Potential role of the X circular code in the regulation of gene expression

Thompson, Julie; Ripp, Raymond; Mayer, Claudine; Poch, Olivier; Michel, Christian

doi:10.1016/j.biosystems.2021.104368

Cited by 6 publications

(2 citation statements)

References 88 publications

(87 reference statements)

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“…The first coding rule is that X 0 , X 1, and X 2 frames of the circular code distinguish three possible reading frames of the protein-coding sequence since hidden stop codons in X 1 and X 2 prevent off-X 0 -frame protein translation-this procedure is often named ambush hypothesis [53,54], and it is thought to ensure accurate translation.…”

Section: Amino Acid Coding Complementarity and Frameshiftsmentioning

confidence: 99%

Antisense Peptide Technology for Diagnostic Tests and Bioengineering Research

Štambuk

Konjevoda

Pavan

2021

IJMS

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Antisense peptide technology (APT) is based on a useful heuristic algorithm for rational peptide design. It was deduced from empirical observations that peptides consisting of complementary (sense and antisense) amino acids interact with higher probability and affinity than the randomly selected ones. This phenomenon is closely related to the structure of the standard genetic code table, and at the same time, is unrelated to the direction of its codon sequence translation. The concept of complementary peptide interaction is discussed, and its possible applications to diagnostic tests and bioengineering research are summarized. Problems and difficulties that may arise using APT are discussed, and possible solutions are proposed. The methodology was tested on the example of SARS-CoV-2. It is shown that the CABS-dock server accurately predicts the binding of antisense peptides to the SARS-CoV-2 receptor binding domain without requiring predefinition of the binding site. It is concluded that the benefits of APT outweigh the costs of random peptide screening and could lead to considerable savings in time and resources, especially if combined with other computational and immunochemical methods.

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Section: Amino Acid Coding Complementarity and Frameshiftsmentioning

confidence: 99%

Antisense Peptide Technology for Diagnostic Tests and Bioengineering Research

Štambuk

Konjevoda

Pavan

2021

IJMS

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“…The genetic code is a surjective map between the 64 trinucleotides and the 20 amino acids plus 1 stop signal. Thus, there are codons, called synonymous, coding the same (LUCA) (Dila et al 2019); identification of a circular code periodicity (modulo 3) in a large region of the 16 S rRNA including the 3' major domain corresponding to the primordial proto-ribosome decoding centre, containing numerous sites that interact with the tRNA and messenger RNA (mRNA) during translation and surrounding the mRNA channel ; potential role of the circular code X in the regulation of gene expression (Thompson et al 2021); and characterisation of accessory genes in coronavirus genomes using the circular code information .…”

Section: Introductionmentioning

confidence: 99%

Reading Frame Retrieval of Genes: A New Parameter of Codon Usage Based on the Circular Code Theory

Michel

Sereni

2023

Bull Math Biol

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Based on the circular code theory, we define a new function f that quantifies the property of reading frame retrieval (RFR) of genes from their codon usage. This RFR function f is computed on a massive scale in genes of genomes of bacteria, eukaryotes and archaea. By expressing f as a function of the mean number n of codons per gene, a "universal" property is identified, whatever the kingdom: the reading frame retrieval is enhanced in large genes. By investigating this property according to the theory developed, a Spearman's rank correlation with a strong negative coefficient is observed between the codon usage dispersion d (from the uniform codon distribution 1 64 ) and the RFR function f , whatever the kingdom ( p-values < 10 −180 in bacteria, < 10 −61 in eukaryotes and < 10 −159 in archaea). Thus, the reading frame retrieval is enhanced with the codon usage dispersion. Furthermore, this approach identifies a "genome centre" from which emerge two distinct "genome arms": an upper arm and a lower arm, respectively, above and below the linear regression. The RFR function by itself or combined with classical methods (alignment, phylogeny) could also be a new approach to classify the genomes in the future.

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Genes on the circular code alphabet

Michel

2021

Biosystems

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Potential role of the X circular code in the regulation of gene expression

Cited by 6 publications

References 88 publications

Antisense Peptide Technology for Diagnostic Tests and Bioengineering Research

Antisense Peptide Technology for Diagnostic Tests and Bioengineering Research

Reading Frame Retrieval of Genes: A New Parameter of Codon Usage Based on the Circular Code Theory

Genes on the circular code alphabet

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