title: Codon pair utilization biases influence translational elongation step times.
abstract: Two independent assays capable of measuring the relative in vivo translational step times across a selected codon pair in a growing polypeptide in the bacterium Escherichia coli have been employed to demonstrate that codon pairs observed in protein coding sequences more frequently than predicted (over-represented codon pairs) are translated slower than pairs observed less frequently than expected (under-represented codon pairs). These results are consistent with the findings that translational step times are influenced by codon context and that these context effects are related to the compatabilities of adjacent tRNA isoacceptor molecules on the surface of a translating ribosome. These results also support our previous suggestion that the frequency of one codon next to another has co-evolved with the structure and abundance of tRNA isoacceptors in order to control the rates of translational step times without imposing additional constraints on amino acid sequences or protein structures.
authors.affiliation: Department of Microbiology and Molecular Genetics, College of Medicine, University of California, Irvine 92717, USA.
authors.forename: B
authors.initials: B
authors.lastname: Irwin
authors.forename: J D
authors.initials: JD
authors.lastname: Heck
authors.forename: G W
authors.initials: GW
authors.lastname: Hatfield
mesh_terms: D000595:Amino Acid Sequence; D001482:Base Composition; D003062:Codon; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism*; D005798:Genes, Bacterial; D007700:Kinetics; D008969:Molecular Sequence Data; D009876:Operon; D010441:Peptide Chain Elongation, Translational; D010957:Plasmids; D014176:Protein Biosynthesis; D012345:RNA, Transfer, Amino Acid-Specific / Q000378:metabolism*; D012364:RNA, Transfer, Trp / Q000378:metabolism; D011993:Recombinant Fusion Proteins / Q000096:biosynthesis / Q000378:metabolism; D012270:Ribosomes / Q000378:metabolism; D013045:Species Specificity; D014158:Transcription, Genetic; D014364:Tryptophan / Q000096:biosynthesis; D001616:beta-Galactosidase / Q000096:biosynthesis / Q000378:metabolism
chemical_list: D003062:Codon; D012345:RNA, Transfer, Amino Acid-Specific; D012364:RNA, Transfer, Trp; D011993:Recombinant Fusion Proteins; D014364:Tryptophan; D001616:beta-Galactosidase