Transcriptional profiling of an enterotoxigenic E. coli isolate

Ribo-Zero Kits have rapidly established themselves as the method of choice for depleting ribosomal RNA (rRNA) for RNA-Seq studies. Their utility extends to microarray-based analysis of gene expression. Sahl et al. describe the use of RNA-Seq and microarray analysis to study the effects of chemical signaling factors in the pathogenesis of enterotoxigenic Escherichia coli (ETEC). This organism is an important pathogenic variant (pathovar) of E. coli in developing countries and is associated with significant morbidity and mortality rates.

The research focused on providing various stimulants to the cells in culture followed by RNA extraction to measure the up- or down-regulation of the enterotoxins being produced by the cells. The Ribo-Zero Gram-Negative Kit was used to remove rRNA from the total RNA preparations, simplifying data analysis from RNA-Seq libraries and microarray expression analysis. RNA-Seq results demonstrated bile salts regulate many virulence factors; one of the most differentially expressed genes in the presence of bile is a unique plasmid-encoded AraC-like transcriptional regulator (peaR).

The authors conclude: "These results provide transcriptional targets and putative mechanisms to better understand the global regulatory networks and virulence expression in this important human pathogen."

Sahl, J. and Rasko, D. (2012). Analysis of the global transcriptional profiles of enterotoxigenic Escherichia coli (ETEC) isolate E24377A Infection and Immunity DOI: 10.1128/IAI.06138-11