STRAND COMPOSITIONAL ASYMMETRY IN BACTERIAL AND LARGE VIRAL GENOMES

Several bacterial genomes exhibit preference for G over C on the DNA l eading strand extending from tile origin of replication to the ter-reg ion in the genomes of Escherichia coli, Mycoplasma genitalium, Bacillu s subtilis, and marginally in Haemophilus influenzae, Mycoplasma pneum oniae, and Helicobacter pylori, Strand compositional asymmetry is not observed in the cyanobacterium Synechocystis sp. genome nor in the arc haeal genomes of Methanococcus jannaschii, Methanobacterium thermoauto trophicum, and Archaeoglobus fulgidus. A strong strand compositional a symmetry is observed in beta-type but not alpha- or gamma-type human h erpesviruses featuring G > C downstream of oriL and C > G upstream of oriL, Dinucleotide relative abundances (i.e., dinucleotide representat ions normalized by the component nucleotide frequencies) are consonant with respect to the leading and lagging strands, Strand compositional asymmetry may reflect on differences in replication synthesis of the leading versus lagging strand, on differences between template and cod ing strand associated with transcription-coupled repair mechanisms, on differences in gene density between the two strands, on differences i n residue and codon biases in relation to gene function, expression le vel, or operon organization, or on differences in single as context de pendent base mutational rates, The absence of strand asymmetry in the archaeal genomes may reflect the presence of multiple origins of repli cation.