Expression data from Shewanella oneidensis MR-1 in time series experiment
Ontology highlight
ABSTRACT:
ORGANISM(S): Shewanella oneidensis MR-1
SUBMITTER: Qasim Beg
PROVIDER: E-GEOD-25821 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The sumitted data compares gene expression profile of Shewnaella oneidensis MR-1 on two different sets of media conditions (nutritionally rich LB medium and Lactate minimal medium)
2012-05-01 | GSE25821 | GEO
Project description:Anaerobic respiration in the metal reducer Shewanella oneidensis MR-1, unlike other bacteria, is regulated by the cAMP receptor protein, CRP. Three putative genes, cyaA, cyaB, and cyaC, predicted to encode class I, class IV, and class III adenylate cyclases respectively, have been identified in the genome sequence of this bacterium. Functional validation through complementation of an E. coli cya mutant confirmed that these genes encode proteins with adenylate cyclase activities. Chromosomal deletion of either cyaA or cyaB did not affect anaerobic respiration with fumarate, DMSO, or Fe(III), whereas the deletion of cyaC caused deficiencies in respiration with DMSO and Fe(III), and to a lesser extent with fumarate. A phenotype similar to that of a crp mutant, which lacks the ability to grow anaerobically with DMSO, fumarate, and Fe(III), was obtained when both cyaA and cyaC were deleted. Microarray analysis of gene expression in the crp and the cyaC mutants revealed the involvement of both genes in the regulation of key respiratory pathways that include DMSO, fumarate, and Fe(III) reduction. Additionally, several genes associated with plasmid replication, flagella biosynthesis, and electron transport, were differentially expressed in the cyaC mutant, but not in the crp mutant. Our results indicated that CyaC plays a major role in regulating anaerobic respiration, and may contribute to additional signaling pathways independent of CRP. To explore the roles of CyaC and CRP in the regulation of anaerobic respiration in Shewanella oneidensis MR-1, the genome-wide transcriptome profiles of ÎcyaC and Îcrp mutants were compared to those of the wild type. Given the growth deficiencies displayed by Îcrp and ÎcyaC under anaerobic conditions, all strains were cultured in chemostats under O2 limitation. Since both Îcrp and ÎcyaC strains are not impaired in aerobic respiration, oxygen-limited conditions provided the means to maintain equal growth rates (0.06 h-1) among the mutant and wild-type strains thus eliminating the effect of growth on the overall transcriptome profiles. At the same time, while growing aerobically, the cells decreased dissolved O2 concentration in the medium below the detection threshold (DOTâ¤1%) allowing for the expression of anaerobic respiratory genes. The latter was confirmed by the reduction of fumarate by the wild-type culture which produced stoichiometric amounts of succinate under O2-limited conditions. The optical density (OD600) of the wild type, ÎcyaC, and Îcrp chemostat cultures used for transcriptome profiling was 0.50, 0.45 and 0.40, respectively. All the experiments were carried out in duplicate.
2010-06-19 | E-GEOD-15657 | biostudies-arrayexpress
Project description:We investigated the anode-specific responses of Shewanella oneidensis MR-1, an exoelectroactive ammaproteobacterium, using for the first time iTRAQ and 2D-LC MS/MS driven membrane proteomics to compare protein abundances in S. oneidensis when generating power in MFCs, and growing in a continuous culture.
2016-12-08 | PXD004090 | Pride
Project description:Comparison of gene expression and mutant fitness in Shewanella oneidensis MR-1 Expression data for 15 growth conditions in mid-exponential phase and expression data across growth phases for 3 of those conditions
2012-07-18 | E-GEOD-39462 | biostudies-arrayexpress
Project description:We combined high-resolution tiling microarrays and 5'-end RNA sequencing to obtain a genome-wide map of transcription start sites (TSSs) for Shewanella oneidensis MR-1. To test the reliability of these TSSs, we compared our result to those from differential RNA sequencing (dRNA-seq), which discriminates primary and processed ends of transcripts. We found that our identified TSSs tend to have significantly more mapped reads in the TEX(+) sample than the TEX(-) sample. Overall, the dRNA-seq results support the validity of our predictions for TSS. S. oneidensis MR-1 was grown to mid-log phase in Luria-Bertani broth (LB) or defined lactate minimal medium, and total RNA was isolated and used for differential RNA-sequencing (dRNA-seq) by next-generation sequencing, which is used to verify genome-wide transcription start sites. For dRNA-seq, total RNA was partially treated with Terminator Exonuclease (TEX) to digest processed RNA and thereby enrich for primary transcript ends.
2014-06-12 | E-GEOD-58292 | biostudies-arrayexpress
Project description:S. oneidensis MR-1 was grown with different electron acceptors: an electrode at 0.4 V vs. SHE, 50 mM Fe(III)citrate, and oxygen. The gene expression pattern for each experiment was analyzed and the differences in gene expression for the different experimental conditions were compared. For two samples S. oneidensis was grown with a graphite anode electrode (at 0.4 V. vs. SHE) as the only electron acceptor - one sample was directly fed with 20 mM lactate, one sample was fed with lactate produced during fermentation of glucose by Lactococcus lactis. Four samples were grown anaerobically with 50 mM Fe(III)citrate as the only electron acceptor, and 20 mM lactate for 20 h. Three samples were grown aerobically with 20 mM lactate for 20 h. The same modified M4 medium was used for all samples. For RNA extraction, the biofilm was scraped off the frozen (-80M-BM-0C) carbon electrode with a sterile razor blade. Biofilm-carbon sludge was combined with 7 mL ice-cold phosphate buffer saline (PBS), vortexed, sonicated at 7 W for 30 s on ice (3 repetitions), and centrifuged. For the liquid cultures, 2 mL of each culture were combined with 2 mL RNA protect, vortexed, and centrifuged at 5,500g for 10 min. The pellets were resuspended in NAES buffer (50 mM sodium acetate buffer, 10 mM EDTA and 1 % SDS at pH 5). RNA was isolated with a phenol:chloroform extraction protocol.
2011-02-01 | E-GEOD-20379 | biostudies-arrayexpress
Project description:5' RNA-Seq of mRNA from S. oneidensis MR-1 grown aerobically in defined lactate medium One lane of sequence for a 5' RNASeq library from RNA treated with exonuclease to remove degraded transcripts, with single-end 40-nt reads
2012-07-18 | E-GEOD-39474 | biostudies-arrayexpress
Project description:One of the most striking observations in the S. oneidensis genome regarding nitrate respiration is that napC is missing and nrfBCD is degenerated. To gain insights into candidate genes encoding the protein(s) in place of NapC and NrfBCD function, i.e., delivering electrons to NapA and NrfA, transcriptional profiling was carried out using the S. oneidensis whole-genome cDNA microarray. Cells of MR-1 grown on nitrate or fumarate under anaerobic conditions were sampled at the exponential phase for the analysis. The quality of the array data was statistically assessed using the method reported previously. Keywords: Compararive microarray study Compare transcriptional profiles of MR-1 grown on nitrate and Fumarate aiming at finding the electron transfer proteins to NapA and NrfA.
2010-05-19 | E-GEOD-11198 | biostudies-arrayexpress
Project description:Bioelectrochemical systems employing mixed microbial communities as biocatalysts are gaining importance as potential renewable energy, bioremediation, or biosensing devices. While we are beginning to understand how individual microorganism species interact with an electrode as electron donor, not much is known about the interactions between different microbial species in a community. Here, we compare the bioelectrochemical performance of Shewanella oneidensis in a pure-culture and in a co-culture with the homolactic acid fermenter Lactococcus lactis. While S. oneidensis alone can only use lactate as electron donor for current production, the co-culture is able to convert glucose into current with a similar coulombic efficiency of approximately 17%, respectively. With (electro)-chemical analysis and transcription profiling, we found that the BES performance and S. oneidensis physiology were not significantly different whether grown as a pure- or co-culture. These co-culture experiments represent a first step in understanding microbial interactions in BES communities with the goal to design complex microbial communities, which specifically convert target substrates into electricity. Further, for the first time, we elucidated S. oneidensis gene expression with an electrode as the only electron acceptor. The expression pattern confirms many previous studies regarding the enzymatic requirements for electrode respiration, and it generates new hypotheses on the functions of proteins, which are so far not known to be involved in electrode respiration. The BES was either operated with S. oneidensis alone, fed with lactate, or it was operated with S. oneidensis and L. lactis with glucose as primary substrate. The basic medium was a modified M4 medium containing 0.5 g/L yeast extract, 0.5 g/L trypton and 5 g/L glycerol phosphate, besides the commen M4 incredients. S. oneidensis oxidizes lactate to acetate and electrons in a BES - the latter generate a current at a graphite anode. The anode biofilm was harvested after about 4 weeks of continuous BES operation and subjected to total RNA extraction.
2010-12-01 | E-GEOD-20343 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in a Shewanella oneidensis MR-1 to Fe nanoparticle decorated anodes, compared to the carbon plate anodes in microbial electrolysis cells. Whole genome microarray analysis of the gene expression showed that the encoding biofilm formation genes were significantly up-regulated as response to nanoparticle decorated anodes which indicated thickness improvements contributed to enhance current density. The increased expression genes related to nanowire, flavins and c-type cytochromes also have partially contributed to enhance current density by Fe nanoparticle decorated anode. The majority of additional differentially expressed genes associated with electron transport, anaerobic metabolism in response to the nanostructured anodes possibly play roles in current density enhancement. A six chip study using total RNA recovered from three separate replicates of biofilm on Fe Nanoparticle decorated anode of Shewanella oneidensis MR-1 and three separate replicates of carbon plate control. Each chip measures the expression level of 4,295 genes .
2011-08-19 | E-GEOD-31535 | biostudies-arrayexpress