A highly divergent archaeo-eukaryotic primase from the Thermococcus nautilus plasmid, pTN2

Abstract

We report the characterization of a DNA primase/polymerase protein (PolpTN2) encoded by the pTN2 plasmid from Thermococcus nautilus. Sequence analysis revealed that this protein corresponds to a fusion between an N-terminal domain homologous to the small catalytic subunit PriS of heterodimeric archaeal and eukaryotic primases (AEP) and a C-terminal domain related to their large regulatory subunit PriL. This unique domain configuration is not found in other virus- and plasmid-encoded primases in which PriS-like domains are typically fused to different types of helicases. PolpTN2 exhibited primase, polymerase and nucleotidyl transferase activities and specifically incorporates dNTPs, to the exclusion of rNTPs. PolpTN2 could efficiently prime DNA synthesis by the T. nautilus PolB DNA polymerase, suggesting that it is used in vivo as a primase for pTN2 plasmid replication. The N-terminal PriS-like domain of PolpTN2 exhibited all activities of the full-length enzyme but was much less efficient in priming cellular DNA polymerases. Surprisingly, the N-terminal domain possesses reverse transcriptase activity. We speculate that this activity could reflect an ancestral function of AEP proteins in the transition from the RNA to the DNA world.

A primase subunit essential for efficient primer synthesis by an archaeal eukaryotic-type primase

“…4b). Compatible with this scenario, a recently identified primase from several thermococcal plasmids encompasses the fusion of PriS and PriL-CTD, with the Fe–S binding motif preserved 24 . Thus, PriX might have originated via fission of the ancestral PriS–PriL fusion gene, accompanied by partial degradation of the PriL moiety, such that only the PriL-CTD remained.…”

DNA topoisomerase VIII: a novel subfamily of type IIB topoisomerases encoded by free or integrated plasmids in Archaea and Bacteria

“…However, in this case, it is also possible that these plasmids were transferred from Bacteria to Archaea at the onset of the haloarchaeal lineage, which has experienced the introduction of around 1000 bacterial genes (63). Irrespective of the evolutionary scenario, the discovery of a subfamily of topoisomerases specifically encoded by plasmids confirms that mobile elements are potential reservoirs of novel proteins involved in DNA metabolism (7,36,42,64). …”

‘Ménage à trois’: a selfish genetic element uses a virus to propagate within Thermotogales

“…Genes for DNA polymerases and primases are not commonly found on plasmids; however, Marpi_2127 encodes a protein with both a DnaB (helicase) and a DnaG (primase) domain. Recently, a DNA primase/polymerase protein (PolpTN2) encoded by the pTN2 plasmid from Thermococcus nautilus has been characterized (Gill et al, 2014). To summarize, a large fraction of pMP1-encoded proteins might be involved in DNA binding and possibly replication and propagation of the plasmid.…”