Pressure modulates the self-cleavage step of the hairpin ribozyme

Abstract

The ability of certain RNAs, denoted as ribozymes, to not only store genetic information but also catalyse chemical reactions gave support to the RNA world hypothesis as a putative step in the development of early life on Earth. This, however, might have evolved under extreme environmental conditions, including the deep sea with pressures in the kbar regime. Here we study pressure-induced effects on the self-cleavage of hairpin ribozyme by following structural changes in real-time. Our results suggest that compression of the ribozyme leads to an accelerated transesterification reaction, being the self-cleavage step, although the overall process is retarded in the high-pressure regime. The results reveal that favourable interactions between the reaction site and neighbouring nucleobases are strengthened under pressure, resulting therefore in an accelerated self-cleavage step upon compression. These results suggest that properly engineered ribozymes may also act as piezophilic biocatalysts in addition to their hitherto known properties.

Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme

“…31;32 The hairpin has been studied intensively by a wide variety of experimental and calculational methods. 16;23;24;33–44 NMR structural models of the isolated loops have been determined, as have numerous crystal structures of the docked form. 7;45–53 The docking of ribozyme loops A and B is accompanied by dramatic structural rearrangements of both loops (Figure 2).…”

Ribozyme Chemistry: To Be or Not To Be under High Pressure

“…The two main chemical steps correspond to the nucleophilic attack and the departure of the leaving group. Figure 1: Reaction mechanism of ribozyme self-cleaving cent catalytic studies of hammerhead, 70,71 hairpin, 72 glmS, 73,74 HDV, 75 VS, 76 twister, 77,78 pistol, 79 and twister-sister. 80 Although the chemical reaction is the same in all self-cleaving ribozymes (Figure 1), the reaction mechanisms differ at the atomic scale due to the presence of specific catalysts and cofactors in the surroundings of the active site.…”

“…Besides, their investigation provides some information about the influence of pressure on the different steps of the reaction, confirming that the chemical cleavage step is significantly accelerated by pressure although the entire reaction is negatively affected. 72,212 The higher rate of self-cleavage is conferred by a more favorable in-line configuration associated with the H-bonds formed in the active site with the nucleobases G8 and A38 that act as catalysts (Figure 2c and Figure 12). A recent solvation model of the hairpin ribozyme suggests that the high-pressure regime pushes water molecules that penetrate into the interstitial spaces .…”

“…Schuabb et al, (2017)72 on the same ribozyme that, although pressure slows down the overall reaction, it accelerates the catalytic step of transesterification, an observation which is attributed to a local strengthening of interactions between the catalytic site and neighboring nucleobases. Rate constant determinations confirm that it is the docking of loops A and…”

Nucleic Acid Catalysis under Potential Prebiotic Conditions

“…[166,167] However,d espite the overall retardation of the reaction, the actual self-cleavage step is accelerated by hydrostatic pressure and the decrease in rate is attributed to the positive activation volume of docking between catalytic loops. [168] The overall yields of RNA strand cleavage by certain hairpin (HH) ribozymes are improved by high hydrostatic pressure, whichc an even potentiate catalysis in the absence of the Mg 2 + typically requiredf or cleavage under ambient pressure. [169,170] Whilstt he hammerhead (HH) ribozyme also has a positivea ctivation volume associated with at ransitiont oa n active conformation (although significantly smaller than for HP ribozyme), no observable DV is associated with the cleavage reactionitself.…”