Evolution of intrinsic transcriptional terminators in their genomic context

Abstract

Transcriptional gene expression relies on two fundamental processes - transcription initiation and termination. Transcriptional termination is essential for the coordinated control of gene expression. Intrinsic termination, the major mechanism of transcriptional termination in bacteria, relies on the sequence-dependent folding of nascent mRNA into a hairpin structure that enables RNA polymerase to dissociate from DNA. Despite their central role in regulating expression in prokaryotic genomes, the conservation of intrinsic terminators and the factors that shape their evolution remain poorly understood. Here, we combine comparative genomics with experimental measurements of terminator function, to study the conservation of intrinsic terminators between Escherichia coli and Salmonella enterica subsp. pullorum. While the two species are closely related, the sequence and function of most terminators are not conserved, with less than 20% of all terminators having an identifiable ortholog - in stark contrast to 60% for coding sequences. Terminators with higher sequence conservation also had more conserved function, indicative of stabilizing selection. The local genomic context shapes the evolution of intrinsic terminators, as their sequence conservation is dependent on the conservation of the upstream gene, while their function is affected by the distance to the downstream gene. Ultimately, any theory of gene regulatory network evolution ought to account for how transcriptional terminators evolve.