Delta-uvrY versus wild-type
Ontology highlight
ABSTRACT:
ORGANISM(S): Shewanella oneidensis MR-1
PROVIDER: GSE24994 | GEO | 2011/01/01
SECONDARY ACCESSION(S): PRJNA131975
REPOSITORIES: GEO
Similar Datasets
Project description:The BarA/UvrY two-component system is well conserved in numerous species of the γ-proteobacteria. However, the regulatory output of this system differs significantly between the species. In this study, we characterized the BarA/UvrY two-component system in Shewanella oneidensis MR-1. Sensor kinase BarA and the cognate response regulator UvrY were identified by bioinformatic analysis and subsequent in vivo interaction and phosphotransfer studies. The expression of two putative small regulatory RNAs (sRNAs), CsrB1 and CsrB2, was demonstrated to be dependent on UvrY. In contrast, a third predicted sRNA, CsrC, was expressed independently of UvrY. Transcriptomic analysis by microarrays revealed that UvrY is a global regulator and affects transcription of key enzymes of carbon metabolism such as ackA, aceAB, and pflAB. Subsequent growth experiments demonstrated that mutants lacking UvrY have a significant growth advantage over the wild type during aerobic growth on N-acetylglucosamine while under under anaerobic conditions the mutant grew more slowly. This effect was absent during growth with lactate as carbon source or in complex medium. Based on these results, we conclude that, in S.oneidensis MR-1, the global BarA/UvrY regulatory system is involved in central carbon metabolism processes. In the study presented, expression profiles of three independent replicates of Shewanella oneidensis MR-1 ∆uvrY were compared to three independent replicates of Shewanella oneidensis MR-1 wild type cells. All samples were obtained from exponentially aerobically grown cells in LB to stationary phase (OD600nm=4.0)
2011-01-01 | E-GEOD-24994 | biostudies-arrayexpress
Project description:Colonization of the intestinal tract and dissemination into deeper tissues by the enteric pathogen Yersinia pseudotuberculosis demands expression of a special set of virulence factors important for the initiation and the persistence of the infection. In this study we demonstrate that many virulence-associated functions are coregulated with the carbohydrate metabolism. This link is mediated by the carbon storage regulator (Csr) system, including the regulatory RNAs CsrB and CsrC, and the cAMP receptor protein (Crp), which both control virulence gene expression in response to the nutrient composition of the medium. Here, we show that Crp regulates the synthesis of both Csr RNAs in an opposite manner. A loss of the crp gene resulted in a strong upregulation of CsrB synthesis, whereas CsrC levels were strongly reduced leading to downregulation of the virulence regulator RovA. Switching of the Csr RNA involves Crp-mediated repression of the response regulator UvrY which activates csrB transcription. To elucidate the regulatory links between virulence and carbon metabolism, we performed comparative metabolome, transcriptome and phenotypic microarray analyses and found that Crp promotes oxidative catabolism of many different carbon sources, whereas fermentative patterns of metabolism are favoured when crp is deleted. Mouse infection experiments further demonstrated that Crp is pivotal for a successful Y. pseudotuberculosis infection. In summary, placement of the Csr system and important virulence factors under control of Crp enables this pathogen to link its nutritional status to virulence in order to optimize biological fitness and infection efficiency through the infectious life cycle.
2012-12-31 | GSE42206 | GEO
Project description:Colonization of the intestinal tract and dissemination into deeper tissues by the enteric pathoÂgen Yersinia pseudotuberculosis demands expression of a special set of virulence factors important for the initiation and the persistence of the infection. In this study we demonstrate that many virulence-associated functions are coregulated with the carbohydrate metabolism. This link is mediated by the carbon storage regulator (Csr) system, including the regulatory RNAs CsrB and CsrC, and the cAMP receptor protein (Crp), which both control virulence gene expression in response to the nutrient composition of the medium. Here, we show that Crp regulates the synthesis of both Csr RNAs in an opposite manner. A loss of the crp gene resulted in a strong upregulation of CsrB synthesis, whereas CsrC levels were strongly reduced leading to downregulation of the viruÂlence regulator RovA. Switching of the Csr RNA involves Crp-mediated reÂpression of the response regulator UvrY which activates csrB transcription. To elucidate the regulatory links between virulence and carbon metabolism, we performed comparative metabolome, transÂÂÂcripÂtome and phenotypic microarray analyses and found that Crp promotes oxidative catabolism of many different carbon sources, whereas fermentative patterns of metabolism are favoured when crp is deleted. Mouse infection experiments further demonstrated that Crp is pivotal for a successÂful Y. pseudoÂtuberÂculosis infection. In summary, placement of the Csr system and important virulence factors under control of Crp enables this pathogen to link its nutritional status to virulence in order to optimize bioÂlogical fitness and infection efficiency through the infecÂtious life cycle. Y. pseudotuberculosis YPIII or the isogenic crp mutant strain were grown to late stationary phase at 25°C. Four biological replicates were employed for each experiment consisting of two pooled individual cultures and two pooled RNA preparation samples, respectively. Total RNA was extracted using SV Total RNA Isolation System (Promega). The samples were treated with RNase-free DNase (Roche Applied Science) and the quality of the RNA was confirmed by the lack of PCR amplification of the hns gene and by using an Agilent 2100 Bioanalyzer.
2012-12-31 | E-GEOD-42206 | biostudies-arrayexpress
Project description:The availability of oxygen is a major environmental factor for many microbes, in particular for bacteria, such as Shewanella species, which thrive in redox-stratified environments. One of the best studied systems involved in mediating the response to changes in environmental oxygen levels is the Arc two-component system of Escherichia coli, consisting of the sensor kinase ArcB and the cognate response regulator ArcA. An ArcA ortholog was previously identified in Shewanella, and as in E. coli, Shewanella ArcA is involved in regulating the response to shifts in oxygen levels. Here, we identified the hybrid sensor kinase SO_0577, now designated ArcS, as the previously elusive cognate sensor kinase of the Arc system in S. oneidensis MR-1. Phenotypic mutant characterization, transcriptomic analysis, protein-protein interaction and phosphotransfer studies revealed that the Shewanella Arc system consists of the sensor kinase ArcS, the single phosphotransfer domain protein HptA, and the response regulator ArcA. Phylogenetic analysis suggests that HptA might be a relict of ArcB. Conversely, ArcS is substantially different with respect to overall sequence homologies and domain organization. Thus, we speculate ArcS might have adopted the role of ArcB after loss of the original sensor kinase, perhaps as a consequence of regulatory adaptation to a redox-stratified environment. In the study presented, expression profiles of three independent replicates of Shewanella oneidensis MR-1 delta-arcS were compared to three independent replicates of Shewanella oneidensis MR-1 wild type cells. All samples were obtained from exponentially aerobically grown cells in LB
2010-06-05 | E-GEOD-21044 | biostudies-arrayexpress
Project description:Shewanella oneidensis MR-1 exhibits extracellular electron transfer (EET) activity that is influenced by various cellular components, including outer-membrane cytochromes, cell-surface polysaccharides (CPS), and regulatory proteins. Here, a random transposon-insertion mutant library of S. oneidensis MR-1 was screened after extended cultivation in electrochemical cells (ECs) with a working electrode poised at +0.2 V (vs. Ag/AgCl) to isolate mutants that adapted to electrode-respiring conditions and identify as-yet-unknown EET-related factors. Several mutants isolated from the enrichment culture exhibited rough morphology and extraordinarily large colonies on agar plates compared to wild-type MR-1. One of the isolated mutants, designated strain EC-2, produced 90% higher electric current than wild-type MR-1 in ECs and was found to have a transposon inserted in the SO_1860 (uvrY) gene, which encodes a DNA-binding response regulator of the BarA/UvrY two-component regulatory system. However, an in-frame deletion mutant of SO_1860 (∆SO_1860) did not exhibit a similar level of current generation as that of EC-2, suggesting that the enhanced current-generating capability of EC-2 was not simply due to the disruption of SO_1860. In both EC-2 and ∆SO_1860, the transcription of genes related to CPS synthesis was decreased compared to wild-type MR-1, suggesting that CPS negatively affects current generation. In addition, transcriptome analyses revealed that a number of genes, including those involved in biofilm formation, were differentially expressed in EC-2 compared to those in ∆SO_1860. The present results indicate that the altered expression of the genes related to CPS biosynthesis and biofilm formation is associated with the distinct morphotype and high current-generating capability of strain EC-2, suggesting an important role of these genes in determining the EET activity of S. oneidensis.
2014-07-14 | GSE50443 | GEO
Project description:Shewanella oneidensis MR-1 is a facultative anaerobe that grows by respiration using a variety of electron acceptors. This organism serves as a model to study how bacteria thrive in redox-stratified environments. A glucose-utilizing engineered derivative of MR-1 has been reported to be unable to grow in glucose minimal medium (GMM) in the absence of electron acceptors, despite this strain having a complete set of genes for reconstructing glucose to lactate fermentative pathways. To gain insights into why MR-1 is incapable of fermentative growth, this study examined a hypothesis that this strain is programmed to repress the expression of some carbon metabolic genes in the absence of electron acceptors. Comparative transcriptomic analyses of the MR-1 derivative were conducted in the presence and absence of fumarate as an electron acceptor, and these found that the expression of many genes involved in carbon metabolism required for cell growth, including several tricarboxylic acid (TCA) cycle genes, was significantly downregulated in the absence of fumarate. This finding suggests a possibility that MR-1 is unable to grow fermentatively on glucose in minimal media owing to the shortage of nutrients essential for cell growth, such as amino acids. This idea was demonstrated in subsequent experiments that showed that the MR-1 derivative fermentatively grows in GMM containing tryptone or a defined mixture of amino acids. We suggest that gene regulatory circuits in MR-1 are tuned to minimize energy consumption under electron acceptor-depleted conditions, and that this results in defective fermentative growth in minimal media. IMPORTANCE It is an enigma why S. oneidensis MR-1 is incapable of fermentative growth despite having complete sets of genes for reconstructing fermentative pathways. Understanding the molecular mechanisms behind this defect will facilitate the development of novel fermentation technologies for the production of value-added chemicals from biomass feedstocks, such as electro-fermentation. The information provided in this study will also improve our understanding of the ecological strategies of bacteria living in redox-stratified environments.
2023-06-20 | GSE220284 | GEO
Project description:The availability of oxygen is a major environmental factor for many microbes, in particular for bacteria, such as Shewanella species, which thrive in redox-stratified environments. One of the best studied systems involved in mediating the response to changes in environmental oxygen levels is the Arc two-component system of Escherichia coli, consisting of the sensor kinase ArcB and the cognate response regulator ArcA. An ArcA ortholog was previously identified in Shewanella, and as in E. coli, Shewanella ArcA is involved in regulating the response to shifts in oxygen levels. Here, we identified the hybrid sensor kinase SO_0577, now designated ArcS, as the previously elusive cognate sensor kinase of the Arc system in S. oneidensis MR-1. Phenotypic mutant characterization, transcriptomic analysis, protein-protein interaction and phosphotransfer studies revealed that the Shewanella Arc system consists of the sensor kinase ArcS, the single phosphotransfer domain protein HptA, and the response regulator ArcA. Phylogenetic analysis suggests that HptA might be a relict of ArcB. Conversely, ArcS is substantially different with respect to overall sequence homologies and domain organization. Thus, we speculate ArcS might have adopted the role of ArcB after loss of the original sensor kinase, perhaps as a consequence of regulatory adaptation to a redox-stratified environment.
2010-03-25 | GSE21044 | GEO
Project description:Transcriptional comparisons between wild-type Streptococcus mutans UA159 and two mutant strains (∆ackA and ∆ackA pta).
2013-05-11 | GSE46835 | GEO
Project description:We investigated the way global gene expression changed in E. coli correlated with the metabolism of seven carbon substrates chosen to trigger a large panel of metabolic pathways with features varying in: carbon influx flow rate; entry points in the metabolic network; modes of transport. Quantitative coarse-grained expression-pattern analysis demonstrated that the gene expression trend following immediately the reduction of carbon influx flow rate was determined by its initial expression level. Subsequent fine-grained expression-pattern analysis demonstrated that the Crp regulator, associated to a change in growth rate, governed the response of most carbon influx-dependent genes. By contrast, the Cra, Mlc and Fur regulators governed the expression of genes responding to non-glycolytic substrates, glycolytic substrates or PTS (phosphotransferase system) transported sugars following an idiosyncratic way, with the function of each of these regulators being titrated by the metabolism of the corresponding substrates. This work also allowed us to expand the extent of the gene complement regulated by each regulator with additional genes (27 genes in the Crp regulon, 49 genes in the Cra regulon, 1 gene in the Mlc regulon and 2 genes in Fur regulon) and to elucidate the regulatory functions of each regulator comprehensively. Strikingly, Crp and Cra worked in concert to coordinate central carbon metabolism with amino acids biosynthesis. Together, these results demonstrated the power of physiology-based interperation of global data in revealing regulatory networks of bacteria.
2021-03-02 | GSE156143 | GEO
Project description:Expression of the virulence regulator RovA of Yersinia pseudotuberculosis, is controlled by the ncRNAs CsrB and CsrC through CsrA and RovM. In this study, we show that the regulator YmoA of the Hha family of nucleoid-associated proteins controls expression of the counterregulated Csr-type RNAs and the Csr-RovM-RovA signalling cascade through alterations of the CsrC RNA stability. YmoA-mediated stabilization of CsrC depends on CsrA and H-NS, but not on the RNA chaperone Hfq and involves a stabilizing stem-loop structure within the 5’-region of CsrC. YmoA influence on CsrC stability is complex as YmoA was found to control numerous factors known to affect RNA structures and stability. In addition, YmoA controls temperature-dependent early and later stage virulence genes in an opposite manner and coregulates their expression with bacterial stress responses and metabolic functions. Following oral infections in a mouse model, we demonstrate that a ymoA mutant is strongly reduced in its ability to disseminate to the Peyer’s patches, mesenteric lymph nodes, liver and spleen and exhibits a reduced mortality. We propose a model in which YmoA controls switching from a RovA-dependent early colonization phase towards a virulence plasmid (pYV)-dependent infection phase important for host defense and persistence.
2012-07-31 | GSE35043 | GEO