An in-silico study of alphaherpesviruses ICP0 genes: Positive selection or strong mutational GC-pressure?

Authors

  • Vladislav Victorovich Khrustalev,

    Corresponding author
    1. Department of General Chemistry, Belarussian State Medical University, Minsk, Belarus
    • 7-24 Communisticheskaya Street, Minsk 220029, Belarus. Tel/Fax: 80172845957
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    • Tel/Fax: 80172845957.

  • Eugene Victorovich Barkovsky

    1. Department of General Chemistry, Belarussian State Medical University, Minsk, Belarus
    Current affiliation:
    1. 57-100 Chervyakova Street, Minsk 220022, Belarus
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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. © 2008 IUBMB IUBMB Life, 60(7): 456–460, 2008

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