ArcA deletion mutant/MR-1
Ontology highlight
ABSTRACT:
ORGANISM(S): Shewanella oneidensis MR-1 Shewanella oneidensis
PROVIDER: GSE7973 | GEO | 2008/02/01
SECONDARY ACCESSION(S): PRJNA100733
REPOSITORIES: GEO
Similar Datasets
Project description:Background: Salmonella enterica serovar Typhimurium (S. Typhimurium) is a Gram-negative pathogen that must successfully adapt to the broad fluctuations in the concentration of dissolved dioxygen encountered in the host. In Escherichia coli, ArcA (Aerobic Respiratory Control) helps the cells to sense and respond to the presence of dioxygen. The global role of ArcA in E. coli is well characterized; however, little is known about its role in anaerobically grown S. Typhimurium. Results: We compared the transcriptional profiles of the virulent wild-type (WT) strain (ATCC 14028s) and its isogenic arcA mutant grown under anaerobic conditions. We found that ArcA directly or indirectly regulates 392 genes (8.5% of the genome); of these, 138 genes are poorly characterized. Regulation by ArcA in S. Typhimurium is similar, but distinct from that in E. coli. Thus, genes/operons involved in core metabolic pathways (e.g., succinyl-CoA, fatty acid degradation, cytochrome oxidase complexes, flagellar biosynthesis, motility, and chemotaxis) were regulated similarly in the two organisms. However, genes/operons present in both organisms, but regulated differently by ArcA in S. Typhimurium included those coding for ethanolamine utilization, lactate transport and metabolism, and succinate dehydrogenases. Salmonella-specific genes/operons regulated by ArcA included those required for propanediol utilization, flagellar genes (mcpAC, cheV), Gifsy-1 prophage genes, and a few SPI-3 genes (mgtBC, slsA, STM3784). In agreement with our microarray data, the arcA mutant was non-motile, lacked flagella, and was as virulent in mice as the WT. Furthermore, we identified a set of 120 genes whose regulation was shared with the anaerobic redox regulator, Fnr. Conclusion(s): We have identified the ArcA regulon in anaerobically grown S. Typhimurium. Our results demonstrated that in S. Typhimurium, ArcA serves as a transcriptional regulator coordinating cellular metabolism, flagella biosynthesis, and motility. Furthermore, ArcA and Fnr share in the regulation of 120 S. Typhimurium genes.
2011-02-10 | GSE24564 | GEO
Project description:Mapping the occupancy of ArcA throughout the genome of Escherchia coli MG1655 K-12 using an affinity purified antibody under anaerobic and aerobic growth conditions. As a control, we also performed ChIP-chip onArcA in a ∆arcA mutant strain of Escherchia coli MG1655 K-12. Described in the manuscript The response regulator ArcA uses a diverse binding site architechture to globally regulate carbon oxidation in E. coli
2013-10-17 | GSE46413 | GEO
Project description:Mapping the occupancy of ArcA throughout the genome of Escherchia coli MG1655 K-12 using an affinity purified antibody under anaerobic and aerobic growth conditions. As a control, we also performed ChIP-chip onArcA in a M-bM-^HM-^FarcA mutant strain of Escherchia coli MG1655 K-12. Described in the manuscript The response regulator ArcA uses a diverse binding site architechture to globally regulate carbon oxidation in E. coli Mapping of occupancy of ArcA in the genome of Escherchia coli MG1655 K-12 during anaerobic fermentation and aerobic respiration. Immunoprecipitated DNA compared to INPUT for each sample.
2013-10-17 | E-GEOD-46413 | biostudies-arrayexpress
Project description:RNA-Seq was performed on Avian pathogenic E. coli (APEC) WT and mutant to investigate the pathogenicity of ArcA (Aerobic Respiratory Control), a global regulator important for E. coli’s adaptation from anaerobic to aerobic conditions and control of that bacterium’s enzymatic defenses against ROS.
2017-03-01 | E-MTAB-3396 | biostudies-arrayexpress
Project description:We found many binding sites for ArcA under glucose fermentative anaerobic growth conditions. Descirbed in the manuscript "The response regulator ArcA uses a diverse binding site architechture to globally regulate carbon oxidation in E. coli" Examination of occupancy of ArcA under anaerobic growth conditions.
2013-10-17 | E-GEOD-46414 | biostudies-arrayexpress
Project description:We found many binding sites for ArcA under glucose fermentative anaerobic growth conditions. Descirbed in the manuscript "The response regulator ArcA uses a diverse binding site architechture to globally regulate carbon oxidation in E. coli"
2013-10-17 | GSE46414 | GEO
Project description:Comparisson of expression profiling of a etrA deletion mutant strain (experimental sample) with that of the wild type Shewanella oneidensis MR-1 strain to assess global direct/indirect genetic regulation EtrA in Shewanella oneidensis MR-1 shares 73.6% and 50.8% amino acid sequence identity with the oxygen-sensing regulator Fnr in E. coli and Anr in Pseudomonas aeruginosa, respectively; however, its regulatory role of anaerobic metabolism in Shewanella spp. is complex and not well understood. Whole-genome expression profiling using a etrA gene deletion mutant as the experimental sample and the wild type strain as the reference, determine that EtrA fine-tunes the expression of genes involved in various anaerobic metabolic pathways, including nitrate, fumarate and dimethyl sulfoxide reduction. Moreover, genes involved in prophage activation and and genes implicated in aerobic metabolism were also differentially expressed. In contrast to previous studies that attributed a minor regulatory role to EtrA in Shewanella spp., this study demonstrates that EtrA acts as a global transcriptional regulator and cofers physiological advantages to the strain under certain growth conditions.
2011-01-29 | GSE26935 | GEO
Project description:Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 ∆arcA mutant, compared to the wild-type strain. The mutations engineered into this strain produce a strain lacking the ArcA protein. The results are further described in the manuscript The response regulator ArcA uses a diverse binding site architechture to globally regulate carbon oxidation in E. coli
2013-10-17 | GSE46412 | GEO
Project description:The goal of this analysis is to define the aerobic and anaerobic regulons for the transcription factor Mlc (Makes Large Colonies) in the periodontal pathogen Aggregatibacter actinomycetemcomitans. The objectives were met by comparing the mRNA profile of a wild type strain, JP2, to that of an isogenic mutant deleted of the Mlc gene. Both strains were grown aerobically and anaerobically. The results show that Mlc is involved in the regulation of dozens of genes in both growth conditions. Half of the study (anaerobic samples) was a four biological replicates study using total RNA recovered from four separate anaerobic cultures of wild-type Aggregatibacter (formerly Actinobacillus) actinomycetemcomitans strain JP2 and four separate anaerobic cultures of strain AAM155, an isogenic deletion mutant in which the gene for Mlc (Makes Large Colonies) has been replaced by a spectinomycin resistance gene cassette. The cells were grown anaerobically in pairs (wild type paired with mutant). The second half of the study (aerobic samples) was a four biological replicates study using total RNA recovered from four separate aerobic cultures of wild-type Aggregatibacter actinomycetemcomitans strain JP2 and four separate anaerobic cultures of strain AAM155, an isogenic deletion mutant of Mlc. The cells were grown aerobically in pairs (wild type paired with mutant). Each chip measures the expression level of 2,116 genes from A. actinomycetemcomitans strain HK1651. There were 11 different 60-mer probes /gene for 94% of the genes, and the entire probe set (22,537 probes) was replicated (technical replicates) three times on each array. Each probe set is contained on a quarter of a chip and there were also 4,426 random probes per array. A total of four chips were used in these experiments.
2013-06-01 | E-GEOD-38868 | biostudies-arrayexpress
Project description:High-resolution tiling analysis of the MR-1 transcriptome under diverse growth conditions The conditions include aerobic growth in Luria-Bertani broth (LB), aerobic growth in defined lactate minimal medium, anaerobic growth in defined lactate minimal medium with 20mM dimethyl sulfoxide as the electron acceptor, anaerobic growth in defined lactate minimal medium with 10mM iron (III) citrate as the electron acceptor, 10 minutes post heat shock at 42oC see GSE39468 for tiling data on lactate minimal media
2013-03-18 | GSE45217 | GEO