Composition Bias and Genome Polarity of RNA Viruses

Overview

Journal Virus Res

Specialty Microbiology

Date 2005 Apr 14

PMID 15826910

Citations 25

Authors

Prasert Auewarakul

Affiliations

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Abstract

I have observed a relationship between GC content in coding sequences of RNA viruses and their genome polarity. Positive-stranded RNA viruses have significantly higher GC contents than negative-stranded RNA viruses. Coding sequences of all negative-stranded RNA viruses are biased toward high A in coding strands (high T in genomes), while two distinct patterns were observed among positive-stranded RNA genomes. This finding suggests that RNA viruses with different genome polarity are under different mutational pressure, which may be a consequence of the difference in the strategies of viral genome expression and replication. The GC content directly affects the viral codon adaptation index using highly expressed human genes as the reference set, which may theoretically predict the efficiency of viral gene expression in human cells.

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References

Kanaya S, Yamada Y, Kinouchi M, Kudo Y, Ikemura T . Codon usage and tRNA genes in eukaryotes: correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis. J Mol Evol. 2001; 53(4-5):290-8. DOI: 10.1007/s002390010219. View

Berkhout B, Grigoriev A, Bakker M, Lukashov V . Codon and amino acid usage in retroviral genomes is consistent with virus-specific nucleotide pressure. AIDS Res Hum Retroviruses. 2002; 18(2):133-41. DOI: 10.1089/08892220252779674. View

Cattaneo R, Schmid A, Eschle D, Baczko K, Ter Meulen V, Billeter M . Biased hypermutation and other genetic changes in defective measles viruses in human brain infections. Cell. 1988; 55(2):255-65. PMC: 7126660. DOI: 10.1016/0092-8674(88)90048-7. View

Sharp P, Li W . The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 1987; 15(3):1281-95. PMC: 340524. DOI: 10.1093/nar/15.3.1281. View

Shindo K, Takaori-Kondo A, Kobayashi M, Abudu A, Fukunaga K, Uchiyama T . The enzymatic activity of CEM15/Apobec-3G is essential for the regulation of the infectivity of HIV-1 virion but not a sole determinant of its antiviral activity. J Biol Chem. 2003; 278(45):44412-6. DOI: 10.1074/jbc.C300376200. View

Aota S, Ikemura T . Diversity in G + C content at the third position of codons in vertebrate genes and its cause. Nucleic Acids Res. 1986; 14(16):6345-55. PMC: 311650. DOI: 10.1093/nar/14.16.6345. View

Sueoka N . Directional mutation pressure, mutator mutations, and dynamics of molecular evolution. J Mol Evol. 1993; 37(2):137-53. DOI: 10.1007/BF02407349. View

Ikemura T, Wada K . Evident diversity of codon usage patterns of human genes with respect to chromosome banding patterns and chromosome numbers; relation between nucleotide sequence data and cytogenetic data. Nucleic Acids Res. 1991; 19(16):4333-9. PMC: 328617. DOI: 10.1093/nar/19.16.4333. View

Chen S, Lee W, Hottes A, Shapiro L, McAdams H . Codon usage between genomes is constrained by genome-wide mutational processes. Proc Natl Acad Sci U S A. 2004; 101(10):3480-5. PMC: 373487. DOI: 10.1073/pnas.0307827100. View

10.

Vartanian J, Meyerhans A, Sala M, Wain-Hobson S . G-->A hypermutation of the human immunodeficiency virus type 1 genome: evidence for dCTP pool imbalance during reverse transcription. Proc Natl Acad Sci U S A. 1994; 91(8):3092-6. PMC: 43521. DOI: 10.1073/pnas.91.8.3092. View

11.

Jenkins G, Holmes E . The extent of codon usage bias in human RNA viruses and its evolutionary origin. Virus Res. 2003; 92(1):1-7. DOI: 10.1016/s0168-1702(02)00309-x. View

12.

Mangeat B, Turelli P, Caron G, Friedli M, Perrin L, Trono D . Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts. Nature. 2003; 424(6944):99-103. DOI: 10.1038/nature01709. View

13.

Francino M, Ochman H . Isochores result from mutation not selection. Nature. 1999; 400(6739):30-1. DOI: 10.1038/21804. View

14.

Galinski M, Troy R, Banerjee A . RNA editing in the phosphoprotein gene of the human parainfluenza virus type 3. Virology. 1992; 186(2):543-50. PMC: 7130814. DOI: 10.1016/0042-6822(92)90020-p. View

15.

Haas J, Park E, Seed B . Codon usage limitation in the expression of HIV-1 envelope glycoprotein. Curr Biol. 1996; 6(3):315-24. DOI: 10.1016/s0960-9822(02)00482-7. View

16.

Lobry J, Sueoka N . Asymmetric directional mutation pressures in bacteria. Genome Biol. 2002; 3(10):RESEARCH0058. PMC: 134625. DOI: 10.1186/gb-2002-3-10-research0058. View

17.

Andre S, Seed B, Eberle J, Schraut W, Bultmann A, Haas J . Increased immune response elicited by DNA vaccination with a synthetic gp120 sequence with optimized codon usage. J Virol. 1998; 72(2):1497-503. PMC: 124631. DOI: 10.1128/JVI.72.2.1497-1503.1998. View

18.

Vartanian J, Henry M, Wain-Hobson S . Sustained G-->A hypermutation during reverse transcription of an entire human immunodeficiency virus type 1 strain Vau group O genome. J Gen Virol. 2002; 83(Pt 4):801-805. DOI: 10.1099/0022-1317-83-4-801. View

19.

Polson A, Bass B, Casey J . RNA editing of hepatitis delta virus antigenome by dsRNA-adenosine deaminase. Nature. 1996; 380(6573):454-6. DOI: 10.1038/380454a0. View

20.

Sueoka N . Directional mutation pressure and neutral molecular evolution. Proc Natl Acad Sci U S A. 1988; 85(8):2653-7. PMC: 280056. DOI: 10.1073/pnas.85.8.2653. View