Promoter Activity Buffering Reduces the Fitness Cost of Misregulation

Organisms regulate gene expression through changes in the activity of transcription factors (TFs). In yeast, the response of genes to changes in TF activity is generally assumed to be encoded in the promoter. To directly test this assumption, we chose 42 genes and, for each, replaced the promoter with a synthetic inducible promoter and measured how protein expression changes as a function of TF activity. Most genes exhibited gene-specific TF dose-response curves not due to differences in mRNA stability, translation, or protein stability. Instead, most genes have an intrinsic ability to buffer the effects of promoter activity. This can be encoded in the open reading frame and the 3′ end of genes and can be implemented by both autoregulatory feedback and by titration of limiting trans regulators. We show experimentally and computationally that, when misexpression of a gene is deleterious, this buffering insulates cells from fitness defects due to misregulation. [Display omitted] •Systematic replacement of native promoters by a constant synthetic inducible promoter•Even when the promoters are identical, each gene has a unique TF dose-response curve•Gene-specific DRCs are not from differences in translation, or mRNA or protein stability•Most genes intrinsically buffer protein levels from changes in promoter activity. Transcription factor binding sites are in promoters. It has therefore been assumed that, in organisms without enhancers, the response of a gene to changes in TF activity is encoded only in the promoter. Using a coupled experimental and mathematical system, Schikora-Tamarit et al. show that this assumption is false.