Quantitative analysis of Escherichia coli sigma factor alleles wildtype rpoS, rpoS819 and rpoS92 transcriptomes in stationary-phase (16 hours)

The goal of this study was to compare system level changes in gene-expression in naturally isolated alleles of stationary-phase sigma factor rpoS and two variants of it isolated during evolution under prolonged stationary-phase. We show that while rpoS819 was an attenuated form of wild type rpoS, rpoS92 partially reverses rpoS819 expression compensating rpoS819. Two biological replicates for each strain were grown in Lysogeny Broth culture for sixteen hours and further processed for RNASeq sample preparation. Total RNA was isolated using Trizol method and treated with DNase to remove any genomic DNA contamination. Finally, total RNA was depleted of ribosomal RNA using Microbe express kit from Ambion.