title: Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure.
abstract: 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.
authors.affiliation: Department of Biology, Center for Environmental and Marine Studies, University of Aveiro, Aveiro, Portugal.
authors.forename: Gabriela
authors.initials: G
authors.lastname: Moura
authors.forename: Miguel
authors.initials: M
authors.lastname: Pinheiro
authors.forename: Joel
authors.initials: J
authors.lastname: Arrais
authors.forename: Ana Cristina
authors.initials: AC
authors.lastname: Gomes
authors.forename: Laura
authors.initials: L
authors.lastname: Carreto
authors.forename: Adelaide
authors.initials: A
authors.lastname: Freitas
authors.forename: José L
authors.initials: JL
authors.lastname: Oliveira
authors.forename: Manuel A S
authors.initials: MA
authors.lastname: Santos
mesh_terms: D003062:Codon; D019143:Evolution, Molecular; D016366:Open Reading Frames; D019642:RNA, Archaeal / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics*