Pentamers with Non-redundant Frames: Bias for Natural Circular Code Codons

Demongeot, Jacques; Seligmann, Hervé

doi:10.1007/s00239-019-09925-0

Cited by 14 publications

(6 citation statements)

References 62 publications

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“…Further studies should experimentally investigate the ring ALPHA as a potential catalyzer of peptide synthesis and search for its role in building after the RNA world, the protein and cell worlds and its role in consolidation of the genetic code, in accordance with previous knowledge in the field [98][99][100][101][102][103][104][105][106][107][108].…”

Section: Discussionmentioning

confidence: 82%

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

Demongeot

Henrion‐Caude

2020

Biology

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(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.

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Section: Discussionmentioning

confidence: 82%

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

Demongeot

Henrion‐Caude

2020

Biology

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“…4. This consists of processes that produced the RNA rings, from the presumably stereochemical determination of codon-amino acid assignments [67], and biases for short pentamers with nonredundant coding across frames [68] which could have accreted into RNA rings. The aim is to understand what makes RNA rings such useful, and perhaps efficient, simulators of prebiotic evolution, independently of the possibility that RNA rings are the actual primordial sequences.…”

Section: Discussionmentioning

confidence: 99%

The primordial tRNA acceptor stem code from theoretical minimal RNA ring clusters

Demongeot

Seligmann

2020

BMC Genet

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Background: Theoretical minimal RNA rings code by design over the shortest length once for each of the 20 amino acids, a start and a stop codon, and form stem-loop hairpins. This defines at most 25 RNA rings of 22 nucleotides. As a group, RNA rings mimick numerous prebiotic and early life biomolecular properties: tRNAs, deamination gradients and replication origins, emergence of codon preferences for the natural circular code, and contents of early protein coding genes. These properties result from the RNA ring's in silico design, based mainly on coding nonredundancy among overlapping translation frames, as the genetic code's codon-amino acid assignments determine. RNA rings resemble ancestral tRNAs, defining RNA ring anticodons and corresponding cognate amino acids. Surprisingly, all examined RNA ring properties coevolve with genetic code integration ranks of RNA ring cognates, as if RNA rings mimick prebiotic and early life evolution. Methods: Distances between RNA rings were calculated using different evolutionary models. Associations between these distances and genetic code evolutionary hypotheses detect evolutionary models best describing RNA ring diversification. Results: Here pseudo-phylogenetic analyses of RNA rings produce clusters corresponding to the primordial code in tRNA acceptor stems, more so when substitution matrices from neutrally evolving pseudogenes are used rather than from functional protein coding genes reflecting selection for conserving amino acid properties. Conclusions: Results indicate RNA rings with recent cognates evolved from those with early cognates. Hence RNA rings, as designed by the genetic code's structure, simulate tRNA stem evolution and prebiotic history along neutral chemistry-driven mutation regimes.

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“…It is unclear how the design of theoretical minimal RNA rings implies complex evolutionary properties such as associations between codon affinity and cognate amino acid hydrophobicity. 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].…”

Section: Discussionmentioning

confidence: 99%