論文

査読有り
2017年4月

Nucleic and Amino Acid Sequences Support Structure-Based Viral Classification

JOURNAL OF VIROLOGY
  • Robert M. Sinclair
  • ,
  • Janne J. Ravantti
  • ,
  • Dennis H. Bamford

91
8
記述言語
英語
掲載種別
研究論文(学術雑誌)
DOI
10.1128/JVI.02275-16
出版者・発行元
AMER SOC MICROBIOLOGY

Viral capsids ensure viral genome integrity by protecting the enclosed nucleic acids. Interactions between the genome and capsid and between individual capsid proteins (i.e., capsid architecture) are intimate and are expected to be characterized by strong evolutionary conservation. For this reason, a capsid structure-based viral classification has been proposed as a way to bring order to the viral universe. The seeming lack of sufficient sequence similarity to reproduce this classification has made it difficult to reject structural convergence as the basis for the classification. We reinvestigate whether the structure-based classification for viral coat proteins making icosahedral virus capsids is in fact supported by previously undetected sequence similarity. Since codon choices can influence nascent protein folding cotranslationally, we searched for both amino acid and nucleotide sequence similarity. To demonstrate the sensitivity of the approach, we identify a candidate gene for the pandoravirus capsid protein. We show that the structure-based classification is strongly supported by amino acid and also nucleotide sequence similarities, suggesting that the similarities are due to common descent. The correspondence between structure-based and sequence-based analyses of the same proteins shown here allow them to be used in future analyses of the relationship between linear sequence information and macromolecular function, as well as between linear sequence and protein folds.
IMPORTANCE Viral capsids protect nucleic acid genomes, which in turn encode capsid proteins. This tight coupling of protein shell and nucleic acids, together with strong functional constraints on capsid protein folding and architecture, leads to the hypothesis that capsid protein-coding nucleotide sequences may retain signatures of ancient viral evolution. We have been able to show that this is indeed the case, using the major capsid proteins of viruses forming icosahedral capsids. Importantly, we detected similarity at the nucleotide level between capsid protein-coding regions from viruses infecting cells belonging to all three domains of life, reproducing a previously established structure-based classification of icosahedral viral capsids.

Web of Science ® 被引用回数 : 18

リンク情報
DOI
https://doi.org/10.1128/JVI.02275-16
PubMed
https://www.ncbi.nlm.nih.gov/pubmed/28122979
PubMed Central
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5375668
Web of Science
https://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=JSTA_CEL&SrcApp=J_Gate_JST&DestLinkType=FullRecord&KeyUT=WOS:000399472200025&DestApp=WOS_CPL
URL
http://europepmc.org/abstract/med/28122979
URL
http://orcid.org/0000-0002-9646-4322
ID情報
  • DOI : 10.1128/JVI.02275-16
  • ISSN : 0022-538X
  • eISSN : 1098-5514
  • ORCIDのPut Code : 46045895
  • PubMed ID : 28122979
  • PubMed Central 記事ID : PMC5375668
  • Web of Science ID : WOS:000399472200025

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