Molecular characterization of pHRDV1, a new virus-like mobile genetic element closely related to pleomorphic viruses in haloarchaea

Abstract

A novel haloarchaeal plasmid, pHRDV1 (13,053 bp), was isolated from the haloarchaeal isolate Halorubrum sp. T3. Molecular and bioinformatics analyses showed that this element is a double-stranded circular DNA molecule containing two putative transcripts with opposite directions. The amino acid sequences of six of the nineteen predicted open reading frames were similar to those found in haloarchaeal pleomorphic viruses, such as Halorubrum pleomorphic virus 3 and Halogeometricum pleomorphic virus 1. There was also a strong conservation in gene order between the plasmid and these viruses. All three conserved viral proteins (VPs), which are characteristic of haloarchaeal pleomorphic viruses VP3, VP4 and VP8, were found in pHRDV1. Furthermore, a typical repressor-operator system similar to haloarchaeal myovirus φCh1, was found on the genome of pHRDV1. However, no viral particles were detected in the supernatants of Halorubrum sp. T3, either in the presence or absence of mitomycin C. These results imply that plasmid pHRDV1 is a distinctive virus-like mobile genetic element that harbors some unique properties that make it different from all of the known haloarchaeal plasmids or viruses.

Identification and characterization of SNJ2, the first temperate pleolipovirus integrating into the genome of the SNJ1‐lysogenic archaeal strain

“…Previously, pleolipoproviral regions have been identified in haloarchaeal chromosomes of strains belonging to Haloferax, Haloarcula, Natronomonas, Halomicrobium, Halopiger, Halorhabdus and Natrialba (Bath et al, 2006;Dyall-Smith et al, 2011;Senčilo et al, 2012) as well as in Haloferax lucentense plasmid pHK2 (Pietilä et al, 2009) and Halorubrum spp. plasmid pHRDV1 (Chen et al, 2014) using bioinformatics approaches. Haloquadratum walsbyi plasmid PL6 was also found to contain an ORF related to the conserved ORF19 of SNJ2 (Dyall-Smith et al, 2011).…”

“…Putative proviruses and proviral elements containing homologues to the conserved pleolipoviral gene cluster have been detected in Haloferax lucentense plasmid pHK2 and Halorubrum sp. plasmid pHRDV1, as well as in a set of haloarchaeal chromosomes (Bath et al, 2006;Pietilä et al, 2009;Dyall-Smith et al, 2011;Senčilo et al, 2012;Chen et al, 2014). However, none of these proviral regions have so far been experimentally confirmed to be live viruses.…”

Pleolipoviridae, a newly proposed family comprising archaeal pleomorphic viruses with single-stranded or double-stranded DNA genomes

“…Haloferax plasmid pHK2 and Halorubrum plasmid pHRDV1 show gene synteny and significant amino acid sequence similarity to the pleolipovirus genomes. Thus, these plasmids are most likely proviruses related to the pleolipoviruses [14,34]. Also, a metagenome from a hypersaline lake contained a sequence similar to those of the pleolipoviruses [37].…”

Virus‐host interplay in high salt environments

“…All these viruses harbour a set of conserved core genes encoding the spike and internal membrane protein as well as a putative packaging NTPase, and two assembly factors (Pietil€ a et al, 2012;Li et al, 2014;Liu et al, 2015). In addition, similar related genetic elements, either proviruses or plasmids, have been identified to be associated with many haloarchaeal strains indicating that these viruses are very common and widespread in the environment as well as within cells Senčilo et al, 2012;Chen et al, 2014;Liu et al, 2015). Life cycles of the pleomorphic viruses are nonlytic culminating in the production of virus progeny in high numbers.…”