The emergence and evolution of gene expression in genome regions replete with regulatory motifs

Gene regulation is essential for life and controlled by regulatory DNA. Mutations can modify the activity of regulatory DNA, and also create new regulatory DNA, a process called regulatory emergence. Non-regulatory and regulatory DNA contain motifs to which transcription factors may bind. Prokaryotic gene expression requires a stretch of regulatory DNA called a promoter, which contains two promoter motifs called -10 and -35 boxes. However, these motifs may occur in both promoters and non-regulatory DNA in multiple copies. It is possible that these motifs influence both the evolution and emergence of regulatory DNA, but this has never been thoroughly tested. To understand whether and how promoter motifs influence promoter emergence and evolution, we start from 25 DNA sequences enriched with -10 and -35 box motifs (promoter islands), mutagenize the sequences, and measure gene expression driven by 240’000 mutants. We find that the probability that mutations create an active promoter varies more than 200-fold, but is not correlated with the number of promoter motifs. In most mutants (∼67%), the weakening, strengthening, or emergence of a promoter is caused by mutations that modify already existing motifs. Notably, creating new motifs can either increase or decrease promoter activity. Our work demonstrates how promoter motifs influence promoter emergence and evolution. It has implications for predicting and understanding regulatory evolution, de-novo genes, and phenotypic evolution.