The impact of RNA structure on coding sequence evolution in both bacteria and eukaryotes

Wanjun Gu, Musheng Li, Yuming Xu, Ting Wang, Jae Hong Ko, Tong Zhou

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


Background: Many studies have found functional RNA secondary structures are selectively conserved among species. But, the effect of RNA structure selection on coding sequence evolution remains unknown. To address this problem, we systematically investigated the relationship between nucleotide conservation level and its structural sensitivity in four model organisms, Escherichia coli, yeast, fly, and mouse. Results: We define structurally sensitive sites as those with putative local structure-disruptive mutations. Using both the Mantel-Haenszel procedure and association test, we found structurally sensitive nucleotide sites evolved more slowly than non-sensitive sites in all four organisms. Furthermore, we observed that this association is more obvious in highly expressed genes and region near the start codon. Conclusion: We conclude that structurally sensitive sites in mRNA sequences normally have less nucleotide divergence in all species we analyzed. This study extends our understanding of the impact of RNA structure on coding sequence evolution, and is helpful to the development of a codon model with RNA structure information.

Original languageEnglish (US)
Article number87
JournalBMC Evolutionary Biology
Issue number1
StatePublished - Apr 23 2014


  • Codon usage bias
  • Gene expression
  • Purifying selection
  • Synonymous mutation
  • Translation initiation
  • mRNA structure

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics


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