when Hik31 was deleted. Genes in this category encoded both core and peripheral proteins for Photosystem I and PS II, the main phycobilisome proteins, chaperones, the ATP synthase cluster and virtually all of the ribosomal proteins. These findings, coupled with the fact that ΔHik31 grew better than the wild-type under low O2 conditions, suggested that Hik31 helped to regulate growth and overall cellular homeostasis. We detected changes in the transcription of other regulatory genes that may compensate for the loss of Hik31. We conclude that Hik31 regulates an important series of genes that relate to energy production and growth and that helps to determine how Synechocystis responds to changes in O2 conditions.
2010-10-28 | GSE24882 | GEO
Project description:Carbon fixation plays a central role in determining cellular redox poise, increasingly understood to be a key parameter in cyanobacterial physiology. In the cyanobacterium Prochlorococcus--—the most abundant phototroph in the oligotrophic oceans--—the carbon-concentrating mechanism (CCM) is reduced to the bare essentials. Given the ability of Prochlorococcus populations to grow under a wide range of oxygen concentrations in the ocean, we wondered how carbon and oxygen physiology intersect in this minimal phototroph. We monitored genome-wide transcription in cells shocked with acute limitation of CO2, O2, or both. O2 limitation produced much smaller transcriptional changes than the broad suppression seen under CO2 limitation and CO2/O2 co-limitation. Strikingly, the transcriptional responses evoked by both CO2 limitation conditions were initially similar to that previously seen in high light stress, but at later timepoints we observed O2-dependent recovery of photosynthesis-related transcripts. These results suggest that oxygen plays a protective role in Prochlorococcus when carbon fixation is not a sufficient sink for light energy. Two biological replicates of timecourses under four conditions: medium bubbled with air (control) or three experimental gases (low CO2; low O2; or low CO2 and low O2)
2015-04-15 | E-GEOD-65684 | biostudies-arrayexpress
Project description:Low oxygen conditions are not only common to natural environments but also occur during tissue invasive growth in the human host. Only few cellular factors have been identified up to now that allow the fungus to efficiently adapt its energy metabolism to the lack of O2. In the present study, we cultivated A. fumigatus in an O2-controlled fermenter and analysed its minute-scale responses to O2 limitation. Transcriptome sequencing revealed a group of genes underlying a rapid and highly dynamic regulation. As an initial experimental setup, A. fumigatus was cultivated in an O2-controlled fermenter, which allowed minute-scale variations in O2-fluxes largely independent of other secondary effects. Cultures were initially grown at saturated O2 concentrations (100% saturation M-bM-^IM-^H 260 M-BM-5mol l-1) and rapidly shifted to hypoxic growth conditions at an initial O2 saturation of 5% (M-bM-^IM-^H 13 M-BM-5mol l-1). Dynamics of low and high O2 responses of A. fumigatus cultivated in an O2-controlled fermenter
2014-07-25 | E-GEOD-55943 | biostudies-arrayexpress
Project description:Complete submergence represses photosynthesis and aerobic respiration causing rapid mortality in most terrestrial plants, but some species have evolved traits allowing them to survive prolonged flooding. Here, we studied the response to submergence of two species and their F1 hybrid in the genus Rorippa, which is related to the model Arabidopsis. We showed that these species have high tolerance to complete, deep submergence, but R. sylvestris survived longer than R. amphibia and the F1 hybrid. While the former restricted growth upon submergence, the latter two genotypes showed induced stem and petiole elongation and had higher aerenchyma contents, indicative of a low oxygen escape strategy. Arabidopsis GeneChip microarrays were used for whole-genome transcript profiling of roots of young plants exposed to air or a 24-h submergence treatment, using a probe mask based on hybridisation of genomic DNA of both species to the arrays. The induction by the submergence treatment of genes involved in glycolysis and fermentation and repression of many energy consuming pathways was similar to the response to low oxygen of Arabidopsis and rice. Notably, sucrose synthases, glycolysis and fermentation genes were more strongly induced in the less tolerant R. amphibia than in R. sylvestris, which might indicate faster carbohydrate consumption of the former, while some genes involved in hydrogen peroxide scavenging were strongly and specifically induced in the latter. F1 hybrids showed a generally weaker response to submergence and an additive mode of gene action, which did not change by the submergence treatment. Keywords: stress response and a comparison of genotypes
2009-12-01 | GSE13641 | GEO
Project description:Complete submergence represses photosynthesis and aerobic respiration causing rapid mortality in most terrestrial plants, but some species have evolved traits allowing them to survive prolonged flooding. Here, we studied the response to submergence of two species and their F1 hybrid in the genus Rorippa, which is related to the model Arabidopsis. We showed that these species have high tolerance to complete, deep submergence, but R. sylvestris survived longer than R. amphibia and the F1 hybrid. While the former restricted growth upon submergence, the latter two genotypes showed induced stem and petiole elongation and had higher aerenchyma contents, indicative of a low oxygen escape strategy. Arabidopsis GeneChip microarrays were used for whole-genome transcript profiling of roots of young plants exposed to air or a 24-h submergence treatment, using a probe mask based on hybridisation of genomic DNA of both species to the arrays. The induction by the submergence treatment of genes involved in glycolysis and fermentation and repression of many energy consuming pathways was similar to the response to low oxygen of Arabidopsis and rice. Notably, sucrose synthases, glycolysis and fermentation genes were more strongly induced in the less tolerant R. amphibia than in R. sylvestris, which might indicate faster carbohydrate consumption of the former, while some genes involved in hydrogen peroxide scavenging were strongly and specifically induced in the latter. F1 hybrids showed a generally weaker response to submergence and an additive mode of gene action, which did not change by the submergence treatment. Experiment Overall Design: We used replicated clones of Rorippa amphibia, Rorippa sylvestris and their F1 hybrid. Plants were grown on sand in pots for three weeks, completely submerged in rain water for 24 h, or kept in air as a control. Three biological controls were collected per genotype, each consisting of a pool of three individuals. Roots were separated from the shoots, quickly rinsed and immediately frozen and used for RNA extraction and hybridization to Arabidopsis Ath1 GeneChips. Genomic DNA of Rorippa amphibia and Rorippa sylvestris was also hybridized to the GeneChips in order to filter out badly performing probes due to sequence divergences from Arabidopsis.
2009-12-04 | E-GEOD-13641 | biostudies-arrayexpress
Project description:Spalax, an underground fossoral rodant is exposed to chronic hypoxic environments. Measurements of Spalax burrows indicated 7% oxygen and up to 15% CO2. In the laboratory Spalax can survive 3% oxygen up to 14 hours as compared to rats that survive less than 4 hours at these oxygen levels. we have proposed Spalax as a model species for the investigation of hypoxia tolerance. this research has implications for many biomedical phenomena involving ischemic disease, notably heart disease and cancer. In this work we have subjected Spalax to 3%, 6% and 10% O2 levels for varying lengths of time and have profiled expression patterns and differential expression in muscle and brain, two tissues with high energy requirements. For comparison with a terrestrial mammal we have profiled RNA from rats exposed to either 21% or 6% oxygen. Spalax animals, captured in the field and held in captivity were subjected to 3 different levels of hypoxia. (1) 3% O2 for 6 hrs (2) 6% O2 for 6 hrs (3) 10% O2 for 44hrs (4) 21% O2 (normoxia). For comparison, Rats were subjected to 21% and 6% oxygen. Animals were euthanized according to approved protocols and RNA extracted from muscle and brain. Samples were labeled using the Agilent low input 2-color labeling kit and hybridized to a custom Spalax microarray (8x15K format). Results were normalized and analyzed using Limma from the R bioconductor package. Differentially expressed gens were identified as well as over-represented gene onotolgy defined functions.
2012-12-31 | E-GEOD-37619 | biostudies-arrayexpress
Project description:Low oxygen conditions are not only common to natural environments but also occur during tissue invasive growth in the human host. Only few cellular factors have been identified up to now that allow the fungus to efficiently adapt its energy metabolism to the lack of O2. In the present study, we cultivated A. fumigatus in an O2-controlled fermenter and analysed its minute-scale responses to O2 limitation. Transcriptome sequencing revealed a group of genes underlying a rapid and highly dynamic regulation. As an initial experimental setup, A. fumigatus was cultivated in an O2-controlled fermenter, which allowed minute-scale variations in O2-fluxes largely independent of other secondary effects. Cultures were initially grown at saturated O2 concentrations (100% saturation ≈ 260 µmol l-1) and rapidly shifted to hypoxic growth conditions at an initial O2 saturation of 5% (≈ 13 µmol l-1).
2014-07-25 | GSE55943 | GEO
Project description:Endothelial cells, and many other types of cells too, physiologically reside in low O2 environments (~ 2-13% O2 or 15-60 mmHg pO2; [PCN]) relevantly to atmospheric O2 (~ 21% or 160 mmHg pO2 at sea level) in vivo. Such PCN is critical for endothelial functions. The majority of our current knowledge regarding the cellular and signaling mechanisms governing endothelial functions, however, is built on endothelial models established under atmospheric O2 (~21% O2). Herein, we comapred the transcriptional profiles between HUVE and HUAE cells cultured and expanded under PCN (3% oxygen) and standard culture normoxia (21% O2).
2013-08-30 | GSE49958 | GEO