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Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes
M J McLean1, K H Wolfe, K M Devine
1Department of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland.
Journal of Molecular Evolution
|December 16, 1998
Summary
Genomic base composition skews in prokaryotes reveal insights into DNA replication and mutational biases. Skew patterns at the third codon position primarily reflect mutation, while overall skews can be influenced by gene transcription and replication direction.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Genomic sequences exhibit variations in base composition, including GC and AT content and skew.
- These variations can be influenced by mutational processes and selective pressures.
- Understanding base composition skews provides insights into genome evolution and functional constraints.
Purpose of the Study:
- To investigate variations in GC content, GC skew, and AT skew at third codon positions in prokaryotic genomes.
- To correlate base composition skews with the origin and direction of DNA replication.
- To differentiate between mutational biases and protein-related influences on base composition skews.
Main Methods:
- Analysis of third codon positions in completely sequenced prokaryotic genomes.
- Examination of GC content, GC skew, and AT skew patterns along genomic regions.
- Comparison of skew patterns with the origin and direction of DNA replication.
Main Results:
- Eight out of nine eubacteria showed GC and AT skews changing sign at the replication origin.
- The leading strand was G-T rich at codon position 3 in most eubacteria, but C-T rich in Mycoplasma species.
- Borrelia burgdorferi and Treponema pallidum exhibited significant base composition skews correlated with replication direction.
Conclusions:
- Base composition skews at third codon positions likely indicate mutational biases.
- Skews over all bases can be affected by protein composition and gene transcription-replication direction coupling.
- Different forces shape base composition skews depending on the genomic region and codon position analyzed.