Analysis of the First Genome of a Hyperthermophilic Marine Virus-Like Particle, PAV1, Isolated fromPyrococcus abyssi

Abstract

Only one virus-like particle (VLP) has been reported from hyperthermophilic Euryarchaeotes. This VLP, named PAV1, is shaped like a lemon and was isolated from a strain of "Pyrococcus abyssi," a deep-sea isolate. Its genome consists of a double-stranded circular DNA of 18 kb which is also present at a high copy number (60 per chromosome) free within the host cytoplasm but is not integrated into the host chromosome. Here, we report the results of complete analysis of the PAV1 genome. All the 25 predicted genes, except 3, are located on one DNA strand. A transcription map has been made by using a reverse transcription-PCR assay. All the identified open reading frames (ORFs) are transcribed. The most significant similarities relate to four ORFs. ORF 180a shows 31% identity with ORF 181 of the pRT1 plasmid isolated from Pyrococcus sp. strain JT1. ORFs 676 and 678 present similarities with a concanavalin A-like lectin/glucanase domain, which could be involved in the process of host-virus recognition, and ORF 59 presents similarities with the transcriptional regulator CopG. The genome of PAV1 displays unique features at the nucleic and proteinic level, indicating that PAV1 should be attached at least to a novel genus or virus family.

Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses

“…Marine archaea numerically dominate the mesopelagic oceans (Karner et al, 2001), with increased abundance in some surface waters (for example, the Southern Ocean; DeLong et al, 1994), yet their viruses are represented by a single isolate-a lemon-shaped virus from a hydrothermal deep-sea environment that infects Pyrococcus abyssi (Geslin et al, 2007). We observed no lemon-shaped viruses nor any of the myriad 'exceptional' morphotypes isolated from archaeal extremophiles (reviewed by Prangishvili et al, 2006).…”

Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

“…The circular dsDNA genome of PAV1 did not show similarity to other archaeal spindle-shaped viruses or, indeed, to any known virus (90). However, PAV1 shares several genes with plasmids from the Thermococcales (3 genes with Thermococcus nautilus plasmid pTN2 and an additional gene with Pyrococcus sp.…”

Unification of the Globally Distributed Spindle-Shaped Viruses of the Archaea

“…For example, APSV1 encodes four other proteins with homologues in tailless spindle- shaped viruses, including the DnaA-like AAA ϩ ATPase believed to be involved in genome replication (45). Similarly, in addition to the MCP, PAV1 shares a three-gene cassette with A3-VLP (23,46), while with TPV1, it shares two other genes for putative minor structural proteins (3). Notably, our analysis has shown that all spindle-shaped viruses encode AAA ϩ ATPases.…”

“…Over the years, a number of spindle-shaped viruses that could not be assigned to the existing taxa based on genome similarity have been isolated from phylogenetically distant archaeal lineages, including Thermococcales (Thermococcus prieurii virus 1 [TPV1] [3] and PAV1 [2,23] (22). We used this information to perform an in-depth genome analysis of all known unclassified spindle-shaped viruses.…”