An in-silico study of alphaherpesviruses ICP0 genes: positive selection or strong mutational GC-pressure?
The purpose of our work was to analyze the case of the strong mutational GC-pressure influence on the ratio between nonsynonymous (DN) and synonymous (DS) distances (DN/DS ratio). We have used as the material the genes coding for ICP0 from five completely sequenced genomes of simplexviruses. DN/DS ratio, total GC-content (G + C), and GC-content in first, second, and third codon positions (1GC, 2GC, and 3GC, respectively) have been calculated separately for exon 2, nonconserved part of exon 3, and conserved part of exon 3 from ICP0 genes. Results showed that DN is more than DS only in the conserved part of exon 3 of ICP0 genes from cercopithecine herpesvirus 2 and cercopithecine herpesvirus 16. However, the cause of this result (DN/DS = 2.54) is the GC-pressure acting on the coding districts with 3GC = 99% rather than the biological process called positive selection. Only in these two viruses, because of the strong GC-pressure, 3GC has reached 99% in the conserved part of ICP0 exon 3, and so nucleotide substitutions that increase the GC-content practically cannot occur in third codon positions, where most substitutions are synonymous. In this case, GC-pressure has a substrate for nucleotide substitutions only in first and second codon positions, where most substitutions are nonsynonymous.
Khrustalev
Vladislav Victorovich
VV
Department of General Chemistry, Belarussian State Medical University, Minsk, Belarus. vvkhrustalev@mail.ru
Barkovsky
Eugene Victorovich
EV
D000465:Algorithms; D018138:Alphaherpesvirinae / Q000235:genetics*; D000595:Amino Acid Sequence; D003062:Codon; D019295:Computational Biology; D004252:DNA Mutational Analysis; D019143:Evolution, Molecular; D005091:Exons; D017874:Immediate-Early Proteins / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009154:Mutation; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D044767:Ubiquitin-Protein Ligases / Q000235:genetics*; D014764:Viral Proteins / Q000235:genetics*
D003062:Codon; D017874:Immediate-Early Proteins; D014764:Viral Proteins; C095533:gene 63 protein, Equine herpesvirus 1; D044767:Ubiquitin-Protein Ligases; C051804:Vmw110 protein, Human herpesvirus 1