Transcription Attenuation: a Highly Conserved Regulatory Strategy Used by Bacteria

We employed computational analyses to assess the conservation of sequence elements that are believed to be essential for the various transcription-attenuation (termination) mechanisms that are used to regulate expression of families of orthologous genes in bacteria. We searched the upstream sequence of every predicted transcription unit for a transcription attenuator. These were then clustered by the orthology relationships of the nearby structural genes. Many gene families regulated by transcription attenuation were found to be adjacent to a regulatory region that had a binding site for a specific protein, tRNA or small metabolite. Using our methodology, we predict that at least 80 different clusters of orthologous groups (COGs) are significantly regulated by transcription attenuation.