A single rare sigma 70 variant establishes a different gene expression pattern in the E.coli pathobiont LF82

LF82, an adherent invasive Escherichia coli (AIEC) pathobiont, is associated with Crohn’s disease, an inflammatory bowel disease of unknown etiology. No genetic features have been identified that distinguish AIEC strains, such as LF82, from “commensal” or pathogenic E. coli. We investigated an extremely rare single nucleotide polymorphism (SNP) within the highly conserved rpoD gene, encoding sigma70 [primary sigma factor, RNA polymerase (RNAP)]. We demonstrate that sigma70 D445V results in transcriptome and phenotypic changes consistent with LF82 phenotypes, including increased biofilm formation and antibiotic resistance. The position of D445V within RNAP is predicted to affect spacer interaction; in vitro transcriptions reveal that the variant increases transcription from several promoters with a 16 bp spacer and a -14G:C. Our work demonstrates that a single SNP within the bacterial primary sigma can lead to myriad gene expression changes/ new phenotypes and suggests an underrecognized mechanism by which pathobionts and other strain variants can emerge. To investigate the effect of a rare mutation found in the sigma 70 of E. coli LF82, isogenic LF82 WT and rpoD V445D mutant were created. Gene expresion profilling analysis was performed using the data that was obtained from the RNA-seq of the isogenic pairs that were grown in triplicate. Comparative gene expression profilling analysis of the RNA-seq data for the LF82 isogenic pairs and E.coli MG1655 isogenic pairs (WT and rpoD D445V mutant) grown at 37o C was performed Comparative gene expression profilling analysis of the RNA-seq data for the LF82 isogenic pairs and E.coli MG1655 isogenic pairs (WT and rpoD D445V mutant , GEO: GSE222248, Bioproject: PRJNA918682) grown at 37o C was performed