Footprints of a Singular 22-Nucleotide RNA Ring at the Origin of Life

Abstract

(1) Background: Previous experimental observations and theoretical hypotheses have been providing insight into a hypothetical world where an RNA hairpin or ring may have debuted as the primary informational and functional molecule. We propose a model revisiting the architecture of RNA-peptide interactions at the origin of life through the evolutionary dynamics of RNA populations. (2) Methods: By performing a step-by-step computation of the smallest possible hairpin/ring RNA sequences compatible with building up a variety of peptides of the primitive network, we inferred the sequence of a singular docosameric RNA molecule, we call the ALPHA sequence. Then, we searched for any relics of the peptides made from ALPHA in sequences deposited in the different public databases. (3) Results: Sequence matching between ALPHA and sequences from organisms among the earliest forms of life on Earth were found at high statistical relevance. We hypothesize that the frequency of appearance of relics from ALPHA sequence in present genomes has a functional necessity. (4) Conclusions: Given the fitness of ALPHA as a supportive sequence of the framework of all existing theories, and the evolution of Archaea and giant viruses, it is anticipated that the unique properties of this singular archetypal ALPHA sequence should prove useful as a model matrix for future applications, ranging from synthetic biology to DNA computing.

mRNA COVID-19 Vaccines—Facts and Hypotheses on Fragmentation and Encapsulation

“…An example of the existence of accumulation of small RNA fragments exists in Sclerotinia sclerotiorum infected with the SsHV2-L virus, and these small RNAs derived from the virus measure approximately 22 nt, the same length as the miRs, suggesting a cleavage by a protein Dicer-like [ 51 ]. Regarding SARS-CoV-2, such an influence on protein translation has already been described [ 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 ], causing observed effects on the concentration of certain proteins, such as a dramatic decrease in hemoglobin [ 66 , 67 , 68 , 69 ]. If we assume that short RNA subsequences (about 20 nucleotides long), from the genes of the SARS-CoV-2 virus, can bind to Argonaut proteins and hybridize the mRNA of key human proteins, involved in metabolisms important as oxygen metabolism, it follows that recombinations, mutations and/or deletions observed in the SARS-CoV-2 genome (such as those which appeared in the United Kingdom, South Africa, France, etc., or spontaneously in vitro [ 70 , 71 , 72 , 73 , 74 , 75 , 76 , 77 ]) can reinforce the possible existence of RNA fragments, possibly capable of hybridizing for example the mRNA of subunits of hemoglobin, the gamma-globin ( Figure 6 ) and the beta-globin ( Figure 7 ), impacting the oxygen transport in infected patients.…”

Primitive Oligomeric RNAs at the Origins of Life on Earth

“…The major criticisms that can be made to our approach are three-fold: (i) the proposed structure is too small in size to be functional, but recent works show that very small RNAs of size 12 nt can have an important function, such as being able to modulate the microRNA from which they derive [59], (ii) the experimental testing of the creation of peptide structures by small RNAs can be performed [60,61], and it has already been carried out in the case of two amino acids on an RNA template [62,63] and could be generalized in the near future, and (iii) the proteins conformations alone could be at the origin of the fitness ruling the first steps of evolution, but they are also concerned by the underlying information of the nucleotide sequence of their genes, which allows the choice among sequences having similar shape abilities of enzymatic catalysis for their substrates. The sequence which imposes itself among those realizing a given functional form could the one which resembles the original sequences.…”

Complete Quantum Information in the DNA Genetic Code

“…This prompted the authors of [21,22] to propose a model of the genetic code and its degeneracy distribution based on a boolean number system and/or a tessera code. See also [23] about the ribosomal translation and [24,25] about the hypothesis that life on earth and the genetic code evolved around tRNA and the corresponding anticodons.…”