The Fitness Landscapes of cis-Acting Binding Sites in Different Promoter and Environmental Contexts

The biophysical nature of the interaction between a transcription factor and its target sequences in vitro is sufficiently well understood to allow for the effects of DNA sequence alterations on affinity to be predicted. But even in relatively simple in vivo systems, the complexities of promoter organization and activity have made it difficult to predict how altering specific interactions between a transcription factor and DNA will affect promoter output. To better understand this, we measured the relative fitness of nearly all Escherichia coli [Image: see text] [Image: see text] binding sites in different promoter and environmental contexts by competing four randomized [Image: see text] promoter libraries controlling the expression of the tetracycline resistance gene (tet) against each other in increasing concentrations of drug. We sequenced populations after competition to determine the relative enrichment of each −35 sequence. We observed a consistent relationship between the frequency of recovery of each −35 binding site and its predicted affinity for [Image: see text] that varied depending on the sequence context of the promoter and drug concentration. Overall the relative fitness of each promoter could be predicted by a simple thermodynamic model of transcriptional regulation, in which the rate of transcriptional initiation (and hence fitness) is dependent upon the overall stability of the initiation complex, which in turn is dependent upon the energetic contributions of all sites within the complex. As implied by this model, a decrease in the free energy of association at one site could be compensated for by an increase in the binding energy at another to produce a similar output. Furthermore, these data show that a large and continuous range of transcriptional outputs can be accessed by merely changing the [Image: see text], suggesting that evolved or engineered mutations at this site could allow for subtle and precise control over gene expression.