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Distribution and evolution of sequence characteristics in the E. coli genome
Journal of Biomolecular Structure & Dynamics
|October 1, 1986
Summary
DNA sequences in E. coli show distinct guanine-cytosine (G + C) content biases in coding versus noncoding regions. These biases, influenced by replication and mutation, affect neighbor frequencies and codon usage.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Published DNA sequences (10% of E. coli genome) were analyzed for guanine-cytosine (G + C) composition.
- High-resolution melting data provided a reference for overall DNA distribution.
Purpose of the Study:
- To investigate variations in G + C content and base-pair neighbor frequencies across different genomic regions.
- To understand the influence of replication, repair, and mutation on DNA sequence characteristics.
- To explore the relationship between inherent neighbor biases and codon usage adaptation.
Main Methods:
- Analysis of published DNA sequences for mean (G + C) composition and standard deviation.
- Comparison of sequence composition with high-resolution melting data.
- Neighbor frequency analysis to identify biases in base-pair combinations.
- Examination of G + C content variations in coding and noncoding regions.
Main Results:
- Mean (G + C) composition (51.0%) agrees well with high-resolution melting data.
- Significant differences in G + C content observed between coding (53%) and noncoding (46%) regions.
- Variance in G + C content is six-fold greater in noncoding regions compared to coding regions.
- Strong negative dependence of variance on G + C content, with A-T and G-C pairs showing neighbor preferences.
- Extreme positive biases in AA, TT, GC, and CG dinucleotides, particularly in noncoding regions.
- Evidence of inherent biases in neighbor frequencies during replication/repair influencing mutation.
- Codon usage bias is partly explained by adaptation to preserve these neighbor biases.
Conclusions:
- Genomic DNA sequences exhibit regional variations in G + C content and base-pair neighbor preferences.
- Replication, repair, and mutation processes impose inherent biases on DNA sequence composition.
- Codon usage in E. coli is influenced by selection acting to maintain these underlying neighbor biases.
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