RpoS regulation of gene expression during exponential growth of E. coli K-12
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ABSTRACT:
ORGANISM(S): Escherichia coli K-12
PROVIDER: GSE9814 | GEO | 2007/12/28
SECONDARY ACCESSION(S): PRJNA103767
REPOSITORIES: GEO
Similar Datasets
Project description:This study is to identify the RpoS regulon in MG1655 in early exponential growth. RNA samples from wild type or rpoS mutants were extracted using acidic hot phenol method and hybridized to Affymetrix E. coli Antisense Genome Array. 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 LB media at a starting OD of 0.0001 and grown aerobically at 37C. Cultures were harvested at an OD600 = 0.3 after being maintained in exponential phase for at least eight generations. 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.
2008-06-16 | E-GEOD-9814 | biostudies-arrayexpress
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:Bacteria generally possess multiple σ factors that, based on structural and functional similarity, divide into two families: σD and σN. Among the seven σ factors in Escherichia coli, six belongs to the σD family. Each σ factor recognizes a group of promoters, providing effective control of differential gene expression. Many studies have shown that σ factors of the σD family compete with each other for function. In contrast, the competition between σN and σD families has yet to be fully explored. Here we report a global antagonistic effect on gene expression between two alternative σ factors, σN (RpoN) and σS (RpoS), a σD family protein. Mutations in rpoS and rpoN inversely affected a number of cellular traits, such as expression of flagellar genes, σN-controlled growth on poor nitrogen sources, and σS-directed expression of acid phosphatase AppA. Transcriptome analysis reveals that 40% of genes in the RpoN regulon were under reciprocal RpoS control. Furthermore, loss of RpoN led to increased levels of RpoS, while RpoN levels were unaffected by rpoS mutations. Expression of the flagellar σF factor (FliA), another σD family protein, was controlled positively by RpoN but negatively by RpoS. These findings unveil a complex regulatory interaction among σN, σS and σF, and underscore the need to employ systems biology approaches to assess the effect of such interaction of σ factors on cellular functions, including motility, nutrient utilization, and stress response. Precise deletion mutants of rpoS or rpoN of MG1655 were constructed and employed in this study. Cultures were inoculated in triplicate in M9 minimal media (0.2% glucose) at a starting OD of 0.0001 and grown aerobically at 37C. Cultures were harvested at OD600 = 0.3 in exponential 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.
2010-12-04 | E-GEOD-20095 | 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:StpA is a paralogue of the nucleoid associated protein H-NS that is conserved in a range of enteric bacteria and had no known function in Salmonella enterica serovar Typhimurium. Here, we show that 5% of the Salmonella genome is regulated by StpA, which contrasts with the situation in Escherichia coli where deletion of stpA only had minor effects on gene expression. The StpA-dependent genes of S. Typhimurium are a specific subset of the H-NS regulon that are predominantly under the positive control of sigma38 (RpoS), CRP-cAMP and PhoP. The regulatory role of StpA varied at different growth phases; StpA only controlled sigma38 levels at mid-exponential phase when it prevented inappropriate activation of sigma38 during rapid bacterial growth. In contrast, StpA only activated the CRP-cAMP regulon during late exponential phase.
2009-10-28 | GSE18428 | GEO
Project description:StpA is a paralogue of the nucleoid associated protein H-NS that is conserved in a range of enteric bacteria and had no known function in Salmonella enterica serovar Typhimurium. Here, we show that 5% of the Salmonella genome is regulated by StpA, which contrasts with the situation in Escherichia coli where deletion of stpA only had minor effects on gene expression. The StpA-dependent genes of S. Typhimurium are a specific subset of the H-NS regulon that are predominantly under the positive control of sigma38 (RpoS), CRP-cAMP and PhoP. The regulatory role of StpA varied at different growth phases; StpA only controlled sigma38 levels at mid-exponential phase when it prevented inappropriate activation of sigma38 during rapid bacterial growth. In contrast, StpA only activated the CRP-cAMP regulon during late exponential phase. To test the hypothesis that stpA prevents Sigma38-dependent transcription during mid-exponential growth in S. Typhimurium, we analysed the effect of the stpA deletion on transcription in the presence and absence of rpoS. Three biological replicates were performed for each strain. For this study, we used Salmonella genomic DNA as the comparator which also acted as the control for spot quality.
2010-06-20 | E-GEOD-18428 | biostudies-arrayexpress
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: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: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