Virologica Sinica

, Volume 27, Issue 5, pp 303–315 | Cite as

Characterization of synonymous codon usage bias in the pseudorabies virus US1 gene

  • Meili Li
  • Zhiyao Zhao
  • Jianhong Chen
  • Bingyun Wang
  • Zi Li
  • Jian Li
  • Mingsheng CaiEmail author
Research Article


In the present study, we examined the codon usage bias between pseudorabies virus (PRV) US1 gene and the US1-like genes of 20 reference alphaherpesviruses. Comparative analysis showed noticeable disparities of the synonymous codon usage bias in the 21 alphaherpesviruses, indicated by codon adaptation index, effective number of codons (ENc) and GC3s value. The codon usage pattern of PRV US1 gene was phylogenetically conserved and similar to that of the US1-like genes of the genus Varicellovirus of alphaherpesvirus, with a strong bias towards the codons with C and G at the third codon position. Cluster analysis of codon usage pattern of PRV US1 gene with its reference alphaherpesviruses demonstrated that the codon usage bias of US1-like genes of 21 alphaherpesviruses had a very close relation with their gene functions. ENc-plot revealed that the genetic heterogeneity in PRV US1 gene and the 20 reference alphaherpesviruses was constrained by G+C content, as well as the gene length. In addition, comparison of codon preferences in the US1 gene of PRV with those of E. coli, yeast and human revealed that there were 50 codons showing distinct usage differences between PRV and yeast, 49 between PRV and human, but 48 between PRV and E. coli. Although there were slightly fewer differences in codon usages between E.coli and PRV, the difference is unlikely to be statistically significant, and experimental studies are necessary to establish the most suitable expression system for PRV US1. In conclusion, these results may improve our understanding of the evolution, pathogenesis and functional studies of PRV, as well as contributing to the area of herpesvirus research or even studies with other viruses.


Pseudorabies virus US1 gene Alphaherpesvirus Codon usage bias 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Advani S J, Weichselbaum R R, Roizman B. 2003. Herpes simplex virus 1 activates cdc2 to recruit topoisomerase II alpha for post-DNA synthesis expression of late genes. Proc Natl Acad Sci U S A, 100:4825–4830.PubMedCrossRefGoogle Scholar
  2. 2.
    Ambagala A P, Cohen J I. 2007. Varicella-Zoster virus IE63, a major viral latency protein, is required to inhibit the alpha interferon-induced antiviral response. J Virol, 81:7844–7851.PubMedCrossRefGoogle Scholar
  3. 3.
    Bastian T W, Livingston C M, Weller S K, et al. 2010. Herpes simplex virus type 1 immediate-early protein ICP22 is required for VICE domain formation during productive viral infection. J Virol, 84:2384–2394.PubMedCrossRefGoogle Scholar
  4. 4.
    Bernardi G. 1986. Compositional constraints and genome evolution. J Mol Evol, 24:1–11.PubMedCrossRefGoogle Scholar
  5. 5.
    Blaisdell B E. 1983. Choice of base at silent codon site 3 is not selectively neutral in eucaryotic structural genes: it maintains excess short runs of weak and strong hydrogen bonding bases. J Mol Evol, 19:226–236.PubMedCrossRefGoogle Scholar
  6. 6.
    Blake R D, Hinds P W. 1984. Analysis of the codon bias in E. coli sequences. J Biomol Struct Dyn, 2:593–606.PubMedCrossRefGoogle Scholar
  7. 7.
    Boelaert F, Deluyker H, Maes D, et al. 1999. Prevalence of herds with young sows seropositive to pseudorabies (Aujeszky’s disease) in northern Belgium. Prev Vet Med, 41:239–255.PubMedCrossRefGoogle Scholar
  8. 8.
    Bowman J J, Orlando J S, Davido D J, et al. 2009. Transient expression of herpes simplex virus type 1 ICP22 represses viral promoter activity and complements the replication of an ICP22 null virus. J Virol, 83:8733–8743.PubMedCrossRefGoogle Scholar
  9. 9.
    Burland T G. 2000. DNASTAR’s Lasergene sequence analysis software. Methods Mol Biol, 132:71–91.PubMedGoogle Scholar
  10. 10.
    Cai M S, Cheng A C, Wang M S, et al. 2009. Characterization of synonymous codon usage bias in the duck plague virus UL35 gene. Intervirology, 52:266–278.PubMedCrossRefGoogle Scholar
  11. 11.
    Cohen J I, Cox E, Pesnicak L, et al. 2004. The varicella-zoster virus open reading frame 63 latency-associated protein is critical for establishment of latency. J Virol, 78:11833–11840.PubMedCrossRefGoogle Scholar
  12. 12.
    Cohen J I, Krogmann T, Bontems S, et al. 2005. Regions of the varicella-zoster virus open reading frame 63 latency-associated protein important for replication in vitro are also critical for efficient establishment of latency. J Virol, 79:5069–5077.PubMedCrossRefGoogle Scholar
  13. 13.
    Comeron J M, Aguade M. 1998. An evaluation of measures of synonymous codon usage bias. J Mol Evol, 47:268–274.PubMedCrossRefGoogle Scholar
  14. 14.
    D’Onofrio G, Ghosh T C, Bernardi G. 2002. The base composition of the genes is correlated with the secondary structures of the encoded proteins. Gene, 300:179–187.PubMedCrossRefGoogle Scholar
  15. 15.
    Dass J F, Sudandiradoss C. 2012. Insight into pattern of codon biasness and nucleotide base usage in serotonin receptor gene family from different mammalian species. Gene, 503:92–100.PubMedCrossRefGoogle Scholar
  16. 16.
    Durand L O, Roizman B. 2008. Role of cdk9 in the optimization of expression of the genes regulated by ICP22 of herpes simplex virus 1. J Virol, 82:10591–10599.PubMedCrossRefGoogle Scholar
  17. 17.
    Duret L. 2002. Evolution of synonymous codon usage in metazoans. Curr Opin Genet Dev, 12:640–649.PubMedCrossRefGoogle Scholar
  18. 18.
    Fu M. 2010. Codon usage bias in herpesvirus. Arch Virol, 155:391–396.PubMedCrossRefGoogle Scholar
  19. 19.
    Gouy M, Gautier C. 1982. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res, 10:7055–7074.PubMedCrossRefGoogle Scholar
  20. 20.
    Grantham R, Gautier C, Gouy M, et al. 1981. Codon catalog usage is a genome strategy modulated for gene expressivity. Nucleic Acids Res, 9:r43–r74.PubMedCrossRefGoogle Scholar
  21. 21.
    Grantham R, Gautier C, Gouy M, et al. 1980. Codon catalog usage and the genome hypothesis. Nucleic Acids Res, 8:r49–r62.PubMedGoogle Scholar
  22. 22.
    Grosjean H, Fiers W. 1982. Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes. Gene, 18:199–209.PubMedCrossRefGoogle Scholar
  23. 23.
    Gupta S K, Ghosh T C. 2001. Gene expressivity is the main factor in dictating the codon usage variation among the genes in Pseudomonas aeruginosa. Gene, 273:63–70.PubMedCrossRefGoogle Scholar
  24. 24.
    Hooper S D, Berg O G. 2000. Gradients in nucleotide and codon usage along Escherichia coli genes. Nucleic Acids Res, 28:3517–3523.PubMedCrossRefGoogle Scholar
  25. 25.
    Hou Z C, Yang N. 2003. Factors affecting codon usage in Yersinia pestis. Acta Bioch Bioph Sin, 35:580–586.Google Scholar
  26. 26.
    Ikemura T. 1985. Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol, 2:13–34.PubMedGoogle Scholar
  27. 27.
    Ikemura T. 1981. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J Mol Biol, 151:389–409.PubMedCrossRefGoogle Scholar
  28. 28.
    Jia R, Cheng A, Wang M, et al. 2009. Analysis of synonymous codon usage in the UL24 gene of duck enteritis virus. Virus Genes, 38:96–103.PubMedCrossRefGoogle Scholar
  29. 29.
    Jiang P, Sun X, Lu Z. 2007. Analysis of synonymous codon usage in Aeropyrum pernix K1 and other Crenarchaeota microorganisms. J Genet Genomics, 34:275–284.PubMedCrossRefGoogle Scholar
  30. 30.
    Jones J O, Arvin A M. 2005. Viral and cellular gene transcription in fibroblasts infected with small plaque mutants of varicella-zoster virus. Antiviral Res, 68:56–65.PubMedCrossRefGoogle Scholar
  31. 31.
    Kalamvoki M, Roizman B. 2011. The histone acetyltransferase CLOCK is an essential component of the herpes simplex virus 1 transcriptome that includes TFIID, ICP4, ICP27, and ICP22. J Virol, 85:9472–9477.PubMedCrossRefGoogle Scholar
  32. 32.
    Koppers-Lalic D, Reits E A, Ressing M E, et al. 2005. Varicelloviruses avoid T cell recognition by UL49.5-mediated inactivation of the transporter associated with antigen processing. Proc Natl Acad Sci U S A, 102:5144–5149.PubMedCrossRefGoogle Scholar
  33. 33.
    Kost R G, Kupinsky H, Straus S E. 1995. Varicella-zoster virus gene 63: transcript mapping and regulatory activity. Virology, 209:218–224.PubMedCrossRefGoogle Scholar
  34. 34.
    Li M L, Wang S, Cai M S, et al. 2011. Characterization of molecular determinants for nucleocytoplasmic shuttling of PRV UL54. Virology, 417:385–393.PubMedCrossRefGoogle Scholar
  35. 35.
    Li M L, Wang S, Cai M S, et al. 2011. Identification of nuclear and nucleolar localization signals of pseudorabies virus (PRV) early protein UL54 reveals that its nuclear targeting is required for efficient production of PRV. J Virol, 85:10239–10251.PubMedCrossRefGoogle Scholar
  36. 36.
    Liu Q, Dou S, Ji Z, et al. 2005. Synonymous codon usage and gene function are strongly related in Oryza sativa. Biosystems, 80:123–131.PubMedCrossRefGoogle Scholar
  37. 37.
    Lobry J R, Gautier C. 1994. Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes. Nucleic Acids Res, 22:3174–3180.PubMedCrossRefGoogle Scholar
  38. 38.
    Lu H, Zhao W M, Zheng Y, et al. 2005. Analysis of synonymous codon usage bias in Chlamydia. Acta Biochim Biophys Sin, 37:1–10.PubMedCrossRefGoogle Scholar
  39. 39.
    Maruyama T, Gojobori T, Aota S, et al. 1986. Codon usage tabulated from the GenBank genetic sequence data. Nucleic Acids Res, 14 Suppl:r151–197.PubMedGoogle Scholar
  40. 40.
    Moriyama E N, Powell J R. 1998. Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli. Nucleic Acids Res, 26:3188–3193.PubMedCrossRefGoogle Scholar
  41. 41.
    Mueller N H, Walters M S, Marcus R A, et al. 2010. Identification of phosphorylated residues on varicella-zoster virus immediate-early protein ORF63. J Gen Virol, 91:1133–1137.PubMedCrossRefGoogle Scholar
  42. 42.
    Muller T, Batza H J, Schluter H, et al. 2003. Eradication of Aujeszky’s disease in Germany. J Vet Med B Infect Dis Vet Public Health, 50:207–213.PubMedCrossRefGoogle Scholar
  43. 43.
    Muller T, Hahn E C, Tottewitz F, et al. 2011. Pseudorabies virus in wild swine: a global perspective. Arch Virol, 156:1691–1705.PubMedCrossRefGoogle Scholar
  44. 44.
    Najafabadi H S, Goodarzi H, Salavati R. 2009. Universal function-specificity of codon usage. Nucleic Acids Res, 37:7014–7023.PubMedCrossRefGoogle Scholar
  45. 45.
    Novembre J A. 2002. Accounting for background nucleotide composition when measuring codon usage bias. Mol Biol Evol, 19:1390–1394.PubMedCrossRefGoogle Scholar
  46. 46.
    Ono E, Amagai K, Yoshino S, et al. 2004. Resistance to pseudorabies virus infection in transformed cell lines expressing a soluble form of porcine herpesvirus entry mediator C. J Gen Virol, 85:173–178.PubMedCrossRefGoogle Scholar
  47. 47.
    Orlando J S, Balliet J W, Kushnir A S, et al. 2006. ICP22 is required for wild-type composition and infectivity of herpes simplex virus type 1 virions. J Virol, 80:9381–9390.PubMedCrossRefGoogle Scholar
  48. 48.
    Pomeranz L E, Reynolds A E, Hengartner C J. 2005. Molecular biology of pseudorabies virus: impact on neurovirology and veterinary medicine. Microbiol Mol Biol Rev, 69:462–500.PubMedCrossRefGoogle Scholar
  49. 49.
    Roychoudhury S, Mukherjee D. 2010. A detailed comparative analysis on the overall codon usage pattern in herpesviruses. Virus Res, 148:31–43.PubMedCrossRefGoogle Scholar
  50. 50.
    Sharp P M, Averof M, Lloyd A T, et al. 1995. DNA sequence evolution: the sounds of silence. Philos Trans R Soc Lond B Biol Sci, 349:241–247.PubMedCrossRefGoogle Scholar
  51. 51.
    Sharp P M, Li W H. 1987. The codon Adaptation Index—a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res, 15:1281–1295.PubMedCrossRefGoogle Scholar
  52. 52.
    Wada A, Suyama A. 1986. Local stability of DNA and RNA secondary structure and its relation to biological functions. Prog Biophys Mol Biol, 47:113–157.PubMedCrossRefGoogle Scholar
  53. 53.
    Wain-Hobson S, Nussinov R, Brown R J, et al. 1981. Preferential codon usage in genes. Gene, 13:355–364.PubMedCrossRefGoogle Scholar
  54. 54.
    Weinstein J N, Myers T G, O’Connor P M, et al. 1997. An information-intensive approach to the molecular pharmacology of cancer. Science, 275:343–349.PubMedCrossRefGoogle Scholar
  55. 55.
    White A K, Ciacci-Zanella J, Galeota J, et al. 1996. Comparison of the abilities of serologic tests to detect pseudorabies-infected pigs during the latent phase of infection. Am J Vet Res, 57:608–611.PubMedGoogle Scholar
  56. 56.
    Wright F. 1990. The ‘effective number of codons’ used in a gene. Gene, 87:23–29.PubMedCrossRefGoogle Scholar

Copyright information

© Wuhan Institute of Virology, CAS and Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Meili Li
    • 1
  • Zhiyao Zhao
    • 1
  • Jianhong Chen
    • 2
  • Bingyun Wang
    • 2
  • Zi Li
    • 1
  • Jian Li
    • 1
  • Mingsheng Cai
    • 2
    Email author
  1. 1.Department of Pathogenic Biology and ImmunologyGuangzhou Medical UniversityGuangzhouChina
  2. 2.Department of Veterinary MedicineFoshan Science and Technology UniversityFoshanChina

Personalised recommendations