Transcriptomic analysis to reveal the impact of small RNAs synthesized from within uxuR on gene expression in E. coli.

The aim was to study the influence of potential small RNAs synthesized from within the uxuR gene coding for a regulator of hexuronate metabolism on gene expression in Escherichia coli. For this purpose, RNA was isolated and sequenced from the wild type E. coli MG1655 and its derivatives with deleted uxuR gene and with deleted translation start for UxuR. In the latter case no UxuR synthesis was detected but promoters coding for regulatory RNAs were present. Cultures were grown with D-glucose or with D-glucuronate, the main intermediate of the Ashwell pathway which is regulated by UxuR. The results clearly show that small RNAs from within the uxuR coding region play an independent role affecting transcription of genes coding for proteins related to flagellar assembly and chemotaxis.