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 hetero...

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Bibliographic Details
Published in:DNA research 2002-02, Vol.9 (1), p.19-24
Main Authors: YAMAGISHI, Kazuo, OSHIMA, Taku, MASUDA, Yasushi, ARA, Takeshi, KANAYA, Shigehiko, MORI, Hirotada
Format: Article
Language:English
Subjects:
Bacteriology
Base Sequence
Biological and medical sciences
codon usage
Codon, Initiator
Conserved Sequence
Dinucleotide Repeats
Escherichia coli
Escherichia coli - genetics
Fundamental and applied biological sciences. Psychology
Gene Order
Genes. Genome
Genetics
Microbiology
Molecular and cellular biology
Molecular genetics
Protein Biosynthesis
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Summary: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.
ISSN:1340-2838
1756-1663
DOI:10.1093/dnares/9.1.19