Asymmetric Substitution Patterns in the Two DNA Strands of Bacteria
Lobry JR
Laboratoire de Biometrie, Unversite Claude Bernard, Villeurbanne, France.
lobry@biomserv.univ-lyon 1.fr
Molecular Biology and Evolution, 13(5):660-665 (May 1996)
Abstract
Analyses of the genomes of three prokaryotes, Escherichia coli, Bacillus subtilis, and
Haemophilus influenzae, revealed a new type of genomic 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
asymmetric. The positions of the boundaries between these compartments were found to
coincide with the origin and terminus of chromosome replication, and there were more A-T
and C-G deviations in intergenic regions and third codon positions, suggesting that a
mutational bias was responsible for this asymmetry. The strand asymmetry was found to be
due to a difference in base compositions of transcripts in the leading and lagging strands.
This difference is sufficient to affect codon usage, but it is small compared to the effects of
gene expressivity and amino-acid composition.
