Limited specificity of molecular interactions incurs an environment-dependent fitness cost in bacteria

Reliable operation of cellular programs depends crucially on the specificity of biomolecular interactions. In gene regulatory networks, the appropriate expression of genes is determined through the specific binding of transcription factors (TFs) to their cognate DNA sequences. However, the large genomic background likely contains many DNA sequences showing similarity to TF target motifs, potentially allowing for substantial non-cognate TF binding with low specificity. Whether and how non-cognate TF binding impacts cellular function and fitness remains unclear. We show that increased expression of different transcriptional regulators in Escherichia coli and Salmonella enterica can significantly inhibit population growth across multiple environments. This effect depends upon (i) TF binding to a large number of DNA sequences with low specificity, (ii) TF cooperativity, and (iii) the ratio of TF to DNA. DNA binding due to the limited specificity of promiscuous or non-native TFs can thus severely impact fitness, giving rise to a fundamental biophysical constraint on gene regulatory design and evolution.