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J. Virol. doi:10.1128/JVI.01410-07
Copyright (c) 2007, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Structure of the Lipothrixvirus AFV3 and Comparative Genomics of Related Viruses from the Hyperthermophilic Archaeal Genus Acidianus

Centre for Comparative Genomics and Danish Archaea Centre, Department of Molecular Biology, Biocenter, Copenhagen University, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; Institut de Minéralogie et de Physique des Milieux Condensés, Université Pierre et Marie Curie, IMPMC-UMR7590, Paris, F-75005 France; CNRS, IMPMC-UMR7590, Paris, F-75005 France; Molecular Biology of the Gene in Extremophiles Unit, Institut Pasteur, rue du Dr. Roux 25, 75724 Paris Cedex 15, France; Department of Microbiology, University of Regensburg, Universitätsst. 31, D-93053 Regensburg, Germany

^* To whom correspondence should be addressed. Email: prangish{at}pasteur.fr.

	Abstract

Four novel filamentous viruses with double-stranded (ds) DNA genomes, AFV3, AFV6, AFV7 and AFV8, have been characterised from the hyperthermophilic archaeal genus Acidianus and they are assigned to the Betalipothrixvirus genus of the family Lipothrixviridae. The structures of the approximately 2 µm long virions are similar and one of them, AFV3, was studied in detail. It consists of a cylindrical envelope containing globular subunits arranged in a helical formation that is unique for any known double-stranded DNA virus. The envelope is 3.1 nm thick and encases an inner core with two parallel rows of protein subunits arranged like a zipper. Each end of the virion is tapered and carries three short filaments. Two major structural proteins are identified that are common to all the betalipothrixviruses. The viral genomes were sequenced and analysed and they reveal a high level of conservation in both gene content and gene order over large regions and this similarity extends partly to the earlier described betalipothrixvirus SIFV of Sulfolobus. A few predicted gene products of each virus, in addition to the structural proteins, could be assigned specific functions including a putative helicase involved in Holliday junction branch migration, a nuclease, a protein phosphatase, transcriptional regulators and glycosyl transferases. The AFV7 genome appears to have undergone intergenomic recombination with a large section of an AFV2-like viral genome, apparently resulting in phenotypical changes as revealed by the presence of AFV2-like termini in the AFV7 virions. Shared features of the genomes include: (i) large inverted terminal repeats exhibiting conserved, regularly-spaced, direct repeats; (ii) a highly conserved operon encoding the two major structural proteins; (iii) multiple overlapping ORFs which may be indicative of gene recoding; (iv) putative 12 bp genetic elements, and (v) partial gene sequences corresponding closely to spacer sequences of chromosomal repeat clusters (CRISPR).

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