title: Conservation of translation initiation sites based on dinucleotide frequency and codon usage in Escherichia coli K-12 (W3110): non-random distribution of A/T-rich sequences immediately upstream of the translation initiation codon.
abstract: Dinucleotide frequencies are useful for characterizing consensus elements as a minimum unit of nucleotide sequence because the neighborhood relations of nucleotide sequences are reflected in dinucleotides. Using a consensus score based on dinucleotide frequencies and intra-species codon usage heterogeneity, denoted by the Z1 parameter, we report the relationship between nucleotide conservation at the translation initiation sites of genes in the Escherichia coli K-12 genome (W3110) and codon usage in its downstream genes. Significant positive correlations were obtained in three regions centered at -13, -4, and +7, which correspond to the Shine-Dalgarno element, the A + T element immediately upstream of the translation initiation site, and the downstream box, respectively.
authors.affiliation: Research and Education Center for Genetic Information, Nara Institute of Science and Technology, Ikoma, Japan.
authors.forename: Kazuo
authors.initials: K
authors.lastname: Yamagishi
authors.forename: Taku
authors.initials: T
authors.lastname: Oshima
authors.forename: Yasushi
authors.initials: Y
authors.lastname: Masuda
authors.forename: Takeshi
authors.initials: T
authors.lastname: Ara
authors.forename: Shigehiko
authors.initials: S
authors.lastname: Kanaya
authors.forename: Hirotada
authors.initials: H
authors.lastname: Mori
mesh_terms: D001483:Base Sequence; D018387:Codon, Initiator; D017124:Conserved Sequence; D018900:Dinucleotide Repeats; D004926:Escherichia coli / Q000235:genetics*; D023061:Gene Order; D014176:Protein Biosynthesis
chemical_list: D018387:Codon, Initiator