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


CONCLUSIONS
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.
Research Center for Learning Sciences, Southeast University, Nanjing, Jiangsu 210096, China. wanjungu@gmail.com.
Wanjun
W
Gu
Musheng
M
Li
Yuming
Y
Xu
Ting
T
Wang
Jae-Hong
JH
Ko
Tong
T
Zhou
D000818:Animals; D004331:Drosophila melanogaster / Q000737:chemistry / Q000235:genetics*; D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics*; D019143:Evolution, Molecular; D051379:Mice; D009690:Nucleic Acid Conformation; D017433:Protein Structure, Secondary; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics*; D016364:Reading Frames; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000235:genetics*
D012333:RNA, Messenger