GSE125110
Complete genome sequence of Escherichia coli C - old model organism with a new application in biofilm research
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. Overall design: Total RNA was extracted from a five days old slide biofilms which were transferred to a fresh LB Miller broth daily. As planktonic cells we used cells detached from the biofilm from the last, 5th day passage.  Planktonic (control) or biofilm (experiment)