Analysis of the first genome of a hyperthermophilic marine virus-like particle, PAV1, isolated from Pyrococcus 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.

FIG. 1.

PAV1 genome map. Predicted genes are represented by thick arrows; light gray shading indicates ORFs with no similarity and no assigned function, and dark gray shading indicates either conserved hypothetical ORFs or ORFs with a hypothetical function; hatching indicates ORFs encoding a putative membrane-associated protein. Transcript locations mapped by using RT-PCR (T1 to T6) are shown by arrows inside the circular genome map. The approximate location of the origin (Ori) of replication as predicted by cumulative GC skew is also indicated. Protein motif or domain names: Lam G, laminin G; Leu zip, leucine zipper; P-loop, nucleoside triphosphate binding site or Walker motif A; wHTH, winged helix or winged helix-turn-helix.

FIG. 2.

Structure of the putative DNA replication origin region. (A) Cumulative GC skew (window size of 20 bp). (B) Identification of a DNA unwinding element (DUE) and nucleotide repeats (indicated by arrows). The longer inverted repeats are indicated by the thick black arrows.

FIG. 3.

ORF 676 and ORF 678 possess domains related to laminin G-like jellyroll fold. Amino acid sequence alignment of the internal repeats of ORFs 676 and 678 with various members of the concanavalin A/glucanase structural family (human serum amyloid P component [1sac_A], hypothetical protein from bacteriophage S-PM2 [gi 58532986], VCBS from Pelodyction luteolum [gi 78186255], hypothetical protein from Rhodopirellula baltica [gi 32471540], VCBS from Prosthecochloris vibrioformis [gi 71481241], and S-layer protein from Clostridium thermocellum [gi 67915998]) are shown. The numbers in brackets indicate the positions in the sequences. The secondary elements of the human serum amyloid P component are displayed above the alignment.