The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes

Asymmetries in base composition between the leading and the lagging strands have been observed previously in many prokaryotic genomes. Since a majorit y of genes is encoded on the leading strand in these genomes, previous anal yses have not been able to determine the relative contribution to the base composition skews of replication processes and transcriptional and/or trans lational forces. Using qualitative graphical presentations and quantitative statistical analyses (analysis of variance), we have found that a signific ant proportion of the GC and AT skews can be attributed to replication orie ntation, i.e., the sequence of a gene is influenced by whether it is encode d on the leading or lagging strand. This effect of replication orientation on skews is independent of, and can be opposite in sign to, the effects of transcriptional or translational processes, such as selection for codon usa ge, amino acid preferences, expression levels (inferred from codon adaptati on index), or potential short signal sequences (e.g., chi sequences). Mutat ional differences between the leading and the lagging strands are the most likely explanation for a significant proportion of the base composition ske w in these bacterial genomes. The finding that base composition skews due t o replication orientation are independent of those due to selection for fun ction of the encoded protein may complicate the interpretation of phylogene tic relationships, conserved positions in nucleotide or amino acid sequence alignments, and codon usage patterns.