Toledo-Aparicio, D. | Search bioRxiv

bioRxiv2024

Evolution of intrinsic transcriptional terminators in their genomic context

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.

evolutionary biology↗

bioRxiv2020

Structure and Evolution of Constitutive Bacterial Promoters

Predicting gene expression levels from any DNA sequence is a major challenge in biology. Using libraries with >25,000 random mutants, we developed a biophysical model that accounts for major features of {sigma}70-binding bacterial promoters to accurately predict constitutive gene expression levels of any sequence. We experimentally and theoretically estimated that 10-20% of random sequences lead to expression and 82% of non-expressing sequences are one point mutation away from a functional promoter. Generating expression from random sequences is pervasive, such that selection acts against {sigma}70-RNA polymerase binding sites even within inter-genic, promoter-containing regions. The pervasiveness of {sigma}70- binding sites, which arises from the structural features of promoters captured by our biophysical model, implies that their emergence is unlikely the limiting step in gene regulatory evolution.

evolutionary biology↗