Two novel families of plasmids from hyperthermophilic archaea encoding new families of replication proteins

Abstract

Thermococcales (phylum Euryarchaeota) are model organisms for physiological and molecular studies of hyperthermophiles. Here we describe three new plasmids from Thermococcales that could provide new tools and model systems for genetic and molecular studies in Archaea. The plasmids pTN2 from Thermococcus nautilus sp. 30-1 and pP12-1 from Pyrococcus sp. 12-1 belong to the same family. They have similar size (∼12 kb) and share six genes, including homologues of genes encoded by the virus PAV1 from Pyrococcus abyssi. The plasmid pT26-2 from Thermococcus sp. 26-2 (21.5 kb), that corresponds to another plasmid family, encodes many proteins having homologues in virus-like elements integrated in several genomes of Thermococcales and Methanococcales. Our analyses confirm that viruses and plasmids are evolutionary related and co-evolve with their hosts. Whereas all plasmids previously isolated from Thermococcales replicate by the rolling circle mechanism, the three plasmids described here probably replicate by the theta mechanism. The plasmids pTN2 and pP12-1 encode a putative helicase of the SFI superfamily and a new family of DNA polymerase, whose activity was demonstrated in vitro, whereas pT26-2 encodes a putative new type of helicase. This strengthens the idea that plasmids and viruses are a reservoir of novel protein families involved in DNA replication.

Provirus Induction in Hyperthermophilic Archaea: Characterization of Aeropyrum pernix Spindle-Shaped Virus 1 and Aeropyrum pernix Ovoid Virus 1

“…All integrase genes from known crenarchaeal viruses are of the SSV type. This type of gene is also found on some archaeal plasmids (21,34). The pNOB8-type integrase was found to be encoded on archaeal plasmids (6) and in putative proviruses of the Euryarchaeota (11).…”

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

“…However, PAV1 shares several genes with plasmids from the Thermococcales (3 genes with Thermococcus nautilus plasmid pTN2 and an additional gene with Pyrococcus sp. strain JT1 plasmid pRT1) (254,284), suggesting a dynamic genetic interaction between these different types of mobile elements (253). Haloarchaeal virus His1 was first assigned to the family Fuselloviridae, which includes crenarchaeal viruses of similar morphology (16).…”

Archaeal Extrachromosomal Genetic Elements

“…A number of Thermococcus and Pyrococcus strains have been isolated from hydrothermal vents in the Atlantic, Indian, and Pacific Oceans, and a systematic screening for extrachromosomal genetic elements revealed that a large proportion of archaeal isolates carry plasmids. Fifteen plasmids have been isolated and characterized so far, and they fall into six different groups based on their putative replication proteins (184,185).…”

“…The other replication protein is family specific. In the pTN2 family, a Prim/Pol enzyme, represented by PolpTN2, was characterized recently (165,184). The N-terminal domain of the protein showed both primase and DNA polymerase activities.…”

“…Strikingly, some plasmids isolated from members of these two archaeal orders show a high level of sequence similarity. pT26-2 is the first integrative genetic element isolated from the Thermococcaceae, and this plasmid is closely related to several integrated genetic elements present in the genomes of Thermococcus kodakarensis; Pyrococcus horikoshii; Thermococcus gammatolerans; M. maripaludis S2, C2, and C7; and Methanococcus voltae; the former three belong to the Thermococcales, while the latter four are members of the Methanococcales (184). Since all of these genetic elements encode a putative integrase of the SSV1 type, it has been postulated that the occurrence of ECEs in different phyla of the Archaea may have resulted from events of crossorder HGT (130,184).…”