Intermolecular epistasis shaped the function and evolution of an ancient transcription factor and its DNA binding sites

Abstract

Complexes of specifically interacting molecules, such as transcription factor proteins (TFs) and the DNA response elements (REs) they recognize, control most biological processes, but little is known concerning the functional and evolutionary effects of epistatic interactions across molecular interfaces. We experimentally characterized all combinations of genotypes in the joint protein-DNA sequence space defined by an historical transition in TF-RE specificity that occurred some 500 million years ago in the DNA-binding domain of an ancient steroid hormone receptor. We found that rampant epistasis within and between the two molecules was essential to specific TF-RE recognition and to the evolution of a novel TF-RE complex with unique derived specificity. Permissive and restrictive epistatic mutations across the TF-RE interface opened and closed potential evolutionary paths accessible by the other, making the evolution of each molecule contingent on its partner's history and allowing a molecular complex with novel specificity to evolve.DOI: http://dx.doi.org/10.7554/eLife.07864.001

Distal substitutions drive divergent DNA specificity among paralogous transcription factors through subdivision of conformational space

“…In this case, enhancement of nGRE-binding ability in the GR lineage and the loss of nGRE-binding ability in the MR and AncSR3 lineages were critical for development of divergent DNA specificity. Both computational and directed evolution studies have implicated epistasis as a primary factor in molecular evolution (34,35), and studies of historical protein divergence have established a major role for epistasis in specific cases (28,(36)(37)(38)(39)(40)(41).…”

Resurrecting ancestral structural dynamics of an antiviral immune receptor: adaptive binding pocket reorganization repeatedly shifts RNA preference

“…Previous studies of slow-evolving receptors have revealed instances in which, after a functional shift, subsequent “restrictive” substitutions can occur that prevent the direct reversal of receptor preference [9, 90–92]. However, when we introduced the “reverse” TEE47∆EK substitution into the derived ancMDA5/LGP2a (ancMDA5/LGP2a TEE47∆EK ), we observed a complete reversion to the ancestral ancRLR function, in which blunt-ended and 5′ppp dsRNAs are bound with equal affinity ( p  > 0.13; Fig.…”

Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations

“…Various mechanisms were proposed, including protein-ligand or protein-DNA binding [25,37,38••], protein conformation [33,39], and allostery [40]. However, protein stability appears to be the most prevalent mechanism of intramolecular epistasis [7,41••,42,43].…”

“…Some describe it as rampant [38] and pervasive [55], or even consider it a determining factor of the molecular evolution [22,56], whereas others view it as less important [57,58]. We return to the discussion of prevalence and mechanisms of epistasis later, after introducing the theoretical foundation of protein biophysics-population genetics mapping.…”