The probability of nonsense mutation caused by replication-associated mutational pressure is much higher for bacterial genes from lagging than from leading strands.
We studied nucleotide usage biases in 4-fold degenerated sites of all the genes from leading and lagging strands of 30 bacterial genomes. The level of guanine in 4-fold degenerated sites (G4f) is significantly lower in genes from lagging strands than in genes from leading strands, probably because of the faster rates of guanine oxidation in single-stranded DNA leading to G to T transversions. The rates of cytosine deamination causing C to T transitions are also higher in lagging strands. We showed that the level of codons able to form stop-codons by the way of G to T transversions and C to T transitions is always higher than the level of codons able to form stop-codons by the way of C to A transversions and G to A transitions. This circumstance can be an explanation of the lower percent of ORFs in lagging strands of bacterial replichores than in leading strands.
Khrustalev
Vladislav Victorovich
VV
Department of General Chemistry, Belarussian State Medical University, Minsk, Dzerzinskogo, Belarus. vvkhrustalev@mail.ru
Barkovsky
Eugene Victorovich
EV
D001482:Base Composition / Q000235:genetics; D016000:Cluster Analysis; D003062:Codon / Q000235:genetics; D018389:Codon, Nonsense / Q000235:genetics*; D004261:DNA Replication / Q000235:genetics / Q000502:physiology*; D004277:DNA, Single-Stranded / Q000096:biosynthesis / Q000235:genetics*; D005798:Genes, Bacterial / Q000235:genetics* / Q000502:physiology; D006147:Guanine / Q000378:metabolism; D010084:Oxidation-Reduction; D010802:Phylogeny
D003062:Codon; D018389:Codon, Nonsense; D004277:DNA, Single-Stranded; D006147:Guanine