The Poitiers School of Mathematical and Theoretical Biology: Besson–Gavaudan–Schützenberger’s Conjectures on Genetic Code and RNA Structures

Demongeot, Jacques; Hazgui, Hana

doi:10.1007/s10441-016-9287-y

Cited by 6 publications

(3 citation statements)

References 50 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…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

View full text Add to dashboard Cite

(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.

show abstract

Section: Discussionmentioning

confidence: 82%

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

Demongeot

Henrion‐Caude

2020

Biology

View full text Add to dashboard Cite

show abstract

“…Independently, in parallel, a French team composed of two biologists and one physician-mathematician (J. Besson, P. Gavaudan, and M.P. Schützenberger) worked on the optimality of the genetic code and the existence of primitive RNAs [4] similar to the invariant parts of tRNA loops (see supplementary material in [5]). Unfortunately, Conway’s algorithm did not incorporate realistic genetic considerations in the game that would have made it possible to test, for example, the plausibility of molecular events hypothesized to have led to the appearance of life.…”

Section: Introductionmentioning

confidence: 99%

Emergence of a “Cyclosome” in a Primitive Network Capable of Building “Infinite” Proteins

Demongeot

Norris

2019

Life

View full text Add to dashboard Cite

We argue for the existence of an RNA sequence, called the AL (for ALpha) sequence, which may have played a role at the origin of life; this role entailed the AL sequence helping generate the first peptide assemblies via a primitive network. These peptide assemblies included “infinite” proteins. The AL sequence was constructed on an economy principle as the smallest RNA ring having one representative of each codon’s synonymy class and capable of adopting a non-functional but nevertheless evolutionarily stable hairpin form that resisted denaturation due to environmental changes in pH, hydration, temperature, etc. Long subsequences from the AL ring resemble sequences from tRNAs and 5S rRNAs of numerous species like the proteobacterium, Rhodobacter sphaeroides. Pentameric subsequences from the AL are present more frequently than expected in current genomes, in particular, in genes encoding some of the proteins associated with ribosomes like tRNA synthetases. Such relics may help explain the existence of universal sequences like exon/intron frontier regions, Shine-Dalgarno sequence (present in bacterial and archaeal mRNAs), CRISPR and mitochondrial loop sequences.

show abstract

“…AL has GCC in anticodon position: GCC has already been suggested as the first anticodon, because it "anticodes" for the simplest amino-acid, the glycine 17 AL aligns with the articulation pivot of many tRNAs, AUG, and allows the pairing TGG-ΨCA needed between the D-and Ty-loops for the tRNA folding 18 AL matches well with many viral not coding genomes 29 19 AL matches well with many microRNAs 30 20 AL matches well with IRE and YUNR loops 31 21 AL matches well with many circular RNAs 31 22 AL contains twice all most unexpected dimers as defined by P. Slonimski 32 Table 3. Optimal biochemical properties of the ring AL.…”

mentioning

confidence: 99%