Global importance of RNA secondary structures in protein-coding sequences

Abstract

Motivation: The protein‐coding sequences of messenger RNAs are the linear template for translation of the gene sequence into protein. Nevertheless, the RNA can also form secondary structures by intramolecular base‐pairing. Results: We show that the nucleotide distribution within codons is biased in all taxa of life on a global scale. Thereby, RNA secondary structures that require base‐pairing between the position 1 of a codon with the position 1 of an opposing codon (here named RNA secondary structure class c1) are under‐represented. We conclude that this bias may result from the co‐evolution of codon sequence and mRNA secondary structure, suggesting that RNA secondary structures are generally important in protein‐coding regions of mRNAs. The above result also implies that codon position 2 has a smaller influence on the amino acid choice than codon position 1. Supplementary information: Supplementary data are available at Bioinformatics online.