Project description:Here, we investigated the impact of Stx2 phage carriage on Escherichia coli (E. coli) K-12 MG1655 host gene expression. Using quantitative RNA-seq analysis, we compared the transcriptome of naïve MG1655 and the lysogens carrying the Stx2 phage of the 2011 E. coli O104:H4 outbreak strain or of the E. coli O157:H7 strain PA8, which share high degree of sequence similarity.
Project description:PdeL is a transcription regulator and c-di-GMP specific phosphodiesterase in Escherichia coli. To address the transcription regulator function of PdeL we analyzed the transcriptomes of four E. coli K12 strains during the exponential growth phase by RNA-sequencing. These four strains included (1) wild-type E. coli K12 strain BW30270 carrying an empty vector control plasmid, (2) an isogenic pdeL deletion mutant carrying the control plasmid, as well as the pdeL mutant that was complemented with (3) a plasmid carrying pdeL under control of the IPTG-inducible tac promoter or (4) a plasmid encoding a fusion protein of the PdeL’s DNA-binding domain and the C-terminal dimerization domain of phage Lambda cI repressor (PdeL-DBD_cI-C). Expression of plasmid-encoded pdeL and pdeL-DBD_cI-C, respectively, was induced by addition of IPTG for 15 minutes prior to RNA isolation. Analyses of the RNA-seq data revealed that plasmid-provided PdeL (and PdeL-DBD_cI-C) repress transcription of class II flagellar genes and presumably regulate the transcription of additional loci, while only little differences were observed between the transcriptomes of wild-type strain BW30270 and its isogenic pdeL mutant.
2020-07-31 | GSE136273 | GEO
Project description:Transcriptome of knockout strain Escherichia coli C600
Project description:Escherichia coli strain C is the last of five E. coli strains (C, K12, B, W, Crooks) designated as safe for laboratory purposes whose genome has not been sequenced. We found that E. coli C forms more robust biofilms than the other four laboratory strains. Here we present the complete genomic sequence of this strain in which we utilized high resolution optical mapping to confirm a large inversion in comparison to other strains. DNA sequence comparison revealed the absence of several genes involved in biofilm formation, such as antigen 43, waaSBOJYZUL for LPS synthesis, and cpsB for curli synthesis. The main difference affecting biofilm formation is the presence of an IS3-like insertion sequence in front of the carbon storage regulator csrA gene. This insertion is located 86 bp upstream of the csrA start codon inside the -35 region of P4 promoter and blocks the transcription from the sigma32 and sigma70 promoters P1-P3 located further upstream. Analysis of gene expression profiles in planktonic and biofilm attached cells by the RNAseq method allows better understanding of this regulatory pathway in E. coli.
