Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure.
BACKGROUND
Codon usage and codon-pair context are important gene primary structure features that influence mRNA decoding fidelity. In order to identify general rules that shape codon-pair context and minimize mRNA decoding error, we have carried out a large scale comparative codon-pair context analysis of 119 fully sequenced genomes.


RESULTS
We have developed mathematical and software tools for large scale comparative codon-pair context analysis. These methodologies unveiled general and species specific codon-pair context rules that govern evolution of mRNAs in the 3 domains of life. We show that evolution of bacterial and archeal mRNA primary structure is mainly dependent on constraints imposed by the translational machinery, while in eukaryotes DNA methylation and tri-nucleotide repeats impose strong biases on codon-pair context.


CONCLUSIONS
The data highlight fundamental differences between prokaryotic and eukaryotic mRNA decoding rules, which are partially independent of codon usage.
Moura
Gabriela
G
Department of Biology, Center for Environmental and Marine Studies, University of Aveiro, Aveiro, Portugal.
Pinheiro
Miguel
M
Arrais
Joel
J
Gomes
Ana Cristina
AC
Carreto
Laura
L
Freitas
Adelaide
A
Oliveira
José L
JL
Santos
Manuel A S
MA
D003062:Codon; D019143:Evolution, Molecular; D016366:Open Reading Frames; D019642:RNA, Archaeal / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics*