Project description:Mapping the occupancy of FNR, HNS, and IHF throughout the genome of Escherchia coli MG1655 K-12 using an affinity purified antibody under anerobic growth conditions. We also mapped the binding of the ß subunit of RNA Polymerase under both aerobic and anaerobic growth conditions. As a control, we also performed ChIP-chip on FNR in a ∆fnr mutant strain of Escherchia coli MG1655 K-12. We also examined FNR immunoprecipitation at various FNR concentrations using IPTG and Ptac::fnr (PK8263). The ∆hns/∆stpA strains were also used. Descirbed in the manuscript Genome-scale Analysis of E. coli FNR Reveals the Complexity of Bacterial Regulon Structure
Project description:Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 ∆hns/∆stpA strain from exponental growth under aerobic and anaerobic growth conditions. The results are further described in the article Genome-scale Analysis of E.coli FNR Reveals the Complex Features of Transcrtipion Factor Binding.
Project description:This entry refers to transcriptome analysis of E. coli with single deletions of hns, stpA, hha and ydgT and double deletions of hns with each of the other three regulators mentioned.
Project description:This entry refers to transcriptome analysis of E. coli with single deletions of hns, stpA, hha and ydgT and double deletions of hns with each of the other three regulators mentioned. 8 samples with 2 replicates each
Project description:Bacterial genomes encode in many instances more than one copy of genes coding for global modulators. In the Enterobacteriaceae, cells express the global modulator H-NS and its paralogue StpA. The enteroaggregative E. coli strain 042 encodes, in addition to the hns and stpA genes, an additional hns gene. We used RNA-seq to compare the transcriptome of the wt strain and its hns, hns2 and double hns hns2 derivatives, as well as of an hha null mutant (hhahha2). It is well known that the Hha protein co-modulates gene expression with H-NS. The results obtained have shown that the main role of H-NS2 is to modulate a subset of H-NS modulated genes, those that also are targeted by Hha, which are mainly HGT genes. When compared with H-NS, H-NS2 also shows a differential expression level and a different regulatory pattern.
Project description:The aim of the study was to compare the transcriptome of E. coli K12 MG1655 cells lacking hydroperoxidase (Hpx-) and therefore unable to detoxify hydrogen peroxide, to wild-type cells; both when the Rtc RNA repair system is active and when it is inhibited; at 8 and 24 hpi. A very large number of genes (up to 1/3) were found to be differentially expressed in Hpx- as compared to wild-type. Inhibition of the Rtc system had dramatic effects on Hpx- but not on wild-type.
Project description:The global regulator, H-NS, controls genes related to stress response, biofilm formation, and virulence expression by recognizing the curved DNA and silences gene transcription acquired from lateral gene transfer. Here, we rewired H-NS to control biofilm formation using protein engineering. One H-NS variant, H-NS K57N was obtained to reduce biofilm formation 10-fold compared to H-NS wild-type. Whole-transcriptome analysis (BW25113 hha hns / pCA24N-hns K57N vs. BW25113 hha hns / pCA24N-hns) revealed that H-NS K57N represses biofilm formation through the interactinon with other nucleoid proteins, Cnu and StpA. Remarkably, H-NS K57N enhanced the excision of defective prophage Rac while H-NS wild-type represses it, and H-NS controlled only Rac excision among E. coli prophages. These results imply that the repression of Rac excision is one of the silencing manner for foreign genes by H-NS. Also, the prophage excision not only led to the change of biofilm formation but also resulted in cell lysis through the expression of toxin protein HokD with reduced viability, which are important for cell physiology in response to the change of environmental conditions. Hence, H-NS regulatory system may be evolved easily with specialized functions in terms of biofilm formation, prophage control, and cell lysis.
