Vibrio cholerae
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: GSE6220
PROVIDER: PRJNA104215 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:For expression analysis of wild-type V. cholerae, hapR, and rpoS deletion mutants in mid-exponential or stationary phase, the strains were grown to either OD600 of 0.3 or for 11 h in LB media at 37 0C, and bacteria from 2-ml culture were quickly pelleted, resuspended in Trizol reagent (GIBCO/BRL, San Diego, California, United States), and frozen on dry ice. RNA was isolated from the Trizol agent, treated with DNaseI (Ambion, Austin, Texas, United States), and cleaned by using the RNeasy kit (Qiagen, Valencia, California, United States). Labeling of cDNA and microarray hybridizations were performed as described [Yiliz et al. 2001, Mol. Micro. 53: 497-515]. Microarrays were scanned with a GenePix 400A instrument (Axon Instruments), using the GENEPIX 5.0 software. At least four microarray experiments were performed for each of two biological replicates for the tested strains. Gene expression of V. cholerae, rpoS, and hapR deletion mutants in stationary phase LB cultures was analyzed and compared to the wild-type parent under identical conditions. Gene expression of the wild-type parent during stationary phase after 11 h growth in LB was analyzed using RNA from an exponentially growing culture as a reference.
2006-11-06 | E-SMDB-3833 | biostudies-arrayexpress
Project description:The role of rpoS gene in the formation of Escherichia coli biofilms were investigated. The gene expression was compared among E. coli MG1655 wild type strain and rpoS knock-out strain in the biofilms, the planktonic exponential phase, and the planktonic stationary phase. The analysis revealed that the wild type bilfilms (WBF) showed similar pattern of gene expression with the WT planktonic stationary phase (WS), whereas the rpoS knock-out biofilms (MBF) showed similar pattern of gene expression with the wild type planktonic exponential phase (WE). Genes involved in the energy metabolism and the flagella synthesis showed higher expression in the rpoS knock-out biofilms (MBF), but not in the wild type biofilms (WBF). Moreover, genes involved in the stress responses showed higher expression in the wild type biofilms (WBF), but not in the rpoS knock-out biofilms (MBF). Keywords: cell type comparison (biofilms vs planktonic cells, wild type vs rpoS knock-out strains)
2008-05-23 | GSE7885 | GEO
Project description:RpoS is a conserved stress regulator that plays a critical role in survival under stress conditions in Escherichia coli and other γ-proteobacteria. RpoS is also involved in virulence of many pathogens including Salmonella and Vibrio species. Though well characterized in non-pathogenic E. coli K12 strains, the effect of RpoS on transcriptome expression has not been examined in pathogenic isolates. E. coli O157:H7 is a serious human enteropathogen, possessing a genome 20% larger than that of E. coli K12, and many of the additional genes are required for virulence. The genomic difference may result in substantial changes in RpoS-regulated gene expression. To test this, we compared the transcriptional profile of wild type and rpoS mutants of the E. coli O157:H7 EDL933 type strain. The rpoS mutation had a pronounced effect on gene expression in stationary phase, and more than 1,000 genes were differentially expressed (two-fold, p<0.05). By contrast, we found 11 genes expressed differently in exponential phase. Western blot analysis revealed that, as expected, RpoS level was low in exponential phase and substantially increased in stationary phase. The defect in rpoS resulted in impaired expression of genes responsible for stress response (e.g., gadA, katE and osmY), arginine degradation (astCADBE), putrescine degradation (puuABCD), fatty acid oxidation (fadBA and fadE), and virulence (ler, espI and cesF). For EDL933-specific genes on O-islands, we found 50 genes expressed higher in wild type EDL933 and 49 genes expressed higher in the rpoS mutants. The protein levels of Tir and EspA, two LEE-encoded virulence factors, were elevated in the rpoS mutants under LEE induction conditions. Our results show that RpoS has a profound effect on global gene expression in the pathogenic strain O157:H7 EDL933, and the identified RpoS regulon, including many EDL933-specific genes, differs substantially from that of laboratory K12 strains. In this study, we characterized the RpoS regulon of E. coli O157:H7 strain EDL933 using microarray analysis.
2009-08-03 | GSE17420 | GEO
Project description:For expression analysis of wild-type V. cholerae, hapR, and rpoS deletion mutants in mid-exponential or stationary phase, the strains were grown to either OD600 of 0.3 or for 11 h in LB media at 37 0C, and bacteria from 2-ml culture were quickly pelleted, resuspended in Trizol reagent (GIBCO/BRL, San Diego, California, United States), and frozen on dry ice. RNA was isolated from the Trizol agent, treated with DNaseI (Ambion, Austin, Texas, United States), and cleaned by using the RNeasy kit (Qiagen, Valencia, California, United States). Labeling of cDNA and microarray hybridizations were performed as described [Yiliz et al. 2001, Mol. Micro. 53: 497-515]. Microarrays were scanned with a GenePix 400A instrument (Axon Instruments), using the GENEPIX 5.0 software. At least four microarray experiments were performed for each of two biological replicates for the tested strains. Gene expression of V. cholerae, rpoS, and hapR deletion mutants in stationary phase LB cultures was analyzed and compared to the wild-type parent under identical conditions. Gene expression of the wild-type parent during stationary phase after 11 h growth in LB was analyzed using RNA from an exponentially growing culture as a reference. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
2006-11-03 | GSE6218 | GEO
Project description:RpoS, an alternative sigma factor, is critical for stress response in Escherichia coli. The RpoS regulon expression has been well characterized in rich media that support fast growth and high growth yields. In contrast, though RpoS levels are high in minimal media, how RpoS functions under such conditions has not been clearly resolved. In this study, we compared the global transcriptional profiles of wild type and an rpoS mutant of E. coli grown in glucose minimal media using microarray analyses. The expression of over 200 genes was altered by loss of RpoS in exponential and stationary phases, with only 48 genes common to both conditions. The nature of the RpoS-controlled regulon in minimal media was substantially different from that expressed in rich media. Specifically, the expression of many genes encoding regulatory factors (e.g., hfq, csrA and rpoE) and genes in metabolic pathways (e.g., lysA, lysC and hisD) were regulated by RpoS in minimal media. In early exponential phase, protein levels of RpoS in minimal media were much higher than that in LB media, which may at least partly account for the observed difference in the expression of RpoS-controlled genes. Expression of genes required for flagellar function and chemotaxis was elevated in the rpoS mutant. Western blot analyses show that the flagella sigma factor FliA was expressed much higher in rpoS mutants than in WT in all phase of growth. Consistent with this, the motility of rpoS mutants was enhanced relative to WT. In conclusion, RpoS and its controlled regulators form a complex regulatory network that mediates the expression of a large regulon in minimal media.
2008-10-10 | GSE12797 | GEO
Project description:Question Addressed: What is the level of expression of genes in Vibrio cholerae recovered from various conditions. These conditions include samples recovered directly from patients (O139 from stool samples from ICDDR,B and N16961 from stool samples from a vaccine trial held in Cincinnati) as well as standard logarithmic and stationary phase grown bacteria. Labeling reactions were performed in duplicate for each stool derived and in quadruplicate for each in vitro grown strain. A common reference was used for each slide, it was composed of RNA from the exponentially growing 92A1552 V. cholerae strain
2013-05-23 | GSE38178 | GEO
Project description:RpoS, an alternative sigma factor, is critical for stress response in Escherichia coli. The RpoS regulon expression has been well characterized in rich media that support fast growth and high growth yields. In contrast, though RpoS levels are high in minimal media, how RpoS functions under such conditions has not been clearly resolved. In this study, we compared the global transcriptional profiles of wild type and an rpoS mutant of E. coli grown in glucose minimal media using microarray analyses. The expression of over 200 genes was altered by loss of RpoS in exponential and stationary phases, with only 48 genes common to both conditions. The nature of the RpoS-controlled regulon in minimal media was substantially different from that expressed in rich media. Specifically, the expression of many genes encoding regulatory factors (e.g., hfq, csrA and rpoE) and genes in metabolic pathways (e.g., lysA, lysC and hisD) were regulated by RpoS in minimal media. In early exponential phase, protein levels of RpoS in minimal media were much higher than that in LB media, which may at least partly account for the observed difference in the expression of RpoS-controlled genes. Expression of genes required for flagellar function and chemotaxis was elevated in the rpoS mutant. Western blot analyses show that the flagella sigma factor FliA was expressed much higher in rpoS mutants than in WT in all phase of growth. Consistent with this, the motility of rpoS mutants was enhanced relative to WT. In conclusion, RpoS and its controlled regulators form a complex regulatory network that mediates the expression of a large regulon in minimal media. Experiment Overall Design: A precise rpoS deletion mutant of MG1655 was constructed using the red recombinase method. Wild type and rpoS mutants were inoculated in triplicate into M63 glucose (0.2%) minimal media at a starting OD of 0.0001 and grown aerobically at 37oC. Cultures were harvested at OD600= 0.3 in exponential phase and at OD600= 1.5 in stationary phase. For RNA extraction, cultures were mixed directly with a boiling lysis buffer containing SDS and EDTA followed by acidic hot phenol (65C) to minimize RNA degradation. RNA samples were hybridized to Affymetrix E. coli Antisense Genome Array according to Affymetrix's standard protocols.
2008-10-26 | E-GEOD-12797 | biostudies-arrayexpress
Project description:RpoS is a conserved stress regulator that plays a critical role in survival under stress conditions in Escherichia coli and other γ-proteobacteria. RpoS is also involved in virulence of many pathogens including Salmonella and Vibrio species. Though well characterized in non-pathogenic E. coli K12 strains, the effect of RpoS on transcriptome expression has not been examined in pathogenic isolates. E. coli O157:H7 is a serious human enteropathogen, possessing a genome 20% larger than that of E. coli K12, and many of the additional genes are required for virulence. The genomic difference may result in substantial changes in RpoS-regulated gene expression. To test this, we compared the transcriptional profile of wild type and rpoS mutants of the E. coli O157:H7 EDL933 type strain. The rpoS mutation had a pronounced effect on gene expression in stationary phase, and more than 1,000 genes were differentially expressed (two-fold, p<0.05). By contrast, we found 11 genes expressed differently in exponential phase. Western blot analysis revealed that, as expected, RpoS level was low in exponential phase and substantially increased in stationary phase. The defect in rpoS resulted in impaired expression of genes responsible for stress response (e.g., gadA, katE and osmY), arginine degradation (astCADBE), putrescine degradation (puuABCD), fatty acid oxidation (fadBA and fadE), and virulence (ler, espI and cesF). For EDL933-specific genes on O-islands, we found 50 genes expressed higher in wild type EDL933 and 49 genes expressed higher in the rpoS mutants. The protein levels of Tir and EspA, two LEE-encoded virulence factors, were elevated in the rpoS mutants under LEE induction conditions. Our results show that RpoS has a profound effect on global gene expression in the pathogenic strain O157:H7 EDL933, and the identified RpoS regulon, including many EDL933-specific genes, differs substantially from that of laboratory K12 strains. In this study, we characterized the RpoS regulon of E. coli O157:H7 strain EDL933 using microarray analysis. A precise rpoS deletion mutant of EDL933 was constructed and employed in this study. EDL933 wild type and rpoS mutants were inoculated in triplicate into LB media at a starting OD of 0.0001 and grown aerobically at 37C. Cultures were harvested at OD600 = 0.3 in exponential phase and OD600=1.5 in stationary phase. For RNA extraction, cultures were mixed directly with a boiling lysis buffer containing SDS and EDTA followed by acidic hot phenol to minimize RNA degradation. RNA samples were hybridized to Affymetrix E. coli Genome 2.0 Array according to Affymetrix's standard protocols.
2009-08-03 | E-GEOD-17420 | biostudies-arrayexpress
Project description:The role of rpoS gene in the formation of Escherichia coli biofilms were investigated. The gene expression was compared among E. coli MG1655 wild type strain and rpoS knock-out strain in the biofilms, the planktonic exponential phase, and the planktonic stationary phase. The analysis revealed that the wild type bilfilms (WBF) showed similar pattern of gene expression with the WT planktonic stationary phase (WS), whereas the rpoS knock-out biofilms (MBF) showed similar pattern of gene expression with the wild type planktonic exponential phase (WE). Genes involved in the energy metabolism and the flagella synthesis showed higher expression in the rpoS knock-out biofilms (MBF), but not in the wild type biofilms (WBF). Moreover, genes involved in the stress responses showed higher expression in the wild type biofilms (WBF), but not in the rpoS knock-out biofilms (MBF). Experiment Overall Design: Affymetrix E. coli antisense genome array was used to compare the gene expression among E. coli wild type and rpoS konck-out strains in the biofilms, the planktonic exponential phase, and the planktonic stationary phase. All samples were grown in MOPS minimal media with 0.2% glucose. Biofilms were grown for 72 hours on glass surface in flow cells (1x4x40 mm), and planktonic cells were grown for 8 hours (exponential phase) and 12 hours (stationary phase). Experiments were repeated 3 times, which resulted in 3 replicates of 6 different samples.
2008-06-18 | E-GEOD-7885 | biostudies-arrayexpress
Project description:The goal of this study was to compare system level changes in gene-expression in naturally isolated alleles of stationary-phase sigma factor rpoS and two variants of it isolated during evolution under prolonged stationary-phase. We show that while rpoS819 was an attenuated form of wild type rpoS, rpoS92 partially reverses rpoS819 expression compensating rpoS819.
2018-08-25 | GSE119046 | GEO