Sense and antisense RNA products of the gene can affect motility and chemotaxis acting independent of the UxuR protein.

Small non-coding and antisense RNAs are widespread in all kingdoms of life, however, the diversity of their functions in bacteria is largely unknown. Here, we study RNAs synthesised from divergent promoters located in the 3'-end of the gene, encoding transcription factor regulating hexuronate metabolism in These overlapping promoters were predicted with rather high scores, effectively bound RNA polymerase and and were capable of initiating transcription in sense and antisense directions. The genome-wide correlation between promoter scores and RNA polymerase binding and was higher for promoters located on the antisense strands of the genes, however, sense promoters within the gene were more active. Both regulatory RNAs synthesised from the divergent promoters inhibited expression of genes associated with the motility and chemotaxis independent of a carbon source on which bacteria had been grown. Direct effects of these RNAs were confirmed for the gene encoding σ subunit of RNA polymerase. In addition to intracellular sRNAs, promoters located within the gene could initiate synthesis of transcripts found in the fraction of RNAs secreted in the extracellular medium. Their profile was also carbon-independent suggesting that intragenic transcripts have a specific regulatory role not directly related to the function of the protein in which gene they are encoded.