Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Identification of genes induced on nitrate, role of OxyR

ABSTRACT: The study aimed to identify role of OxyR during growth on different electron acceptors when E. coli are growing anaerobically. Wt and OxyR null cells were grown on nitrate and fumarate medium anaerobically. Each condition was done in duplicate. RNA was extracted using Qiagen RNeasy kit after stabilization of RNA with RNA protect bacteria reagent. Hybridization and further processing was done based on Affymetrix protocols on E. coli Genome 2.0 arrays.

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

SUBMITTER: Divya Seth

PROVIDER: E-GEOD-24524 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Endogenous protein S-Nitrosylation in E. coli: regulation by OxyR.

Seth Divya D Hausladen Alfred A Wang Ya-Juan YJ Stamler Jonathan S JS

Science (New York, N.Y.) 20120401 6080

Endogenous S-nitrosylation of proteins, a principal mechanism of cellular signaling in eukaryotes, has not been observed in microbes. We report that protein S-nitrosylation is an obligate concomitant of anaerobic respiration on nitrate in Escherichia coli. Endogenous S-nitrosylation during anaerobic respiration is controlled by the transcription factor OxyR, previously thought to operate only under aerobic conditions. Deletion of OxyR resulted in large increases in protein S-nitrosylation, and S ...[more]

PMID: 22539721

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Project description:Oxidative stress caused by exposure to reactive oxygen species (ROS), is a major challenge for aerobic and especially anaerobic organisms. Bacteria coordinate the response to oxidative stress through the LysR-type transcriptional regulator (LTTR) OxyR. Extensive studies have focused on the classical Escherichia coli system to shed light on the mode of action of defensive weapons against oxidative stress. The underlying mechanism is mediated via the formation of redox-dependent disulfide bond between two conserved cysteines of OxyR, thus activating transcription of members of the OxyR regulon. However, only fragmentary information on the regulation and function of OxyR has been gleaned through genetic and biochemical analyses in the important opportunistic pathogen P. aeruginosa. In this report, we used a comprehensive transcriptional profiling analysis to delineate the OxyR regulon under three conditions (KingM-bM-^@M-^Ys A medium [Pseudomonas medium or PM], Luria Broth (LB), and LB when oxyR is overexpressed), to investigate its roles in different cellular aspects that are independent of the classical oxidative stress response. Interestingly, when grown in LB, OxyR was found to regulating many genes involved in the process of inter-cellular communication known as quorum sensing (QS). In contrast, when grown in PM, OxyR regulate the expression of a newly identified CSS (cell-surface signaling) system in an OxyR-dependent fashion. In addition, the results from oxyR overexpression further confirmed that OxyR was linked to regulation of QS and Type 3 Secretion (T3SS) in addition to the regulation of antioxidative genes. Taken together, our results show that, apart from its dominant role in defense against oxidative stress in P. aeruginosa, OxyR acts as a global regulator that provides a link between the regulation of oxidative stress response, QS and virulence. 15 samples, representing 5 different biological conditions, including 3 biological replicates for each condition

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.

Dataset Information

Identification of genes induced on nitrate, role of OxyR

Publications

Endogenous protein S-Nitrosylation in E. coli: regulation by OxyR.

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