Project description:Directional RNAseq analyses was undertaken in Klebsiella pneumoniae Ecl8 and isogenic mutants Ecl8delta ramA and Ecl8delta ramR to determine the RamA regulon. All samples were grown in Luria Bertani broth until OD600 approx 0.6 prior to RNA extraction. Differential expression was determined using DEseq upon pairwise comparisons of Ecl8 vs Ecl8delta ramA, Ecl8deltaramA vs Ecl8deltaramR, Ecl8 vs Ecl8deltaramR.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Project description:To get a high resolution understanding of the effect of Fur on global gene expression, we compared by high-resolution RNAseq the transcriptomes of a wild-type E. coli K-12 strain and its Fur deletion derivative grown in minimal medium with or without supplementation of iron. Three independent total RNA extraction and RNAseq assays were performed for each strain in each condition.
Project description:Regulation of EHEC gene expression by the gut commensal bacterium B. thetaiotaomicron. EHEC is a human pathogen that colonizes in the colon where B. thetaiotaomicron is a predominant commensal. We used microarrays to evaluate global regulation of EHEC when cultured with B. thetaiotaomicron.
Project description:Investigation of whole genome gene expression level changes in E. coli O103:H25 in co-culture with Bacteroides thetaiotaomicron CCUG 10774 compared to when E. coli is cultured individually.
Project description:Helicobacter pylori encounters a wide range of pH within the human stomach. In a comparison of H. pylori cultured in vitro under neutral or acidic conditions, about 15% of genes are26 differentially expressed, and corresponding changes are detectable for many of the encoded proteins. The ArsRS two-component system (TCS), comprised of the sensor kinase ArsS and its cognate response regulator ArsR, has an important role in mediating pH-responsive changes in H. pylori gene expression. In this study, we sought to delineate the pH-responsive ArsRS regulon and further define the role of ArsR in pH-responsive gene expression. We compared H. pylori strains containing an intact ArsRS system with an arsS null mutant or strains containing site32 specific mutations of a conserved aspartate residue (D52) in ArsR, which is phosphorylated in response to signals relayed by the cognate sensor kinase ArsS. We identified 178 genes that were pH-responsive in strains containing an intact ArsRS system but not in ∆arsS or arsR mutants. These constituents of the pH-responsive ArsRS regulon include genes involved in acid acclimatization (ureAB, amidases), oxidative stress responses (katA, sodB), transcriptional regulation related to iron or nickel homeostasis (fur, nikR), and genes encoding outer membrane proteins [including sabA, alpA, alpB, hopD (labA), and horA]. When comparing H. pylori strains containing an intact ArsRS TCS with arsRS mutants, each cultured at neutral pH, relatively few genes are differentially expressed. Collectively, these data suggest that ArsRS41 mediated gene regulation has an important role in H. pylori adaptation to changing pH conditions.
Project description:The Bradyrhizobium japonicum NtrC regulatory protein influences gene expression in response to changes in intracellular nitrogen status. Under conditions of low nitrogen, phosphorylation of NtrC results in up-regulation of a number of genes involved in nitrogen metabolism and nitrogen acquisition. To better define the exact nature of NtrC’s influence on gene expression, a ntrC mutation was created in B. japonicum and transcriptional profiling was performed by DNA microarray analysis of both the mutant and wild type strains.
Project description:The Bradyrhizobium japonicum NtrC regulatory protein influences gene expression in response to changes in intracellular nitrogen status. Under conditions of low nitrogen, phosphorylation of NtrC results in up-regulation of a number of genes involved in nitrogen metabolism and nitrogen acquisition. To better define the exact nature of NtrC’s influence on gene expression, a ntrC mutation was created in B. japonicum and transcriptional profiling was performed by DNA microarray analysis of both the mutant and wild type strains.
