A single rare s70 variant establishes a unique gene expression pattern in the E. coli pathobiont LF82

Authors: ARROYO - MENDOZA, MELISSA - National Institute Of Diabetes And Digestive And Kidney Diseases; PROCTOR, ALEXANDRA - Iowa State University; CORREA-MEDINA, ABRAHAM - National Institute Of Diabetes And Digestive And Kidney Diseases; DEWOLF, SARAH - Iowa State University; Wymore Brand, Meghan; ROSA, VIRGINIA - National Institute Of Diabetes And Digestive And Kidney Diseases; LORENZI, HERNAN - National Institute Of Diabetes And Digestive And Kidney Diseases; WANNEMUEHLER, MICHAEL - National Institute Of Diabetes And Digestive And Kidney Diseases; PHILLIPS, GREGORY - Iowa State University; HINTON, DEBORAH - Iowa State University

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/16/2024
Publication Date: 9/11/2024
Citation: Arroyo - Mendoza, M., Proctor, A., Correa-Medina, A., Dewolf, S., Wymore Brand, M.J., Rosa, V., Lorenzi, H., Wannemuehler, M.J., Phillips, G.J., Hinton, D.M. 2024. A single rare s70 variant establishes a unique gene expression pattern in the E. coli pathobiont LF82. Nucleic Acids Research. https://doi.org/10.1093/nar/gkae773.
DOI: https://doi.org/10.1093/nar/gkae773

Interpretive Summary: The microbial population of the gastrointestinal tract, the gut microbiota, is associated with many gastrointestinal and non-gastrointestinal diseases. Inflammatory bowel disease is a severe chronic inflammatory gastrointestinal disorder in humans with a complex etiology, including contributions from the microbiota. A specific type of E. coli, adherent invasive E. coli (AIEC), have been associated with inflammatory bowel disease, but it is unknown how AIEC are genetically different from human intestinal nonpathogenic E. coli and what genes determine AIEC pathogenicity. This study investigated a genetic change (single nucleotide polymorphism) discovered in part of an E.coli RNA polymerase that controls bacterial gene expression. This genetic change resulted in alterations in gene expression and impacted characteristics of pathogenic bacteria including biofilm formation and antibiotic resistance. This genetic change may be contributing to the pathogenicity of AIEC in inflammatory bowel disease. Additionally, genetic changes in bacterial RNA polymerases may be an underappreciated mechanism for the emergence of new strains of pathogenic bacteria such as AIEC.

Technical Abstract: 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 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 -14 G: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.