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

Jacques Demongeot1, Hervé Seligmann2,3

  • 1Laboratory AGEIS EA 7407, Team Tools for E-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecoms4Health, Faculty of Medicine, Université Grenoble Alpes, 38700, La Tronche, France.

Journal of Molecular Evolution
|January 8, 2020
PubMed
Summary
This summary is machine-generated.

The natural circular code, comprising specific codon sets (X0, X1, X2), evolved from ancient RNA rings. Selection for non-redundant overlap coding in nucleotide sequences led to the modern genetic code.

Keywords:
Comma-free codeOverlap codingOverprintingPunctuation codeSelf-correcting codes

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Area of Science:

  • Genetics
  • Molecular Biology
  • Bioinformatics

Background:

  • The natural circular code involves specific codon overrepresentations (X0, X1, X2) across different reading frames.
  • Theoretical minimal RNA rings suggest an evolutionary transition from X1 bias in ancient rings to X0 bias in recent ones.

Purpose of the Study:

  • To investigate the biases for X0, X1, and X2 in nucleotide sequences across various genetic codes.
  • To explore the evolutionary origins and selection pressures that shaped the natural circular code.

Main Methods:

  • Analysis of biases for X0, X1, and X2 in non-redundant nucleotide tetra- and pentamers.
  • Comparison of codon biases across different genetic codes, including nuclear and mitochondrial codes.

Main Results:

  • Biases for X0 are observed in nucleotide pentamers, with stronger prevalence in nuclear genetic codes compared to mitochondrial codes.
  • Conversely, X1 biases show opposite tendencies, being more pronounced in mitochondrial codes.
  • Evidence suggests X1 emerged in ancient single-stranded protogenomes, while X0 evolved later with double-stranded genomes.

Conclusions:

  • Selection for non-redundant overlap coding in short nucleotide sequences was a key driver in the formation of the natural circular code.
  • The evolution of the circular code reflects a shift from single-stranded to double-stranded genomes and changes in replication mechanisms.