Mobile DNA is replete with hotspots for the de novo emergence of gene regulation

Abstract

ABSTRACTDNA mutations that create new gene expression are important raw materials for Darwinian evolution. One potential source of new gene regulation is mobile DNA, which can sometimes drive the expression of genes near its insertion site in a genome through outward-directed promoters. However, we do not know how frequent this ability is, nor how frequently mobile DNA may evolve such promotersde novo. Here we address these questions for the insertion sequence family IS3, the most abundant family of a simple form of prokaryotic mobile DNA. First, we estimate that at least 30% of IS3 sequences harbor outward-directed promoters. Second, we combine high-throughput mutagenesis with a massively parallel reporter assay to show that single point mutations suffice to create outward-directed promoters in all the IS3 sequences we studied. We found that in 5.6% of 18’607 mutant IS3 sequences, promoter activity emerged de novo. Promoters preferentially arise at emergence hotspots in each IS3 sequence. These hotspots overlap with promoter motifs that already exist or are newly created by mutation. One common route to promoter activity is gaining a -10 box downstream of an existing -35 box, which we call “Shiko Emergence.” Overall, we show that mobile DNA has a high latent potential to drive new gene expression. This makes mobile DNA ideal for domestication by its host organism. It also raises intriguing questions about how this potential has evolved.