Korean Journal of Microbiology (미생물학회지)

The Microbiological Society of Korea (한국미생물학회)
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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
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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

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