Thermophilic Adaptation of a Minimal Hammerhead Ribozyme Comes with a Functional Penalty

Life has adapted to extreme environments, such as elevated pH, extreme temperatures, and environments with a lack of oxygen. The biomolecules made by organisms that live in extreme environments must adapt to remain folded and functional. Recent computational studies have shown that rRNA, tRNA, and certain mRNAs adapt in thermophilic organisms through an increased GC content. However, few previous studies have assessed the efficiency of adapted thermophilic RNAs. The work presented herein uses minimal hammerhead ribozymes as a model system to determine the effects of high-temperature adaptation, through increased GC base pairing in the ribozyme secondary structure. Two hammerhead ribozymes were designed based upon the minimal hammerhead 16 (HH16) ribozyme, a well-characterized model system. The mesophilic ribozyme has a moderate GC content (44%) in stems I, II, and III, while the thermophilic ribozyme has nearly double the GC content (76%) in those same stems. Both ribozymes share a conserved catalytic core and loop. Thermal denaturation experiments show that the model thermophilic ribozyme is more thermostable with a higher single (cooperative) melting temperature than the model mesophilic ribozyme. However, thermostability is accompanied by a functional penalty. While at certain temperatures, the thermophilic ribozyme reaches the lower observed rates of the mesophilic ribozyme, the thermophilic ribozyme never reaches the same maximal rate of catalysis as the mesophilic ribozyme.