The ribosome as a missing link in prebiotic evolution II: Ribosomes encode ribosomal proteins that bind to common regions of their own mRNAs and rRNAs

Abstract

We have proposed that the ribosome may represent a missing link between prebiotic chemistries and the first cells. One of the predictions that follows from this hypothesis, which we test here, is that ribosomal RNA (rRNA) must have encoded the proteins necessary for ribosomal function. In other words, the rRNA also functioned pre-biotically as mRNA. Since these ribosome-binding proteins (rb-proteins) must bind to the rRNA, but the rRNA also functioned as mRNA, it follows that rb-proteins should bind to their own mRNA as well. This hypothesis can be contrasted to a "null" hypothesis in which rb-proteins evolved independently of the rRNA sequences and therefore there should be no necessary similarity between the rRNA to which rb-proteins bind and the mRNA that encodes the rb-protein. Five types of evidence reported here support the plausibility of the hypothesis that the mRNA encoding rb-proteins evolved from rRNA: (1) the ubiquity of rb-protein binding to their own mRNAs and autogenous control of their own translation; (2) the higher-than-expected incidence of Arginine-rich modules associated with RNA binding that occurs in rRNA-encoded proteins; (3) the fact that rRNA-binding regions of rb-proteins are homologous to their mRNA binding regions; (4) the higher than expected incidence of rb-protein sequences encoded in rRNA that are of a high degree of homology to their mRNA as compared with a random selection of other proteins; and (5) rRNA in modern prokaryotes and eukaryotes encodes functional proteins. None of these results can be explained by the null hypothesis that assumes independent evolution of rRNA and the mRNAs encoding ribosomal proteins. Also noteworthy is that very few proteins bind their own mRNAs that are not associated with ribosome function. Further tests of the hypothesis are suggested: (1) experimental testing of whether rRNA-encoded proteins bind to rRNA at their coding sites; (2) whether tRNA synthetases, which are also known to bind to their own mRNAs, are encoded by the tRNA sequences themselves; (3) and the prediction that archaeal and prokaryotic (DNA-based) genomes were built around rRNA "genes" so that rRNA-related sequences will be found to make up an unexpectedly high proportion of these genomes.

Self-Referential Encoding on Modules of Anticodon Pairs—Roots of the Biological Flow System

“…Ribosomal proteins belong to the category of Intrinsically Disordered [35], which is a character of the early encodings in the SRM. Recent studies have even detected the possibility of ribosomal proteins being coded for by ribosomal RNA [87], extending and updating our older propositions [84,85] on tRNA-rRNA homologies that are consistent also with [95].…”

“…Our approach is centered on the elements proper to the encoding / decoding machinery -tRNAs and their anticodons, synthetases and amino acids, considering the strings of codons later developments, either enchained triplets derived from pre-encoded tRNAs [84][85][86][87][88] or exogenous strings that acquired the ability of being translated through evolutionary adjustments. Such strings and the decoding machinery would have coevolved with focus on e. g. speed while maintaining accuracy in translation, in a process that might have not preserved the details of the process of encoding.…”

Evolution of Nucleotide Punctuation Marks: From Structural to Linear Signals

“…Translation by ribosomes is complex and was probably absent at molecular evolution’s first steps (Baranov et al, 2009; Root-Bernstein and Root-Bernstein, 2015, 2016). Hence proteins were probably first produced by ribosome-free systems, such as non-ribosomal peptide synthesis (Roy and Ibba, 2010; Chen Y. et al, 2016).…”

Self-Referential Encoding on Modules of Anticodon Pairs—Roots of the Biological Flow System

“…Our approach is centered on the elements proper to the encoding / decoding machinery -tRNAs and their anticodons, synthetases and amino acids, considering the strings of codons later developments, either enchained triplets derived from pre-encoded tRNAs [99][100][101][102][103] or exogenous strings that acquired the ability of being translated through evolutionary adjustments. Such strings and the decoding machinery would have coevolved with focus on e. g. speed while maintaining accuracy in translation, in a process that might have not preserved the details of the process of encoding.…”