  Evolutionary trajectories and phenotypic states available to cell populations
are ultimately dictated by intermolecular interactions between DNA, RNA,
proteins, and other molecular species. Here we study how evolution of gene
regulation in a single-cell eukaryote S. cerevisiae is affected by the
interactions between transcription factors (TFs) and their cognate genomic
sites. Our study is informed by high-throughput in vitro measurements of TF-DNA
binding interactions and by a comprehensive collection of genomic binding
sites. Using an evolutionary model for monomorphic populations evolving on a
fitness landscape, we infer fitness as a function of TF-DNA binding energy for
a collection of 12 yeast TFs, and show that the shape of the predicted fitness
functions is in broad agreement with a simple thermodynamic model of two-state
TF-DNA binding. However, the effective temperature of the model is not always
equal to the physical temperature, indicating selection pressures in addition
to biophysical constraints caused by TF-DNA interactions. We find little
statistical support for the fitness landscape in which each position in the
binding site evolves independently, showing that epistasis is common in
evolution of gene regulation. Finally, by correlating TF-DNA binding energies
with biological properties of the sites or the genes they regulate, we are able
to rule out several scenarios of site-specific selection, under which binding
sites of the same TF would experience a spectrum of selection pressures
depending on their position in the genome. These findings argue for the
existence of universal fitness landscapes which shape evolution of all sites
for a given TF, and whose properties are determined in part by the physics of
protein-DNA interactions.
