ASYMMETRIC SUBSTITUTION PATTERNS IN THE 2 DNA STRANDS OF BACTERIA

Analyses of the genomes of three prokaryotes, Escherichia coli, Bacill us subtilis, and Haemophilus influenzae, revealed a new type of genomi c compartmentalization of base frequencies. There was a departure from intrastrand equifrequency between A and T or between C and G, showing that the substitution patterns of the two strands of DNA were asymmet ric. The positions of the boundaries between these compartments were f ound to coincide with the origin and terminus of chromosome replicatio n, and there were more A-T and C-G deviations in intergenic regions an d third codon positions, suggesting that a mutational bias was respons ible for this asymmetry. The strand asymmetry was found to be due to a difference in base compositions of transcripts in the leading and lag ging strands. This difference is sufficient to affect codon usage, but it is small compared to the effects of gene expressivity and amino-ac id composition.