P. Andrade, M. J. Martín, R. Juá-rez, F. Ló-pez-de-saro, and L. Blanco, Limited terminal transferase in human DNA polymerase mu defines the required balance between accuracy and efficiency in NHEJ, Proc. Natl. Acad. Sci. USA, vol.106, pp.16203-16208, 2009.

D. Baidyaroy, G. Hausner, B. , and H. , In vivo conformation and replication intermediates of circular mitochondrial plasmids in Neurospora and Cryphonectria parasitica, Fungal Biol, vol.116, pp.919-931, 2012.

C. Bath, T. Cukalac, K. Porter, and M. L. Smith, His1 and His2 are distantly related, spindle-shaped haloviruses belonging to the novel virus group, Salterprovirus. Virology, vol.350, pp.228-239, 2006.

K. Beck, A. Vannini, P. Cramer, and G. Lipps, The archaeo-eukaryotic primase of plasmid pRN1 requires a helix bundle domain for faithful primer synthesis, Nucleic Acids Res, vol.38, pp.6707-6718, 2010.

P. Bé-guin, N. Charpin, E. V. Koonin, P. Forterre, and M. Krupovic, Casposon integration shows strong target site preference and recapitulates protospacer integration by CRISPR-Cas systems, Nucleic Acids Res, vol.44, pp.10367-10376, 2016.

M. Berjó-n-otero, L. Villar, M. De-vega, M. Salas, and M. Redrejo-rodríguez, DNA polymerase from temperate phage Bam35 is endowed with processive polymerization and abasic sites translesion synthesis capacity, Proc. Natl. Acad. Sci. USA, vol.112, pp.3476-3484, 2015.

M. Berjó-n-otero, L. Villar, M. Salas, and M. Redrejo-rodríguez, Disclosing early steps of protein-primed genome replication of the Gram-positive tectivirus Bam35, Nucleic Acids Res, vol.44, pp.9733-9744, 2016.

A. J. Berman, S. Kamtekar, J. L. Goodman, J. M. Lá-zaro, M. De-vega et al., Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases, EMBO J, vol.26, pp.3494-3505, 2007.

A. Bernad, J. M. Lá-zaro, M. Salas, and L. Blanco, The highly conserved amino acid sequence motif Tyr-Gly-Asp-Thr-Asp-Ser in alphalike DNA polymerases is required by phage phi 29 DNA polymerase for protein-primed initiation and polymerization, Proc. Natl. Acad. Sci. USA, vol.87, pp.4610-4614, 1990.

M. A. Blasco, J. Mé-ndez, J. M. Lá-zaro, L. Blanco, and M. Salas, Primer terminus stabilization at the phi 29 DNA polymerase active site. Mutational analysis of conserved motif KXY, J. Biol. Chem, vol.270, pp.2735-2740, 1995.

A. Bonnín, J. M. Lá-zaro, L. Blanco, and M. Salas, A single tyrosine prevents insertion of ribonucleotides in the eukaryotic-type phi29 DNA polymerase, J. Mol. Biol, vol.290, pp.241-251, 1999.

D. K. Braithwaite and J. Ito, Compilation, alignment, and phylogenetic relationships of DNA polymerases, Nucleic Acids Res, vol.21, pp.787-802, 1993.

C. A. Brautigam and T. A. Steitz, Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes, Curr. Opin. Struct. Biol, vol.8, pp.54-63, 1998.

J. A. Brown and Z. Suo, Unlocking the sugar ''steric gate'' of DNA polymerases, Biochemistry, vol.50, pp.1135-1142, 2011.

S. Broyde, L. Wang, O. Rechkoblit, N. E. Geacintov, P. et al., Lesion processing: high-fidelity versus lesion-bypass DNA polymerases, Trends Biochem. Sci, vol.33, pp.209-219, 2008.

E. Cannavo, C. , and P. , Sae2 promotes dsDNA endonuclease activity within Mre11-Rad50-Xrs2 to resect DNA breaks, Nature, vol.514, pp.122-125, 2014.

J. Y. Choi, S. Lim, E. J. Kim, A. Jo, and F. P. Guengerich, Translesion synthesis across abasic lesions by human B-family and Y-family DNA polymerases a, d, h, i, k, and REV1, J. Mol. Biol, vol.404, pp.34-44, 2010.

W. C. Copeland, W. , and T. S. , Mutational analysis of the human DNA polymerase alpha. The most conserved region in alpha-like DNA polymerases is involved in metal-specific catalysis, J. Biol. Chem, vol.268, pp.11028-11040, 1993.

E. Dufour, J. Mé-ndez, J. M. Lá-zaro, M. De-vega, L. Blanco et al., An aspartic acid residue in TPR-1, a specific region of protein-priming DNA polymerases, is required for the functional interaction with primer terminal protein, J. Mol. Biol, vol.304, pp.289-300, 2000.

S. D. Dyall, M. T. Brown, J. , and P. J. , Ancient invasions: from endosymbionts to organelles, Science, vol.304, pp.253-257, 2004.

, Cell Reports, vol.21, pp.1574-1587, 20171585-11-07.

J. Filé-e, P. Forterre, T. Sen-lin, L. , and J. , Evolution of DNA polymerase families: evidences for multiple gene exchange between cellular and viral proteins, J. Mol. Evol, vol.54, pp.763-773, 2002.

P. Forterre, Darwin's goldmine is still open: variation and selection run the world, Front. Cell. Infect. Microbiol, vol.2, p.106, 2012.

D. N. Frick and C. C. Richardson, DNA primases, Annu. Rev. Biochem, vol.70, pp.39-80, 2001.

S. García-gó-mez, A. Reyes, M. I. Martínez-jimé-nez, E. S. Chocró-n, S. Mouró-n et al., , 2013.

, Mol. Cell, vol.52, pp.541-553

S. Gill, M. Krupovic, N. Desnoues, P. Bé-guin, G. Sezonov et al., A highly divergent archaeo-eukaryotic primase from the Thermococcus nautilus plasmid, pTN2, Nucleic Acids Res, vol.42, pp.3707-3719, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01332620

E. Gobbi, A. Carpanelli, G. Firrao, and R. Locci, The Cryphonectria parasitica plasmid pUG1 contains a large ORF with motifs characteristic of family B DNA polymerases, Nucleic Acids Res, vol.25, pp.3275-3280, 1997.

M. W. Gray, Mitochondrial evolution, Cold Spring Harb. Perspect. Biol, vol.4, p.11403, 2012.

T. A. Guilliam and A. J. Doherty, PrimPol-Prime Time to Reprime, Genes, 2017.

T. A. Guilliam, B. A. Keen, N. C. Brissett, and A. J. Doherty, Primasepolymerases are a functionally diverse superfamily of replication and repair enzymes, Nucleic Acids Res, vol.43, pp.6651-6664, 2015.

R. C. Heller and K. J. Marians, Replication fork reactivation downstream of a blocked nascent leading strand, Nature, vol.439, pp.557-562, 2006.

R. C. Hoeben and T. G. Uil, Adenovirus DNA replication, Cold Spring Harb. Perspect. Biol, vol.5, p.13003, 2013.

C. A. Hutchison, H. O. Smith, C. Pfannkoch, and J. C. Venter, Cellfree cloning using phi29 DNA polymerase, Proc. Natl. Acad. Sci. USA, vol.102, pp.17332-17336, 2005.

L. M. Iyer, E. V. Koonin, D. D. Leipe, A. , and L. , Origin and evolution of the archaeo-eukaryotic primase superfamily and related palmdomain proteins: structural insights and new members, Nucleic Acids Res, vol.33, pp.3875-3896, 2005.

S. Kamtekar, A. J. Berman, J. Wang, J. M. Lá-zaro, M. De-vega et al., The phi29 DNA polymerase:protein-primer structure suggests a model for the initiation to elongation transition, EMBO J, vol.25, pp.1335-1343, 2006.

V. V. Kapitonov, J. , and J. , Self-synthesizing DNA transposons in eukaryotes, Proc. Natl. Acad. Sci. USA, vol.103, pp.4540-4545, 2006.

D. Kazlauskas and C. Venclovas, Computational analysis of DNA replicases in double-stranded DNA viruses: relationship with the genome size, Nucleic Acids Res, vol.39, pp.8291-8305, 2011.

D. Kazlauskas, M. Krupovic, and C. Venclovas, The logic of DNA replication in double-stranded DNA viruses: insights from global analysis of viral genomes, Nucleic Acids Res, vol.44, pp.4551-4564, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01977379

T. Kent, P. A. Mateos-gomez, A. Sfeir, and R. T. Pomerantz, Polymerase q is a robust terminal transferase that oscillates between three different mechanisms during end-joining, p.13740, 2016.

R. Klassen and F. Meinhardt, Linear protein-primed replicating plasmids in eukaryotic microbes, Microbial Linear Plasmids, pp.187-226, 2007.

E. V. Koonin, Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases, Biol. Direct, vol.1, p.39, 2006.

A. Kornberg and T. A. Baker, , 1992.

M. Krupovic and E. V. Koonin, Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution, Nat. Rev. Microbiol, vol.13, pp.105-115, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01977391

M. Krupovic and E. V. Koonin, Self-synthesizing transposons: unexpected key players in the evolution of viruses and defense systems, Curr. Opin. Microbiol, vol.31, pp.25-33, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01977380

M. Krupovic, D. H. Bamford, and E. V. Koonin, Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses, Biol. Direct, vol.9, p.6, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-00994115

M. Krupovic, K. S. Makarova, P. Forterre, D. Prangishvili, and E. V. Koonin, Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity, BMC Biol, vol.12, p.36, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-01001796

M. Krupovic, P. Bé-guin, and E. V. Koonin, Casposons: mobile genetic elements that gave rise to the CRISPR-Cas adaptation machinery, Curr. Opin. Microbiol, vol.38, pp.36-43, 2017.
URL : https://hal.archives-ouvertes.fr/pasteur-01977358

R. D. Kuchta and G. Stengel, Mechanism and evolution of DNA primases, Biochim. Biophys. Acta, vol.1804, pp.1180-1189, 2010.

D. J. Laverty, A. M. Averill, S. Doublié, and M. M. Greenberg, The A-Rule and Deletion Formation During Abasic and Oxidized Abasic Site Bypass by DNA Polymerase q, ACS Chem. Biol, vol.12, pp.1584-1592, 2017.

Q. Li and F. E. Nargang, Two Neurospora mitochondrial plasmids encode DNA polymerases containing motifs characteristic of family B DNA polymerases but lack the sequence Asp-Thr-Asp, Proc. Natl. Acad. Sci. USA, vol.90, pp.4299-4303, 1993.

G. Lipps, S. Rö-ther, C. Hart, and G. Krauss, A novel type of replicative enzyme harbouring ATPase, primase and DNA polymerase activity, EMBO J, vol.22, pp.2516-2525, 2003.

P. Ló-pez-garcía and D. Moreira, Open Questions on the Origin of Eukaryotes, Trends Ecol. Evol, vol.30, pp.697-708, 2015.

K. S. Makarova, Y. I. Wolf, P. Forterre, D. Prangishvili, M. Krupovic et al., Dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes, Extremophiles, vol.18, pp.877-893, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-01977394

M. I. Martínez-jimé-nez, S. García-gó-mez, K. Bebenek, G. Sastre-moreno, P. A. Calvo et al., Alternative solutions and new scenarios for translesion DNA synthesis by human PrimPol, DNA Repair (Amst.), vol.29, pp.127-138, 2015.

S. Mouró-n, S. Rodriguez-acebes, M. I. Martínez-jimé-nez, S. García-gó-mez, S. Chocró-n et al., Repriming of DNA synthesis at stalled replication forks by human PrimPol, Nat. Struct. Mol. Biol, vol.20, pp.1383-1389, 2013.

P. Nevin, C. C. Gabbai, and K. J. Marians, Replisome-mediated translesion synthesis by a cellular replicase, J. Biol. Chem, vol.292, pp.13833-13842, 2017.

X. Peng, T. Basta, M. Hä-ring, R. A. Garrett, P. et al., , 2007.

, Genome of the Acidianus bottle-shaped virus and insights into the replication and packaging mechanisms, Virology, vol.364, pp.237-243

A. J. Picher, B. Budeus, O. Wafzig, C. Kr?-uger, S. García-gó-mez et al., TruePrime is a novel method for whole-genome amplification from single cells based on TthPrimPol, Nat. Commun, vol.7, p.13296, 2016.

I. Rodríguez, J. M. Lá-zaro, L. Blanco, S. Kamtekar, A. J. Berman et al., A specific subdomain in phi29 DNA polymerase confers both processivity and strand-displacement capacity, Proc. Natl. Acad. Sci. USA, vol.102, pp.6407-6412, 2005.

W. D. Rupp, H. , and P. , Discontinuities in the DNA synthesized in an excision-defective strain of Escherichia coli following ultraviolet irradiation, J. Mol. Biol, vol.31, pp.291-304, 1968.

M. Salas, Protein-priming of DNA replication, Annu. Rev. Biochem, vol.60, pp.39-71, 1991.

M. Salas and M. Vega, Protein-Primed Replication of Bacteriophage F29 DNA, pp.137-167, 2016.

M. Salas, I. Holguera, M. Redrejo-rodríguez, and M. Vega, DNAbinding proteins essential for protein-primed bacteriophage F29 DNA replication, Front. Mol. Biosci, vol.3, p.37, 2016.

J. Sambrook, R. , and D. , Molecular cloning: a laboratory manual, 2001.

, Cell Reports, vol.21, pp.1574-1587, 2017.

U. Schulte and A. M. Lambowitz, The LaBelle mitochondrial plasmid of Neurospora intermedia encodes a novel DNA polymerase that may be derived from a reverse transcriptase, Mol. Cell. Biol, vol.11, pp.1696-1706, 1991.

A. M. Sidore, F. Lan, S. W. Lim, and A. R. Abate, Enhanced sequencing coverage with digital droplet multiple displacement amplification, Nucleic Acids Res, vol.44, p.66, 2016.

M. S. Soengas, J. A. Esteban, J. M. Lá-zaro, A. Bernad, M. A. Blasco et al., Site-directed mutagenesis at the Exo III motif of phi 29 DNA polymerase; overlapping structural domains for the 3 0-5 0 exonuclease and strand-displacement activities, EMBO J, vol.11, pp.4227-4237, 1992.

B. S. Strauss, The ''A'' rule revisited: polymerases as determinants of mutational specificity, DNA Repair (Amst.), vol.1, pp.125-135, 2002.

B. Sun, M. Pandey, J. T. Inman, Y. Yang, M. Kashlev et al., T7 replisome directly overcomes DNA damage, Nat. Commun, vol.6, p.10260, 2015.

N. Tanguy-le-gac, E. Delagoutte, M. Germain, and G. Villani, Inactivation of the 3 0-5 0 exonuclease of the replicative T4 DNA polymerase allows translesion DNA synthesis at an abasic site, J. Mol. Biol, vol.336, pp.1023-1034, 2004.

A. Vaisman, W. , and R. , Translesion DNA polymerases in eukaryotes: what makes them tick?, Crit. Rev. Biochem. Mol. Biol, vol.52, pp.274-303, 2017.

J. S. Valentine, D. L. Wertz, T. J. Lyons, L. L. Liou, J. J. Goto et al., The dark side of dioxygen biochemistry, Curr. Opin. Chem. Biol, vol.2, pp.253-262, 1998.

G. Villani, N. Tanguy-le-gac, L. Wasungu, D. Burnouf, R. P. Fuchs et al., Effect of manganese on in vitro replication of damaged DNA catalyzed by the herpes simplex virus type-1 DNA polymerase, Nucleic Acids Res, vol.30, pp.3323-3332, 2002.

J. Wang, A. K. Sattar, C. C. Wang, J. D. Karam, W. H. Konigsberg et al., Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69, Cell, vol.89, pp.1087-1099, 1997.

W. Yang, An overview of Y-Family DNA polymerases and a case study of human DNA polymerase h, Biochemistry, vol.53, pp.2793-2803, 2014.

Y. Zhu, L. Song, J. Stroud, and D. S. Parris, Mechanisms by which herpes simplex virus DNA polymerase limits translesion synthesis through abasic sites, DNA Repair (Amst.), vol.7, pp.95-107, 2008.

B. Zhu, L. Wang, H. Mitsunobu, X. Lu, A. J. Hernandez et al., Deep-sea vent phage DNA polymerase specifically initiates DNA synthesis in the absence of primers, Proc. Natl. Acad. Sci. USA, vol.114, pp.2310-2318, 2017.

, Cell Reports, vol.21, pp.1574-1587, 20171587-11-07.

, Cell Reports, vol.21

M. Redrejo-rodríguez, C. D. Ordóñez, M. Berjón-otero, J. Morenogonzález, C. Aparicio-maldonado et al.,

S. F. Altschul, T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang et al., , 1997.

. Gapped, PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res, vol.25, pp.3389-3402

S. Capella-gutierrez, J. M. Silla-martinez, and T. Gabaldon, trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, vol.25, pp.1972-1973, 2009.

S. García-gómez, A. Reyes, M. I. Martínez-jiménez, E. S. Chocron, S. Mourón et al., PrimPol, an archaic primase/polymerase operating in human cells, Mol Cell, vol.52, pp.541-553, 2013.

S. Guindon, J. F. Dufayard, V. Lefort, M. Anisimova, W. Hordijk et al., New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0, Syst Biol, vol.59, pp.307-321, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511784

M. Krupovic and E. V. Koonin, Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution, Nat Rev Microbiol, vol.13, pp.105-115, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01977391

K. Okonechnikov, O. Golosova, M. Fursov, T. , and U. , Unipro UGENE: a unified bioinformatics toolkit, Bioinformatics, vol.28, pp.1166-1167, 2012.

J. Pei and N. V. Grishin, PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information, Methods Mol Biol, vol.1079, pp.263-271, 2014.

J. Soding, A. Biegert, and A. N. Lupas, The HHpred interactive server for protein homology detection and structure prediction, Nucleic Acids Res, vol.33, pp.244-248, 2005.

A. Spriestersbach, J. Kubicek, F. Schafer, H. Block, and B. Maertens, Purification of HisTagged Proteins, Methods Enzymol, vol.559, pp.1-15, 2015.

F. W. Studier, Protein production by auto-induction in high density shaking cultures, Protein Expr Purif, vol.41, pp.207-234, 2005.

M. J. Sullivan, N. K. Petty, and S. A. Beatson, Easyfig: a genome comparison visualizer, Bioinformatics, vol.27, pp.1009-1010, 2011.