title: A role for codon order in translation dynamics.
abstract: The genetic code is degenerate. Each amino acid is encoded by up to six synonymous codons; the choice between these codons influences gene expression. Here, we show that in coding sequences, once a particular codon has been used, subsequent occurrences of the same amino acid do not use codons randomly, but favor codons that use the same tRNA. The effect is pronounced in rapidly induced genes, involves both frequent and rare codons and diminishes only slowly as a function of the distance between subsequent synonymous codons. Furthermore, we found that in S. cerevisiae codon correlation accelerates translation relative to the translation of synonymous yet anticorrelated sequences. The data suggest that tRNA diffusion away from the ribosome is slower than translation, and that some tRNA channeling takes place at the ribosome. They also establish that the dynamics of translation leave a significant signature at the level of the genome.
authors.affiliation: Institute of Computational Science, ETH Zurich, 8092 Zurich, Switzerland.
authors.forename: Gina
authors.initials: G
authors.lastname: Cannarozzi
authors.forename: Gina
authors.initials: G
authors.lastname: Cannarrozzi
authors.forename: Nicol N
authors.initials: NN
authors.lastname: Schraudolph
authors.forename: Mahamadou
authors.initials: M
authors.lastname: Faty
authors.forename: Peter
authors.initials: P
authors.lastname: von Rohr
authors.forename: Markus T
authors.initials: MT
authors.lastname: Friberg
authors.forename: Alexander C
authors.initials: AC
authors.lastname: Roth
authors.forename: Pedro
authors.initials: P
authors.lastname: Gonnet
authors.forename: Gaston
authors.initials: G
authors.lastname: Gonnet
authors.forename: Yves
authors.initials: Y
authors.lastname: Barral
mesh_terms: D000596:Amino Acids / Q000378:metabolism; D003062:Codon / Q000378:metabolism*; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000378:metabolism; D012343:RNA, Transfer / Q000378:metabolism*; D012270:Ribosomes / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000166:cytology / Q000235:genetics* / Q000378:metabolism
chemical_list: D000596:Amino Acids; D003062:Codon; D012333:RNA, Messenger; D012343:RNA, Transfer