Abstract
Circular codes represent a form of coding allowing detection/correction of frame-shift errors. Building on recent theoretical advances on circular codes, we provide evidence that protein coding sequences exhibit in-frame circular code marks, that are absent in introns and are intimately linked to the keto-amino transformation of codon bases. These properties strongly correlate with translation speed, codon influence and protein synthesis levels. Strikingly, circular code marks are absent at the beginning of coding sequences, but stably occur 40 codons after the initiator codon, hinting at the translation elongation process. Finally, we use the lens of circular codes to show that codon influence on translation correlates with the strong-weak dichotomy of the first two bases of the codon. The results can lead to defining new universal tools for sequence indicators and sequence optimization for bioinformatics and biotechnological applications, and can shed light on the molecular mechanisms behind the decoding process.
Highlights
Circular codes represent a form of coding allowing detection/correction of frame-shift errors
We have shown that circular codes theory provides a new and powerful key to understanding the influence of codon bias on gene expression
There are recurring properties, linking the coverage inside equivalence classes with the set of transformations of the codons of the codes. These properties strongly correlate with translation speed, codon influence and protein synthesis level
Summary
Circular codes represent a form of coding allowing detection/correction of frame-shift errors. To explore whether the universal ranking property shown above, is valid out of frame, we extended the analysis of the coverage of circular codes to the three reading frames of coding sequences for 25 well-annotated eukaryotic species (Table 3 of the Supplementary Information).
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