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Theoretical minimal RNA rings designed according to coding constraints mimic deamination gradients

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Abstract

Deaminations (A->G, C->T) increase with DNA singlestrandedness during replication, presumably creating spontaneous genomic mutational and nucleotide frequency gradients. Alternatively, genes are positioned to avoid deaminations. Deamination gradients affect directly mitogene third codon positions; conserved vertebrate mitochondrial tRNA and protein coding gene arrangements minimize deaminations in anticodons, and first and second codon positions in mitogenes. Here we describe deamination gradients across theoretical minimal RNA rings, 22 nucleotide-long RNAs designed to simulate prebiotic RNAs. These RNA rings code for a start/stop codon and a single codon for each amino acid, and form stem-loop hairpins slowing degradation. They resemble consensus tRNAs, defining potential anticodons and cognate amino acids. Theoretical minimal RNA rings are not designed to include deamination gradients, yet deamination gradients occur in RNA rings. tRNA homology produces stronger evidence for deamination gradients than RNA ring homology defined by coding properties. Deamination gradients start at predicted RNA ring anticodons, corresponding to known homologies between mitochondrial tRNAs and replication origins, and between bacterial tRNA synthetases and mitochondrial DNA polymerase gamma. Deamination gradients are strongest for RNA rings with predicted anticodons matching cognate amino acids that integrated early the genetic code. Presumably protections against deaminations evolved while amino acids integrated the genetic code. Results confirm tRNA-RNA ring homologies. Coding constraints defining RNA rings presumably produce deamination gradients starting at predicted anticodons. Hence, the universal genetic code determines nucleotide deamination gradients in theoretical minimal RNA rings, suggesting adaptation to prevent consequences of deamination mutations. Results also indicate that the genetic code’s structure determined evolution of tRNAs, their cognates, tRNA synthetases, and polymerases.

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Authors and Affiliations

  1. Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, Université Grenoble Alpes, 38700, La Tronche, France

    Jacques Demongeot

  2. The National Natural History Collections, The Hebrew University of Jerusalem, IL-91904, Jerusalem, Israel

    Hervé Seligmann

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  1. Jacques Demongeot
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  2. Hervé Seligmann
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Correspondence to Hervé Seligmann.

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Communicated by: Matthias Waltert

This article is dedicated to the memory of Manfred Eigen, an immense pioneer in the field of theoretical biology of evolution.

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Demongeot, J., Seligmann, H. Theoretical minimal RNA rings designed according to coding constraints mimic deamination gradients. Sci Nat 106, 44 (2019). https://doi.org/10.1007/s00114-019-1638-5

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