HF2: a double‐stranded DNA tailed haloarchaeal virus with a mosaic genome

Abstract

Summary HF2 is a haloarchaeal virus infecting twoHalorubrum species (Family Halobacteriaceae). It is lytic, has a head-and-tail morphology and belongs to the Myoviridae (contractile tails). The linear double-stranded DNA genome was sequenced and found to be 77 670 bp in length, with a mol% G+C of 55.8. A total of 121 likely open reading frames (ORFs) were identified, of which 37 overlapped at start and stop codons. The predicted proteins were usually acidic (average pI of 4.8), and less than about 12% of them had homologues in the sequence databases. Four complete tRNA-like sequences (tRNA-Arg, -Asx, -Pro and -Tyr) and an incomplete tRNA-Thr were detected. A transcription map showed that most of the genome was transcribed and that the synthesis of transcripts occurred in a highly organized and reproducible pattern over a 5 h infection cycle. Transcripts often spanned multiple ORFs, suggesting that viral genes were organized into operons. The predicted ORF and observed transcript directions matched well and showed that transcription is mainly directed inwards from the genome termini, meeting at about 45-48 kb, and this was also a turning point in a cumulative GCskew plot. The low point in cumulative GC-skew, near the left end, was a region rich in short repeats and lacking ORFs, which is likely to be an origin of replication. The HF2 genome is a mosaic of components from widely different sources, demonstrating clearly that viruses of haloarchaea, like their bacteriophage counterparts, are vectors for the exchange and trans-

Insights into Head-Tailed Viruses Infecting Extremely Halophilic Archaea

“…The GϩC content of the genome is 60%. The HSTV-2 genome is similar in sequence and gene arrangement to the previously characterized archaeal myoviruses HF1 and HF2 (20,21). Dot plot comparison shows that the overall similarity of the HSTV-2 and HF1 and HF2 genomes is moderate, 70.4 and 59.8% nucleotide identities, respectively, over the length of HSTV-2, with the degree of similarity falling off at the right end of the HSTV-2 genome (data not shown).…”

“…Although no head-tailed viruses infecting hyperthermophilic archaea have yet been isolated, such virus-like particles have been observed in hydrothermal environments (16). So far, detailed characterization of archaeal head-tailed viruses has been limited mostly to the genome level (17)(18)(19)(20)(21), and, in contrast to the extensive structural research on head-tailed bacteriophages, no virion structures are available for archaeal head-tailed viruses.…”

Constituents of SH1, a Novel Lipid-Containing Virus Infecting the Halophilic Euryarchaeon Haloarcula hispanica

“…2), similar to haloarchaeal organisms (4,67). However, based on the calculated pI, some of the SH1 gene products were extremely basic in character (pI Ͼ 10).…”

“…For Thermoproteales the only sequenced isolate is the Pyrobaculum spherical virus, which has been proposed to possess a lipid envelope surrounding a helical nucleoprotein core (30). The kingdom Euryarchaeota contains physiologically diverse members of methanogenic, halophilic, and thermoacidophilic organisms, and viruses of this group include the Methanothermobacter viruses psiM1 and psiM2 (47,54), the lytic HF1 that infects cells of the Haloferax and Haloterrigena genera (68), the lytic HF2 that infects Halorubrum cariense (67), and the temperate Natrialba magadii virus Ch1 (40). All have head-tail morphology reminiscent of bacteriophages belonging to the families Myoviridae (such as T4) and Siphoviridae (such as ).…”

“…Such viruses probably infect most if not all bacterial and some archaeal species. The genomes of tailed phages are mosaics that have likely experienced global genetic exchange (44,67,68). On the other hand, tailless bacterial viruses with an internal membrane belonging to the family Tectiviridae do not seem to obey this rule.…”