Rhodospirillum rubrum whole transcriptome data comparison between anaerobic versus aerobic growth conditions
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ABSTRACT:
ORGANISM(S): Rhodospirillum rubrum
PROVIDER: GSE130635 | GEO | 2019/05/03
REPOSITORIES: GEO
Similar Datasets
Project description:Rhodospirillum rubrum whole transcriptome data comparison between anaerobic versus aerobic growth conditions
| PRJNA540842 | ENA
Project description:In the context of the Micro-Ecological Life Support System Alternative (MELiSSA) project, the quorum sensing system (QS) of R. rubrum S1H has been shown to rely on acyl homoserine lactones (AHLs) as communication signals. In addition, previous studies in our lab have suggested that pigment content and photosynthetic membrane production could be under the control of QS. In the present study, the transcriptomic and proteomic profiles of a QS-deficient mutant (R. rubrum strain M68) that does not produce AHLs as the WT strain (R. rubrum S1H) were compared when cultivated in light anaerobic conditions using acetate as carbon source. Transcriptomic and proteomic approaches revealed that 330 genes and 217 proteins were differentially expressed in M68 compared to S1H, indicating that several operons were QS-regulated i.e. flagellar assembly, chemotaxis, photosynthesis, electron transport, stress proteins. These results showed the importance of a functional QS system in R. rubrum.
2019-02-01 | GSE76666 | GEO
Project description:Investigation of whole genome gene expression level changes in Thermoplasma acidophilum cultured under aerobic and anaerobic conditions. The analysis are further described in Na Sun, Cuiping Pan, Stephan Nickell, Matthias Mann, Wolfgang Baumeister, and István Nagy, Quantitative proteome and transcriptome analysis of the archaeon Thermoplasma acidophilum cultured under aerobic and anaerobic conditions (submitted).
2011-09-27 | GSE21956 | GEO
Project description:In the present study, the susceptibility of the purple pigmented photosynthetic alphaproteobacterium Rhodospirillum rubrum S1H to gamma irradiation was investigated and its molecular response was characterised by means of gene expression analysis. R. rubrum S1H appears to be about 4 times more sensitive than the model strain Escherichia coli MG1655 to cobalt-60 gamma irradiation. Whole genome response of R. rubrum to 25 Gy revealed the common expression of SOS response related genes in both rich and minimal media. Quantitative expression of the lexA gene was followed after various recovery time following gamma irradiation and showed differential gene expression pattern between minimal and rich medium. This work paves the way for forthcoming molecular studies on the effect of ionizing radiation on R. rubrum S1H and the other MELiSSA strains. Keywords: Rhodospirillum rubrum; ionizing radiation tolerance; microarray; quantitative PCR.
2015-11-10 | GSE23799 | GEO
Project description:Transcript abundance profiles were examined over the first 24 hours of germination in rice grown under anaerobic conditions. Transcript abundance profiles were also examined for rice grown under aerobic conditions for 24 h and then switched to anaerobic conditions and vice versa.
2009-07-24 | E-MEXP-2267 | biostudies-arrayexpress
Project description:In the present study, the susceptibility of the purple pigmented photosynthetic alphaproteobacterium Rhodospirillum rubrum S1H to gamma irradiation was investigated and its molecular response was characterised by means of gene expression analysis. R. rubrum S1H appears to be about 4 times more sensitive than the model strain Escherichia coli MG1655 to cobalt-60 gamma irradiation. Whole genome response of R. rubrum to 25 Gy revealed the common expression of SOS response related genes in both rich and minimal media. Quantitative expression of the lexA gene was followed after various recovery time following gamma irradiation and showed differential gene expression pattern between minimal and rich medium. This work paves the way for forthcoming molecular studies on the effect of ionizing radiation on R. rubrum S1H and the other MELiSSA strains. Keywords: Rhodospirillum rubrum; ionizing radiation tolerance; microarray; quantitative PCR. Two-condition experiments. Comparing samples after exposure to gamma (Co-60) irradiation with a non-irradiated sample. At least biological duplicates. Each array contains 3 technical replicates.
2015-11-10 | E-GEOD-23799 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE14239: MESSAGE 2 space experiment with Rhodospirillum rubrum S1H GSE14241: BASE-A space experiment with Rhodospirillum rubrum S1H Refer to individual Series
2010-05-16 | E-GEOD-14265 | biostudies-arrayexpress
Project description:The changes in protein composition of E. coli were studied in a global proteomic approach for aerobic growth without or with fumarate as carbon source (glycerol + O2, fumarate + O2, respectively) and anaerobic growth without or with fumarate as carbon source (glycerol + DMSO, glycerol + DMSO + fumarate, respectively). The experiments should unravel the changes in response to fumarate under aerobic (i) and anaerobic (ii) conditions, and more generally (iii) the fumarate proteome under aerobic versus anaerobic conditions. Fumarate was used as the C4DC due to its capability to support aerobic and anaerobic growth, and glycerol was used as the alternative carbon source that exerts no or only weak carbon catabolite repression.
2019-11-20 | PXD011760 | Pride
Project description:We found many binding sites for FNR under glucose fermentative anaerobic growth conditions. Also, many binding sites were identified for σ70 under both aerobic and anaerobic growthin conditions. Descirbed in the manuscript "Genome-scale Analysis of E. coli FNR Reveals the Complexity of Bacterial Regulon Structure"
2013-06-20 | GSE41187 | GEO
Project description:The Lactobacillus buchneri CD034 strain, known to improve the ensiling process of green fodder and the quality of the silage itself was transcriptionally analyzed by sequencing of transcriptomes isolated under anaerobic vs. aerobic conditions. L. buchneri CD034 was first cultivated under anaerobic conditions and then shifted to aerobic conditions by aeration with 21% oxygen. Cultivations already showed that oxygen was consumed by L. buchneri CD034 after aeration of the culture while growth of L. buchneri CD034 was still observed. RNA sequencing data revealed that irrespective of the oxygen status of the culture, the most abundantly transcribed genes are required for basic cell functions such as protein biosynthesis, energy metabolism and lactic acid fermentation. Under aerobic conditions, 283 genes were found to be transcriptionally up-regulated while 198 genes were found to be down-regulated (p-value < 0.01). Up-regulated genes i. a. play a role in oxygen consumption via oxidation of pyruvate or lactate (pox, lctO). Additionally, genes encoding proteins required for decomposition of reactive oxygen species (ROS) such as glutathione reductase or NADH peroxidase were also found to be up-regulated. Genes related to pH homeostasis and redox potential balance were found to be down-regulated under aerobic conditions. Overall, genes required for lactic acid fermentation were hardly affected by the growth conditions applied. Genes identified to be differentially transcribed depending on the aeration status of the culture are suggested to specify the favorable performance of the strain in silage formation.
2017-02-10 | GSE67802 | GEO