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.
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.
Yamagishi
Kazuo
K
Research and Education Center for Genetic Information, Nara Institute of Science and Technology, Ikoma, Japan.
Oshima
Taku
T
Masuda
Yasushi
Y
Ara
Takeshi
T
Kanaya
Shigehiko
S
Mori
Hirotada
H
D001483:Base Sequence; D018387:Codon, Initiator; D017124:Conserved Sequence; D018900:Dinucleotide Repeats; D004926:Escherichia coli / Q000235:genetics*; D023061:Gene Order; D014176:Protein Biosynthesis
D018387:Codon, Initiator