Comparisons between small ribosomal RNA and theoretical minimal RNA ring secondary structures confirm phylogenetic and structural accretion histories

Abstract

Ribosomal RnAs are complex structures that presumably evolved by tRnA accretions. Statistical properties of tRnA secondary structures correlate with genetic code integration orders of their cognate amino acids. Ribosomal RnA secondary structures resemble those of tRnAs with recent cognates. Hence, rRNAs presumably evolved from ancestral tRNAs. Here, analyses compare secondary structure subcomponents of small ribosomal RnA subunits with secondary structures of theoretical minimal RNA rings, presumed proto-tRNAs. Two independent methods determined different accretion orders of rRNA structural subelements: (a) classical comparative homology and phylogenetic reconstruction, and (b) a structural hypothesis assuming an inverted onion ring growth where the three-dimensional ribosome's core is most ancient and peripheral elements most recent. comparisons between (a) and (b) accretions orders with RnA ring secondary structure scales show that recent rRnA subelements are: 1. more like RNA rings with recent cognates, indicating ongoing coevolution between tRNA and rRNA secondary structures; 2. less similar to theoretical minimal RNA rings with ancient cognates. Our method fits (a) and (b) in all examined organisms, more with (a) than (b). Results stress the need to integrate independent methods. theoretical minimal RnA rings are potential evolutionary references for any sequence-based evolutionary analyses, independent of the focal data from that study. Ribosomes presumably evolved through serial accretions of tRNAs and tRNA-like RNAs 1-11. The ribosomal dimeric RNA core surrounding the peptide synthesis site 12-14 also resembles tRNA dimers linked by complementary anticodons, according to the self-referential hypothesis on the origin of translation 15-19. Evidence for this process exists also in modern vertebrate mitochondrial ribosomes: regular mitochondrial tRNAs constitutively fulfill 5S rRNA functions 20,21. In the latter case, extreme mitogenome reduction perhaps reversed evolution to a tRNA-insertion stage, enabling further mitogenome reduction. These evidences suggest that rRNAs derived from tRNAs.

Further Characterization of the Pseudo-Symmetrical Ribosomal Region

“…On the other hand, despite discordant visions [ 15 , 16 ] there is a widely accepted hypothesis that assumes that the ribosome is a molecular fossil whose structure recapitulates its history and states that the most ancient part of it is represented by the PTC and the ribonucleotides that delineate it [ 9 , 10 , 11 , 12 , 13 , 14 ]. By assuming this scenario, we classified Mg 2+ ions that interact with the SymR in three classes that might say something about the relative time in which these interactions were established.…”

“…The most widely accepted hypothesis on the evolution of the ribosome states that the most ancient part of it is represented by the PTC and the ribonucleotides that delineate it [ 9 , 10 , 11 , 12 , 13 , 14 ]. Alternative views suggest that components of the small subunit evolved earlier than the PTC [ 15 ] or that the rRNA evolved by accretion from preexisting tRNA-like molecules [ 16 ].…”

Theoretical minimal RNA rings mimick molecular evolution before tRNA-mediated translation: codon-amino acid affinities increase from early to late RNA rings

“…However, this system actually mimicks unexpectedly numerous and complex properties of the genetic code [96,98], tRNAs [43], protein coding genes [99,100], their proteins [101] and of replication origins [102]. This RNA ring system enables to recover probable evolutionary scenarios of tRNAs and rRNAs [101,[103][104][105][106][107][108], and the assignment of AUG as universal initiation codon [109]. The design of RNA rings implies that the genetic code pre-existed the emergence of RNA rings.…”

SARS-CoV-2 and miRNA-like inhibition power

“…Moreover, RNA viruses can also form complexes with existing mRNAs and/or proteins of host cells. Thereby they might prevent protein function, behave like microRNAs [3] , [4] , [5] , [6] or ribosomal RNAs [6] , [7] , [8] , inhibiting or favoring the translation of specific proteins of host cells [9] , [10] , [11] , [12] , [13] , [14] , [15] , [16] , [17] . If these proteins are vital for the host, viral pathogenicity is much greater than that caused by viral replication.…”