Proviral regions have been identified in the genomes of many haloarchaea, but only a few archaeal halophilic temperate viruses have been studied. Here, we report a new virus, SNJ2, originating from archaeal strainNatrinemasp. J7-1. We demonstrate that this temperate virus coexists with SNJ1 virus and is dependent on SNJ1 for efficient production. Here, we show that SNJ1 is an icosahedral membrane-containing virus, whereas SNJ2 is a pleomorphic one. Instead of producing progeny virions and forming plaques, SNJ2 integrates into the host tRNAMet gene. The virion contains a discontinuous, circular, double-stranded DNA genome of 16 992 bp, in which both nicks and single-stranded regions are present preceded by a ‘GCCCA’ motif. Among 25 putative SNJ2 open reading frames (ORFs), five of them form a cluster of conserved ORFs homologous to archaeal pleolipoviruses isolated from hypersaline environments. Two structural protein encoding genes in the conserved cluster were verified in SNJ2. Furthermore, SNJ2-like proviruses containing the conserved gene cluster were identified in the chromosomes of archaea belonging to 10 different genera. Comparison of SNJ2 and these proviruses suggests that they employ a similar integration strategy into a tRNA gene.
We report a novel temperate pleolipovirus SNJ2 that integrates into the tRNAMet gene of Natrinema sp. strain J7-1. The SNJ2 genome is circular, double-stranded DNA with interruptions preceded by a conserved “GCCCA” motif. The viral genome contains a cluster of five ORFs homologous to archaeal pleolipoviruses isolated from hypersaline environments. We identified 17 SNJ2-like proviruses in several haloarchaea belonging to 10 different genera, which all employ a similar integration strategy into a tRNA gene.