Haloviruses HF1 and HF2: Evidence for a Recent and Large Recombination Event

Abstract

Haloviruses HF1 and HF2 were isolated from the same saltern pond and are adapted to hypersaline conditions, where they infect a broad range of haloarchaeal species. The HF2 genome has previously been reported. The complete sequence of the HF1 genome has now been determined, mainly by PCR and primer walking. It was 75,898 bp in length and was 94.4% identical to the HF2 genome but about 1.8 kb shorter. A total of 117 open reading frames and five tRNA-like genes were predicted, and their database matches and characteristics were similar to those found in HF2. A comparison of the predicted restriction digest patterns based on nucleotide sequence with the observed restriction digest patterns of viral DNA showed that, unlike the case for HF2, some packaged HF1 DNA had cohesive termini. Except for a single base change, HF1 and HF2 were identical in sequence over the first 48 kb, a region that includes the early and middle genes. The remaining 28 kb of HF1 showed many differences from HF2, and the similarity of the two genomes over this late gene region was 87%. The abrupt shift in sequence similarity around 48 kb suggests a recent recombination event between either HF1 or HF2 and another HF-like halovirus that has swapped most of the right-end 28 kb. This example indicates there is a high level of recombination among viruses that live in this extreme environment.Our understanding of viral and prokaryotic evolution has been radically changed over the last 10 years as a result of the ability to sequence whole genomes of organisms, including a large number of viruses (3). One of the most striking discoveries is that viral genomes are often mosaics (22), consisting of many small genetic fragments from different sources yet making up a functional whole (17,38). Despite this mosaicism, the arrangement and order of genes (synteny), particularly within functional modules such as DNA packaging and virus structural genes, are often well conserved (2,4,17,18,21).About 204 prokaryotic viruses have been fully sequenced (National Center for Biotechnology Information [NCBI] database, December 2003), and many are related (for example, the dairy bacteriophages and the lambdoid phages). Comparison of related viruses is important as it can shed light on their evolution and structure-function relationships, but to adequately assess the breadth of virus diversity and the degree of genetic exchange between viruses, novel viruses from across the two prokaryotic domains need to be isolated and sequenced (13). While thousands of bacteriophages are known, it is unfortunate that only a small number of archaeal viruses have been isolated and few of these have had their genomes completely sequenced (20,24,(33)(34)(35)38). Most of these genome sequences are very different from each other (and from those of other viruses), but some are sufficiently close that comparisons can be made (e.g., viruses of Sulfolobus [36] and Methanobacterium [24]), and these have given some indication about how archaeal viruses have evolved.The first haloarchaeal virus t...

Virion Architecture Unifies Globally Distributed Pleolipoviruses Infecting Halophilic Archaea

“…It has been shown that viral genes responsible for functions like replication are not inherited vertically within a viral lineage but are changed by horizontal gene transfer (2,3,8,40). Recombination is most probably frequent in hypersaline habitats, where the viral particle concentration reaches high levels and viruses infect the same limited range of host organisms (30,46,61). Thus, the pleolipoviruses most likely employ different replication mechanisms, resulting in different genome types.…”

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

“…Comparative analyses of these (pro)viral genomes revealed that the evolution of tailed archaeal virus genomes is governed by the same mechanisms as those described for their bacterial counterparts (37,112), i.e., diversification, gene acquisition from different sources, illegitimate recombination, and intergenome rearrangements (136,149,195,203,270). Comparative genomics has also uncovered a set of conserved genes (149), which was found to include genes for the major capsid protein, prohead protease, portal, and the terminase complex.…”

“…Although head-and-tail viruses represent the majority of reported halovirus isolates, they seem to constitute only a minor part of euryarchaeal viruses (213,252). The isolation and genome characterization of tailed archaeal viruses have so far been restricted to organisms of only two taxonomic orders of Archaea: the Halobacteriales (136,195,270) and Methanobacteriales (169,203). owever, proviruses clearly related to tailed dsDNA viruses have also been reported for organisms of the orders Methanococcales, Methanosarcinales (149), and Archaeoglobales (M. Krupovic, unpublished data).…”

Archaeal viruses—novel, diverse and enigmatic

“…This has been observed for the crenarchaeal fuselloviruses [32,33,46], the Sulfolobus conjugative plasmids [47], and also for the head-tail haloarchaeal viruses HF1 and HF2 [48]. Recently, a hypothesis was proposed to explain this phenomenon for fuselloviruses, which may extend to other archaeal integrative genetic elements and could have more general implications for the evolution of archaeal viruses and plasmids [33].…”