Radiotolerance of Rhodospirillum rubrum S1H
Ontology highlight
ABSTRACT:
ORGANISM(S): Rhodospirillum rubrum
SUBMITTER: Natalie Leys
PROVIDER: E-GEOD-23799 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
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:R. rubrum S1H inoculated on solid minimal media was sent to the ISS in September 2006 (BASE-A experiment). After 10 days flight, R. rubrum cultures returned back to Earth. These cultures were then subjected to both transcriptomic and proteomic analysis and compared with the corresponding ground control. Whole-genome oligonucleotide microarray and high throughput proteomics, which offer the possibility to survey respectively the global transcriptional and translational response of an organism, were used to test the effect of space flight. Moreover, in an effort to identify a specific stress response of R. rubrum to space flight, ground simulation of space ionizing radiation and space gravity were performed under identical culture setup and growth conditions encountered during the actual space journey. This study is unique in combining the results from an actual space experiment with the corresponding space ionizing radiation and modeled microgravity ground simulations, which lead to a more solid dissection of the different factors contribution acting in space flight conditions. Total RNA was extracted from R. rubrum S1H grown after 10 days in space flight or after 10 days in simulated ionizing radiation or simulated microgravity. Each microarray slide contained 3 technical repeats.
2010-05-16 | E-GEOD-14241 | biostudies-arrayexpress
Project description:Aiming at the development of a micropollutant biosensor in the frame of the Micro-Ecological Life Support System Alternative (MELiSSA), a pilot study was initiated to identify triclosan (TCS)-responsive biomarker genes in the MELiSSA carbon-mineralizing microorganism, Rhodospirillum rubrum S1H. TCS is a biocide, commonly found in human excrements and is considered an emerging pollutant in wastewater and the environment. Chronic exposure to MELiSSA-relevant concentrations (≥25 µg L-1) TCS caused a significant extension of the lag phase without affecting the growth rate. Analytical determination gave no indication of TCS biodegradation during the growth experiment and flow cytometric viability analyses revealed that TCS is only slightly toxic to R. rubrum. Through microarray analyses, the genetic mechanisms supporting the reversibility of TCS-induced inhibition were scrutinized. Hence, an extremely TCS-responsive cluster of four small adjacent genes was revealed, with up to 34-fold induction at 25 µg L-1. These four genes, for which the name micropollutant-upregulated factor (muf) was proposed; appear to be unique to R. rubrum and are shown for the first time to be involved in the response to stress. Moreover, numerous other systems that are associated with the proton-motive force were shown to be responsive to TCS, but never as highly upregulated as the muf genes. Hence, R. rubrum induced the phage shock protein operon (pspABC), numerous major facilitator efflux systems, cell envelope consolidation mechanisms, oxidative stress response, beta-oxidation, and carbonic anhydrase; while downregulating bacterial conjugation- and carboxysome synthesis genes. The muf genes and three efflux-related genes showed most potential as low-dose biomarkers. The two microarray experiments (10 and 25 µg l-1 Triclosan) were all performed in biological triplicate and containing three (in-slide) technical repeats. For all conditions, the Triclosan exposed sample (Cy5) was compared with the non-exposed solvent control (Cy3) to identify those genes that were differentially expressed upon Triclosan exposure.
2010-05-19 | E-GEOD-16189 | biostudies-arrayexpress
Project description:The present study explores the potential of compound-specific gene-upregulation profiles in the ubiquitous purple nonsulfur bacterium Rhodospirillum rubrum S1H as biomarkers for exposure to surface water contaminants, i.e. high production-volume pharmaceuticals. Even though the pharmaceuticals [i.e., acetylsalicylic acid (ASA), diclofenac (DCF), and 17M-NM-1-ethinylestradiol (EE2)] did not affect the bacterial growth kinetics at environmentally-relevant concentrations (86nM), whole-genome microarray analyses revealed the upregulation of 128, 49, and 47 genes upon exposure to DCF, ASA, and EE2, respectively. A strong overlap (27-48%) was observed between transcriptional responses, but a total of 93 genes were found to be upregulated in a compound-specific manner. Hence, we were able to identify 74 and 15 potential biomarker genes for DCF and ASA, respectively. DCF specifically induced genes involved mainly in stress response, signal transduction, response regulation, the electron transport chain, and transcription, while ASA specifically induced genes predominantly involved in signal transduction, response regulation, and trans-membrane translocation. Moreover, our findings validated triclosan-specific biomarker genes that were identified previously. As only 4 genes were specifically-upregulated for EE2, no representative biomarker profile was identified. This study illustrates that a pollutant-specific molecular response can be generated in R. rubrum S1H, which could become a relevant model-microorganism to screen for the ecological impact of surface water contaminants in situ. KEYWORDS: environmental impact studies, risk assessment, biosensor, wastewater, micropollutant, aspirin Two-condition experiments. Comparing samples after induction of three pharmaceuticals each with a non-induced samples. Biological triplicate. Each array contains 3 technical replicates.
2013-08-23 | E-GEOD-23794 | biostudies-arrayexpress
Project description:R. rubrum S1H inoculated on solid agar rich media was sent to the ISS in October 2003 (MESSAGE-part 2 experiment). After 10 days flight, R. rubrum cultures returned back to Earth. These cultures were then subjected to both transcriptomic and proteomic analysis and compared with the corresponding ground control. Whole-genome oligonucleotide microarray and high throughput proteomics, which offer the possibility to survey respectively the global transcriptional and translational response of an organism, were used to test the effect of space flight. Moreover, in an effort to identify a specific stress response of R. rubrum to space flight, ground simulation of space ionizing radiation and space gravity were performed under identical culture setup and growth conditions encountered during the actual space journey. This study is unique in combining the results from an actual space experiment with the corresponding space ionizing radiation and modeled microgravity ground simulations, which lead to a more solid dissection of the different factors contribution acting in space flight conditions. Total RNA was extracted from R. rubrum S1H grown after 10 days in space flight or after 10 days in simulated ionizing radiation or simulated microgravity. Each microarray slide contained 3 technical repeats.
2010-05-16 | E-GEOD-14239 | 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.
2015-11-10 | GSE23799 | GEO
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:A cDNA microarray was constructed from the expressed sequence tags (ESTs) of different developmental stages, and comparative genome hybridization based on microarray procedures were carried out. Dermatophyte species are classified into three genera: Epidermophyton, Microsporum, and Trichophyton. To determine the relationship between these three groups comparative genome hybridization were used in our experiment. Trichophyton rubrum genmic DNA was reference DNA and labelled by Cy3 while the other dermatophytes genomic DNA were test DNA and labelled by CY5. Test and reference DNA were co-hybridized with the T. rubrum cDNA microarray and the numbers of genes shared between each species and T. rubrum were determined. Keywords: Comparative Genomic Hybridization We used a Trichophyton rubrum cDNA microarray prepared in our lab through comparative genome hybridization of genomic DNA of 21 dermatophyte strains (belonging to 20 species) to elucidate the taxonomy and evolution profiles of 20 dermatophyte species. The numbers of genes shared between each species and T. rubrum were determined. Each strain DNA hybridized for 3 times. The slides were separated into three groups base on different datasets.
2010-05-03 | E-GEOD-7909 | biostudies-arrayexpress
Project description:In the frame of the European MELiSSA project, which aims to develop a closed biological life support system for forthcoming long term space exploration missions, the study of the alpha-proteobacterium Rhodospirillum rubrum S1H cultivated in space related environmental conditions has started. In the present work, the bacterium was grown using two different microgravity simulators, namely the Rotating Wall Vessel (RWV) and the Random Positioning Machine (RPM) and its response was evaluated at both the transcriptomic and proteomic levels using respectively a dedicated whole-genome microarray and high-througput proteomics. At the transcriptomic level, 13 genes were found significantly induced in the RWV samples and all 13 were included in the more pronounced response of 235 induced genes of R. rubrum S1H to the RPM cultivation. On the other hand, at the proteomic level, a few common proteins were found to be differentially expressed in RWV and RPM while the RWV appeared to induce a higher number of significantly regulated proteins. However, the transcriptomic and the proteomic approaches appeared to be complementary pointing out the likely interrelation between quorum sensing, cell pigmentation and cell aggregation in R. rubrum S1H. Future studies will aim to characterize this unknown quorum sensing regulon.
2010-06-05 | GSE19942 | GEO
Project description:Radiotolerance of Rhodospirillum rubrum S1H
| PRJNA130701 | ENA