Data from: Epistatic interactions influence terrestrial-marine functional shifts in cetacean rhodopsin

Like many aquatic vertebrates, whales have blue-shifting spectral tuning
substitutions in the dim-light visual pigment, rhodopsin, that are thought
to increase photosensitivity in underwater environments. We have
discovered that known spectral tuning substitutions also have surprising
epistatic effects on another function of rhodopsin, the kinetic rates
associated with light-activated intermediates. By using absorbance
spectroscopy and fluorescence-based retinal release assays on
heterologously expressed rhodopsin, we assessed both spectral and kinetic
differences between cetaceans (killer whale) and terrestrial outgroups
(hippo, bovine). Mutation experiments revealed that killer whale rhodopsin
is unusually resilient to pleiotropic effects on retinal release from key
blue-shifting substitutions (D83N and A292S), largely due to a
surprisingly specific epistatic interaction between D83N and the
background residue, S299. Ancestral sequence reconstruction indicated that
S299 is an ancestral residue that predates the evolution of blue-shifting
substitutions at the origins of Cetacea. Based on these results, we
hypothesize that intramolecular epistasis helped to conserve
rhodopsin's kinetic properties while enabling blue-shifting spectral
tuning substitutions as cetaceans adapted to aquatic environments.
Trade-offs between different aspects of molecular function are rarely
considered in protein evolution, but in cetacean and other vertebrate
rhodopsins, may underlie multiple evolutionary scenarios for the selection
of specific amino acid substitutions.