Classification of Viruses Based on the Amino Acid Sequences of Viral Polymerases

바이러스 핵산중합효소의 아미노산 서열에 의한 바이러스 분류

  • Nam, Ji-Hyun (School of Life Sciences, Chungbuk National University) ;
  • Lee, Dong-Hun (School of Life Sciences, Chungbuk National University) ;
  • Lee, Keon-Myung (School of Electrical and Computer Engineering, Chungbuk National University) ;
  • Lee, Chan-Hee (School of Life Sciences, Chungbuk National University)
  • 남지현 (충북대학교 자연과학대학 생명과학부) ;
  • 이동훈 (충북대학교 자연과학대학 생명과학부) ;
  • 이건명 (충북대학교 자연과학대학 전기전자컴퓨터공학부) ;
  • 이찬희 (충북대학교 자연과학대학 생명과학부)
  • Published : 2007.12.30

Abstract

According to the Baltimore Scheme, viruses are classified into 6 main classes based on their replication and coding strategies. Except for some small DNA viruses, most viruses code for their own polymerases: DNA-dependent DNA, RNA-dependent RNA and RNA-dependent DNA polymerases, all of which contain 4 common motifs. We undertook a phylogenetic study to establish the relationship between the Baltimore Scheme and viral polymerases. Amino acid sequence data sets of viral polymerases were taken from NCBI GenBank, and a multiple alignment was performed with CLUSTAL X program. Phylogenetic trees of viral polymerases constructed from the distance matrices were generally consistent with Baltimore Scheme with some minor exceptions. Interestingly, negative RNA viruses (Class V) could be further divided into 2 subgroups with segmented and non-segmented genomes. Thus, Baltimore Scheme for viral taxonomy could be supported by phylogenetic analysis based on the amino acid sequences of viral polymerases.

볼티모어의 분류체계에 의하면 바이러스는 복제 및 단백질합성 전략에 따라 6개의 집단으로나눌 수 있다. 몇 종류의 작은 DNA 바이러스를 제외한 대부분의 바이러스는 게놈 복제를 위한 자신의 핵산중합효소를 유전자로 암호화하고 있다. 바이러스 핵산중합효소에는 DNA-의존DNA 중합효수, RNA-의존RNA 중합효소, RNA-의존 DNA 중합효소 세 종류가 있으며, 이들은 모두 4개의 공통된 모티프(motif)를 가진다. 우리는 볼티모어의 분류체계와 바이러스의 핵산중합효소와의 관계를 아미노산 서열을 통해 분자 계통분류학적 분석을 통해 알아보고자 하였다. NCBI GenBank에서 얻은 바이러스 중합효소의 아미노산 서열을 CLUSTAL X 프로그램으로 다중서열하고, Neighbor-joining, Maximum-likelihood, Bayesian의 세 가지 방법으로 계통도를 그려보았다. 미세한 차이는 있었으나, 세 가지 방법 모두에서 볼티모어의 분류법과 일치하는 결과를 보였고, 특이하게도 두 가닥 RNA 바이러스는 숙주의 종류에 따라, (-)RNA 바이러스는 게놈의 절편화에 따라 각각2개의 소집단으로 나뉘어지는 것을 볼 수 있었다.

Keywords

References

  1. Biswal, B.K., M.M. Cherney, M. Wang, L. Chan, C.G. Yannopoulos, D. Bilimoria, O. Nicolas, J. Bedard, and M.N. James. 2005. Crystal structures of the RNA-dependent RNA polymerase genotype 2a of hepatitis C virus reveal two conformations and suggest mechanisms of inhibition by non-nucleoside inhibitors. J. Biol. Chem. 280, 18202-18210 https://doi.org/10.1074/jbc.M413410200
  2. Braithwaite, D.K. and J. Ito. 1993. Compilation, alignment, and phylogenetic relationships of DNA polymerases. Nucleic Acids Res. 21, 787-802 https://doi.org/10.1093/nar/21.4.787
  3. Bruenn, J.A. 1993. A closely related group of RNA-dependent RNA polymerases from double-stranded RNA viruses. Nucleic Acids Res. 21, 5667-5669 https://doi.org/10.1093/nar/21.24.5667
  4. Bruenn, J.A. 2003. A structural and primary sequence comparison of the viral RNA-dependent RNA polymerases. Nucleic Acids Res. 31, 1821-1829 https://doi.org/10.1093/nar/gkg277
  5. Dmitrievaa, T.M., A.V. Alexeevskia, G.S. Shatskaya, E.A. Tolskaya, A.P. Gmyl, E.V. Khitrina, and V.I. Agol. 2007. Significance of the C-terminal amino acid residue in mengovirus RNA-dependent RNA polymerase. Virology 365, 79-91 https://doi.org/10.1016/j.virol.2007.02.038
  6. Dolja, V.V. and J.C. Carrington. 1992. Evolution of positive-strand RNA viruses. Sem. Virol. 3, 315-326
  7. Falquet, L., M. Pagni, P. Bucher, N. Hulo, C.J. Sigrist, K. Hofmann, and A. Bairoch. 2002. The PROSITE database, its status in 2002. Nucleic Acids Res. 30, 235-238 https://doi.org/10.1093/nar/30.1.235
  8. Felsenstein, J. 2002. PHYLIP (Phylogeny Inference Package) Version 3.6a3. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA
  9. Francki, R.I.B., C.M. Fauquet, D.L. Knudson, and F. Brown. 1991. Virus taxonomy. Classification and nomenclature of Viruses. Fifth report of the international committee on taxonomy of viruses
  10. Goldbach, R. and J. Wellink. 1988. Evolution of plus-strand RNA viruses. Intervirology 29, 260-267 https://doi.org/10.1159/000150054
  11. Habili, N. and R.H. Symons. 1989. Evolutionary relationship between luteoviruses and other RNA plant viruses based on sequence motifs and their putative RNA polymerases and nucleic acid helicases. Nucleic Acids Res. 17, 9543-9555 https://doi.org/10.1093/nar/17.23.9543
  12. Huelsenbeck, J.P. and F. Ronquist. Command reperence for MrBayes ver. 3.0B4, Serial Version. Department of Biology, University of Rochester, USA
  13. Hugot, J.P., J.P. Gonzalez, and C. Denys. 2001. Evolution of the old world arenaviridae and their rodent hosts: generalized hosttransfer or association by descent? Infect. Genet. Evol. 2, 1-8
  14. Iyer, L.M., E.V. Koonin, and L. Aravind. 2003. Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases. BMC Structural Biol. 3, 1 https://doi.org/10.1186/1472-6807-3-1
  15. Koonin, E.V. and V.V. Dolja. 1993. Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Crit. Rev. Biochem. Mol. Biol. 28, 375-430 https://doi.org/10.3109/10409239309078440
  16. Matthews, R.E.F. 1985. Viral taxonomy for the non-virologist. Ann. Rev. Microbiol. 39, 451-474 https://doi.org/10.1146/annurev.mi.39.100185.002315
  17. Mayo, M.A. and C.R. Fringle. 1998. Virus taxonomy-1997. J. Gen. Virol. 79, 649-657 https://doi.org/10.1099/0022-1317-79-4-649
  18. Ng, K.K., N. Pendas-Franco, J. Rojo, J.A. Boga, A. Machin, J.M. Alonso, and F. Parra. 2004. Crystal structure of Norwalk virus polymerase reveals the carboxyl terminus in the active site cleft. J. Biol. Chem. 279, 16638-16645 https://doi.org/10.1074/jbc.M400584200
  19. Poch, O., I. Sauvaget, M. Delarue, and N. Torodo. 1989. Identification of four conserved motifs among the RNA-dependent polymerase encoding elements. EMBO J. 8, 3867-3874
  20. Rybicki, E.P. 1990. The classification of organisms at the edge of life, or problems with virus systematics. South African J. Sci. 86, 182-186
  21. Shwed, P.S., P. Dobos, L.A. Cameron, V.N. Vakharia, and R. Duncan. 2002. Birnavirus VP1 proteins from a distinct subgroup of RNA-dependent RNA polymerases lacking a GDD motif. Virology 296, 241-250 https://doi.org/10.1006/viro.2001.1334
  22. Strauss, J.H. and E.G. Strauss. 1988. Evolution of RNA viruses. Ann. Rev. Microbiol. 42, 657-683 https://doi.org/10.1146/annurev.mi.42.100188.003301
  23. Thompson, J.D., T.J. Gibson, F. Plewniak, F. Jeanmougin, and D.G. Higgins. 1997. The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876-4882 https://doi.org/10.1093/nar/25.24.4876
  24. Vieth, S., A.E. Torda, A. Marcel, S. Herbert, and G. Stephan. 2004. Sequence analysis of L RNA of Lassa virus. Virology 318, 153-168 https://doi.org/10.1016/j.virol.2003.09.009
  25. Ward, C.W. 1993. Progress towards a higher taxonomy of viruses. Res. Virol. 144, 419-453 https://doi.org/10.1016/S0923-2516(06)80059-2
  26. Zanotto, P.M., M.J. Gibbs, E.A. Gould, and E.C. Holmes. 1996. A reevaluation of the higher taxonomy of viruses based on RNA polymerases. J. Virol. 70, 6083-6096