title: An in-silico study of alphaherpesviruses ICP0 genes: positive selection or strong mutational GC-pressure?
abstract: 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.
authors.affiliation: Department of General Chemistry, Belarussian State Medical University, Minsk, Belarus. vvkhrustalev@mail.ru
authors.forename: Vladislav Victorovich
authors.initials: VV
authors.lastname: Khrustalev
authors.forename: Eugene Victorovich
authors.initials: EV
authors.lastname: Barkovsky
mesh_terms: 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*
chemical_list: 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