Template switching in DNA replication can create and maintain RNA hairpins

Abstract

The evolutionary origin of ribonucleic acid (RNA) stem structures and the preservation of their base-pairing under a spontaneous and random mutation process have puzzled theoretical evolutionary biologists. DNA replication-related template switching is a mutation mechanism that creates reverse-complement copies of sequence regions within a genome by replicating briefly either along the complementary or nascent DNA strand. Depending on the relative positions and context of the four switch points, this process may produce a reverse-complement repeat capable of forming the stem of a perfect DNA hairpin, or fix the base-pairing of an existing stem. Template switching is typically thought to trigger large structural changes and its possible role in the origin and evolution of RNA genes has not been studied. Here we show that the reconstructed ancestral history of ribosomal RNA sequences contains compensatory base substitutions that are linked with parallel sequence changes consistent with the DNA replication-related template switching. In addition to compensatory mutations, the mechanism can explain complex changes involving non-Watson-Crick pairing and appearances of novel stem structures, though mutations breaking the structure rarely get fixed in evolution. Our results suggest a solution for the longstanding dilemma of RNA gene evolution and demonstrate how template switching can both create perfect stem structures with a single mutation event and maintain their base pairing over time with matching changes. The mechanism can also generate parallel sequence changes, many inexplicable under the point mutation model, and provides an explanation for the asymmetric base-pair frequencies in stem structures.