Reconstruction of the rRNA Sequences of LUCA, with Bioinformatic Implication of the Local Similarities Shared by Them

SIMPLE SUMMARY: In order to explore the origin of 16S, 5S, and 23S ribosomal RNAs in novel views and methods, full lengths of the three rRNA sequences of the last universal common ancestor were reconstructed for the first time. Within these sequences, repeat short fragments or local self-similarities were shared. Moreover, these short fragments were conserved, clustered around the functional center of ribosome, and contained nearly all types of functional sites of ribosome. These results indicated a possibility that short fragments may act as component elements or parts of them in the origin of rRNAs, which can be practically tested by simulating experiments in the future. ABSTRACT: The theory of the RNA world, especially with the catalytic capability of RNA, provides a reasonable framework explaining the evolution of molecular genetics system before the scenario of the central dogma. However, it remains a challenge to deduce the origin mechanism of rRNAs. Here we reconstructed the phylogenetic relationships of archaea and bacteria with bootstrap values of most nodes, especially the deep ones, higher than 90%. Based on the well-resolved tree, the full lengths of 16S, 5S, and 23S rRNA sequences of the last universal common ancestor (LUCA) were reconstructed for the first time. The potential similarities shared by the three ancestral rRNA sequences were further explored by searching for repeat short fragments in the level of purine–pyrimidine (RY) with certain lengths and arrangements. With the lengths ranging from 2 to 14, functional short fragments could be found in the three RNAs. As a representative, a set with a total of 75 short fragments of 11 nucleotides in length can recover all types of the known functional sites of ribosomes in a most concise manner. The 75 short fragments cluster around the functional center of the ribosome, among which 18 of them are highly conserved across five or six kingdoms and still contain all types of known functional sites except one. Alternatively, according to the strategy using the level of AUGC instead of RY, a similar pattern can be recovered. Such results indicate the local similarities shared by 16S, 5S, and 23S rRNAs and thus suggest a possible general mechanism in the formation of the LUCA rRNAs.