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 journalArticle

5 Citations (Scopus)

Abstract

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
Volume14
Issue number1
DOIs
StatePublished - Apr 23 2014

Fingerprint

eukaryote
eukaryotic cells
RNA
bacterium
nucleotides
bacteria
start codon
secondary structure
organisms
codons
yeast
mutation
divergence
yeasts
Escherichia coli
gene
mice
genes
testing
organism

Keywords

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

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics

Cite this

The impact of RNA structure on coding sequence evolution in both bacteria and eukaryotes. / Gu, Wanjun; Li, Musheng; Xu, Yuming; Wang, Ting; Ko, Jae Hong; Zhou, Tong.

In: BMC Evolutionary Biology, Vol. 14, No. 1, 87, 23.04.2014.

Research output: Contribution to journalArticle

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AU - Zhou, Tong

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