AFV1, a novel virus infecting hyperthermophilic archaea of the genus acidianus

Abstract

We describe a novel virus, AFV1, of the hyperthermophilic archaeal genus Acidianus. Filamentous virions are covered with a lipid envelope and contain at least five different proteins with molecular masses in the range of 23-130 kDa and a 20.8-kb-long linear double-stranded DNA. The virus has been assigned to the family Lipothrixviridae on the basis of morphotypic characteristics. Host range is confined to several strains of Acidianus and the virus persists in its hosts in a stable carrier state. The latent period of virus infection is about 4 h. Viral DNA was sequenced and sequence similarities were found to the lipothrixvirus SIFV, the rudiviruses SIRV1 and SIRV2, as well as to conjugative plasmids and chromosomes of the genus Sulfolobus. Exceptionally for the linear genomes of archaeal viruses, many short direct repeats, with the sequence TTGTT or close variants thereof, are closely clustered over 300 bp at each end of the genome. They are reminiscent of the telomeric ends of linear eukaryal chromosomes.

Structure of the Acidianus Filamentous Virus 3 and Comparative Genomics of Related Archaeal Lipothrixviruses

“…In considering their disposition in our model, this would correspond to a virus length of 2,000 nm, which precisely fits our EM observation. The estimated thickness of the outer layer of the AFV3 virion of 3.1 nm measured on the 2D average map corresponds closely with estimates for virions of other lipothrixviruses, namely, SIFV, AFV1, and AFV2, based on observed particle widths before and after removal of the outer layer (1,5,13). The value is less than the minimal observed widths of cellular or viral membranes (41) and raises the issue of the chemical composition of the outer layer.…”

“…White boxes indicate that no clearly homologous genes were detected in the other four viral genomes. As observed for other crenarchaeal viruses, about one-third of the genes, mainly single genes and first genes of operons, are preceded (ϳ25 to 30 bp upstream) by TATA-like promoter motifs and are predicted to yield leaderless transcripts (5,11,37). Each AFV genome carries a long inverted terminal repeat (ITR), and each terminal region exhibits the motif TGTCATT, repeated two or three times with a constant spacing of 65 bp and ending at a conserved 62-bp sequence near the terminus.…”

“…One of these, ORF166, is the most basic of the proteins and is also the most conserved, with detectable homologs in AFV1 as well as rudiviruses (Table 2), and it is likely to be a DNA binding protein involved in coiling viral DNA. Another operon encoding the putative helicase and nuclease (ORF593 and ORF203) is also conserved in the genomes of AFV1 and AFV2 (5,13) and in rudiviral genomes (Table 2). Moreover, it is the only operon that is conserved among the rudiviruses (26,39).…”

“…Subsequently, three other filamentous viruses were assigned to this family, including Sulfolobus islandicus filamentous virus (SIFV) (1), Acidianus filamentous virus 1 (AFV1) (5), and AFV2 (13). Their enveloped virions range in length from about 900 nm (AFV1) to 2 m (SIFV), with diameters of about 24 nm.…”

Viral assemblage composition in Yellowstone acidic hot springs assessed by network analysis

“…The only viral group containing members from differing families involved the Rudiviridae viruses ARV-1 and SRV, and the unclassified fusiform viruses STSV-1 and STSV-2 (Xiang et al, 2005;Erdmann et al, 2013). A number of other archaeal viruses were found exclusively in single clusters, including ATV; 1.4% network contigs (Prangishvili et al, 2006b) and AFV-1 (1.3% network contigs; Bettstetter et al, 2003). A number of thermophilic viruses were not detected.…”