Nucleotide composition affects codon usage toward the 3'-end

Autoři: Fouad Zahdeh aff001;  Liran Carmel aff001
Působiště autorů: Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel aff001;  Hereditary Research Lab, Life Sciences Department, Bethlehem University, Bethlehem, Palestinian authority aff002
Vyšlo v časopise: PLoS ONE 14(12)
Kategorie: Research Article


The 3’-end of the coding sequence in several species is known to show specific codon usage bias. Several factors have been suggested to underlie this phenomenon, including selection against translation efficiency, selection for translation accuracy, and selection against RNA folding. All are supported by some evidence, but there is no general agreement as to which factors are the main determinants. Nor is it known how universal this phenomenon is, and whether the same factors explain it in different species. To answer these questions, we developed a measure that quantifies the codon usage bias at the gene end, and used it to compute this bias for 91 species that span the three domains of life. In addition, we characterized the codons in each species by features that allow discrimination between the different factors. Combining all these data, we were able to show that there is a universal trend to favor AT-rich codons toward the gene end. Moreover, we suggest that this trend is explained by avoidance from forming RNA secondary structures around the stop codon, which may interfere with normal translation termination.

Klíčová slova:

Eukaryota – Gene expression – Messenger RNA – Prokaryotic cells – Protein translation – RNA structure – Transfer RNA – Translation termination


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