Wild type versus delta vts1
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE3859 | GEO | 2006/02/15
SECONDARY ACCESSION(S): PRJNA94087
REPOSITORIES: GEO
Similar Datasets
Project description:The experiment was designed to look for genes up/downregulated in the absense of Vts1p compared to wild-type cells grown in steady state conditions. Experiment Overall Design: 3 chips delta VTS1 vs. 2 wild type control chips
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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.
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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.
2011-01-01 | GSE24994 | GEO
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)
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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
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