A parallel computation revealing the role of the in vivo environment in shaping the catalytic structure of a mitochondrial RNA transcript

Abstract

We study the search for folded structures performed by an RNA molecule as it is being assembled by sequential incorporation of nucleotides. The specific process we shall focus on is the transcription of intron 4 of the yeast apocytochrome b gene. We prove that the structure generated by sequential folding is endowed with catalytic potential. More specifically, the formation of all conserved interactions in the catalytic core and intramolecular splicing substrate may be achieved by sequential folding in vivo, concurrent with transcription itself. We base our analysis on a parallel Monte Carlo simulation, assigning an individual processor to each competing folding pathway. In this way, we show that the group I mitochondrial intron requires an in vivo environment to aid the folding into a structure presenting the catalytically-active helix P7 and the splicing substrate upon which the catalytic core exerts its function. It is inferred that a base pair disruption caused by interaction with a ribosome is required to bias the folding pathway so that helix P7 is formed. Furthermore, it is shown that a disruption in the early stages of transcription, followed by the perturbation described is essential to shape the 3' splicing site. Our study suggests that pre-mRNAs of group I might achieve catalytic potential in a fundamentally different way from ribosomal RNAs of the same group, where thermodynamics appear to control the formation of the catalytic structural motif. The role of the trans-acting factor, on the other hand, cannot be recovered in vitro by recombination with the transcript.