Thermal adaptation of mRNA secondary structure: stability versus lability

Significance We demonstrate that the free energy change that occurs during folding of the secondary structures (ΔGfold) of messenger RNAs (mRNAs) for cytosolic malate dehydrogenase varies significantly with evolutionary adaption temperature in marine mollusks. These adaptive changes in ΔGfold confer a physiologically important balance between stability and lability of secondary structure. This balance likely is of key importance in ensuring that the many functions of mRNA that depend on reversible changes in secondary structure can be conducted effectively at different species’ normal body temperatures. Synonymous changes in guanine + cytosine (G+C) content are the primary driver of adaptive change in ΔGfold; these G+C adaptations can confer appropriate stability on the mRNAs without altering stability or function of the proteins they encode. Macromolecular function commonly involves rapidly reversible alterations in three-dimensional structure (conformation). To allow these essential conformational changes, macromolecules must possess higher order structures that are appropriately balanced between rigidity and flexibility. Because of the low stabilization free energies (marginal stabilities) of macromolecule conformations, temperature changes have strong effects on conformation and, thereby, on function. As is well known for proteins, during evolution, temperature-adaptive changes in sequence foster retention of optimal marginal stability at a species’ normal physiological temperatures. Here, we extend this type of analysis to messenger RNAs (mRNAs), a class of macromolecules for which the stability–lability balance has not been elucidated. We employ in silico methods to determine secondary structures and estimate changes in free energy of folding (ΔGfold) for 25 orthologous mRNAs that encode the enzyme cytosolic malate dehydrogenase in marine mollusks with adaptation temperatures spanning an almost 60 °C range. The change in free energy that occurs during formation of the ensemble of mRNA secondary structures is significantly correlated with adaptation temperature: ΔGfold values are all negative and their absolute values increase with adaptation temperature. A principal mechanism underlying these adaptations is a significant increase in synonymous guanine + cytosine substitutions with increasing temperature. These findings open up an avenue of exploration in molecular evolution and raise interesting questions about the interaction between temperature-adaptive changes in mRNA sequence and in the proteins they encode.