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J Mol Biol. 2018 Mar 2;430(5):737-750. doi: 10.1016/j.jmb.2017.11.014. Epub 2017 Dec 11.

Novel Families of Archaeo-Eukaryotic Primases Associated with Mobile Genetic Elements of Bacteria and Archaea.

Author information

1
Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania.
2
Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR 7138 Evolution Paris Seine-Institut de Biologie Paris Seine, Paris 75005, France.
3
Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Department of Microbiology, Institut Pasteur, 25 rue du Docteur Roux, Paris 75015, France.
4
Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania. Electronic address: ceslovas.venclovas@bti.vu.lt.
5
Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Department of Microbiology, Institut Pasteur, 25 rue du Docteur Roux, Paris 75015, France. Electronic address: krupovic@pasteur.fr.

Abstract

Cellular organisms in different domains of life employ structurally unrelated, non-homologous DNA primases for synthesis of a primer for DNA replication. Archaea and eukaryotes encode enzymes of the archaeo-eukaryotic primase (AEP) superfamily, whereas bacteria uniformly use primases of the DnaG family. However, AEP genes are widespread in bacterial genomes raising questions regarding their provenance and function. Here, using an archaeal primase-polymerase PolpTN2 encoded by pTN2 plasmid as a seed for sequence similarity searches, we recovered over 800 AEP homologs from bacteria belonging to 12 highly diverse phyla. These sequences formed a supergroup, PrimPol-PV1, and could be classified into five novel AEP families which are characterized by a conserved motif containing an arginine residue likely to be involved in nucleotide binding. Functional assays confirm the essentiality of this motif for catalytic activity of the PolpTN2 primase-polymerase. Further analyses showed that bacterial AEPs display a range of domain organizations and uncovered several candidates for novel families of helicases. Furthermore, sequence and structure comparisons suggest that PriCT-1 and PriCT-2 domains frequently fused to the AEP domains are related to each other as well as to the non-catalytic, large subunit of archaeal and eukaryotic primases, and to the recently discovered PriX subunit of archaeal primases. Finally, genomic neighborhood analysis indicates that the identified AEPs encoded in bacterial genomes are nearly exclusively associated with highly diverse integrated mobile genetic elements, including integrative conjugative plasmids and prophages.

KEYWORDS:

DNA replication; Thermococcus plasmids; evolution; helicases; structural modeling

PMID:
29198957
PMCID:
PMC5862659
DOI:
10.1016/j.jmb.2017.11.014
[Indexed for MEDLINE]
Free PMC Article

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