A. Kornberg, T. A. Baker, and . Dna-replication, , 2005.

P. H. Patel and L. A. Loeb, Getting a grip on how DNA polymerases function, Nat Struct Biol, vol.8, issue.8, p.11473246, 2001.

D. K. Braithwaite and J. Ito, Compilation, alignment, and phylogenetic relationships of DNA polymerases, Nucleic Acids Res, vol.21, issue.4, p.8451181, 1993.

M. Delarue, O. Poch, N. Tordo, D. Moras, and P. Argos, An attempt to unify the structure of polymerases. Protein Eng, vol.3, p.2196557, 1990.

M. Hogg, P. Osterman, G. O. Bylund, R. A. Ganai, . Lundströ-m-e-b et al., Structural basis for processive DNA synthesis by yeast DNA polymerase ?, Nat Struct Mol Biol, vol.21, issue.1, p.24292646, 2014.

R. J. Evans, D. R. Davies, J. M. Bullard, J. Christensen, L. S. Green et al., Structure of PolC reveals unique DNA binding and fidelity determinants, Proc Natl Acad Sci, vol.105, issue.52, p.19106298, 2008.

R. A. Wing, S. Bailey, and T. A. Steitz, Insights into the replisome from the structure of a ternary complex of the DNA polymerase III alpha-subunit, J Mol Biol, vol.382, issue.4, p.18691598, 2008.

M. Imamura, T. Uemori, I. Kato, and Y. Ishino, A non-alpha-like DNA polymerase from the hyperthermophilic archaeon Pyrococcus furiosus, Biol Pharm Bull, vol.18, issue.12, p.8787781, 1995.

Y. Ishino, K. Komori, I. K. Cann, and Y. Koga, A novel DNA polymerase family found in Archaea, J Bacteriol, vol.180, issue.8, p.9555910, 1998.

L. Greenough, Z. Kelman, and A. F. Gardner, The roles of family B and D DNA polymerases in Thermococcus species 9?N Okazaki fragment maturation, J Biol Chem, vol.290, issue.20, p.25814667, 2015.

G. Henneke, D. Flament, U. Hü-bscher, J. Querellou, and J. Raffin, The hyperthermophilic euryarchaeota Pyrococcus abyssi likely requires the two DNA polymerases D and B for DNA replication, J Mol Biol

, Jul, vol.1, issue.1, p.15922358

B. R. Berquist, P. Dassarma, and S. Dassarma, Essential and non-essential DNA replication genes in the model halophilic Archaeon, Halobacterium sp. NRC-1. BMC Genet, vol.8, p.17559652, 2007.

L. Cubonová, T. Richardson, B. W. Burkhart, Z. Kelman, B. A. Connolly et al., Archaeal DNA polymerase D but not DNA polymerase B is required for genome replication in Thermococcus kodakarensis, J Bacteriol, vol.195, issue.10, p.23504010, 2013.

C. J. Castelle and J. F. Banfield, Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life, Cell, vol.172, issue.6, p.29522741, 2018.

L. Sauguet, P. Raia, G. Henneke, and M. Delarue, Shared active site architecture between archaeal PolD and multi-subunit RNA polymerases revealed by X-ray crystallography, Nat Commun, vol.7, p.27548043, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01389383

G. Ruprich-robert and P. Thuriaux, Non-canonical DNA transcription enzymes and the conservation of twobarrel RNA polymerases, Nucleic Acids Res, vol.38, issue.14, p.20360047, 2010.

L. M. Iyer, E. V. Koonin, and L. Aravind, Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases, BMC Struct Biol, vol.3, p.12553882, 2003.

F. Werner and D. Grohmann, Evolution of multisubunit RNA polymerases in the three domains of life, Nat Rev Microbiol, vol.9, issue.2, p.21233849, 2011.

E. Lehmann, F. Brueckner, and P. Cramer, Molecular basis of RNA-dependent RNA polymerase II activity, Nature, vol.450, issue.7168, p.18004386, 2007.

T. Fouqueau, F. Blombach, and F. Werner, Evolutionary Origins of Two-Barrel RNA Polymerases and SiteSpecific Transcription Initiation, Annu Rev Microbiol, vol.71, p.28657884, 2017.

A. Palud, G. Villani, L. 'haridon, S. Querellou, J. Raffin et al., Intrinsic properties of the two replicative DNA polymerases of Pyrococcus abyssi in replicating abasic sites: possible role in DNA damage tolerance? Mol Microbiol, vol.70, p.18826407, 2008.

D. Kimanius, B. O. Forsberg, S. H. Scheres, and E. Lindahl, Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2. eLife, vol.5, 2016.

A. Punjani, J. L. Rubinstein, D. J. Fleet, and M. A. Brubaker, cryoSPARC: algorithms for rapid unsupervised cryoEM structure determination, Nat Methods, vol.14, issue.3, p.28165473, 2017.

A. G. Baranovskiy, J. Gu, N. D. Babayeva, I. Kurinov, Y. I. Pavlov et al., Crystal structure of the human Pol? B-subunit in complex with the C-terminal domain of the catalytic subunit, J Biol Chem, 201722.

, , vol.292, p.28747437

D. Wang, D. A. Bushnell, K. D. Westover, C. D. Kaplan, and R. D. Kornberg, Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis, Cell, vol.127, issue.5, p.17129781, 2006.

P. Emsley, B. Lohkamp, W. G. Scott, and K. Cowtan, Features and development of Coot, Acta Crystallogr D Biol Crystallogr, vol.66, p.20383002, 2010.

A. Drozdetskiy, C. Cole, J. Procter, and G. J. Barton, JPred4: a protein secondary structure prediction server, Nucleic Acids Res, vol.43, issue.W1, p.25883141, 2015.

I. Matsui, Y. Urushibata, Y. Shen, E. Matsui, and H. Yokoyama, Novel structure of an N-terminal domain that is crucial for the dimeric assembly and DNA-binding of an archaeal DNA polymerase D large subunit from Pyrococcus horikoshii, FEBS Lett, vol.585, issue.3, p.21192935, 2011.

L. Holm and P. Rosenström, Dali server: conservation mapping in 3D, Nucleic Acids Res, vol.38, issue.2, pp.545-554, 2010.

N. V. Grishin, KH domain: one motif, two folds, Nucleic Acids Res, vol.29, issue.3, p.11160884, 2001.

X. Chen, D. L. Court, and J. X. , Crystal structure of ERA: A GTPase-dependent cell cycle regulator containing an RNA binding motif, Proc Natl Acad Sci, vol.96, issue.15, p.10411886, 1999.

K. Timinskas and ?. Venclovas, The N-terminal region of the bacterial DNA polymerase PolC features a pair of domains, both distantly related to domain V of the DNA polymerase III ? subunit, FEBS J, 2011.

, , vol.278, p.21740522

B. Beuth, S. Pennell, K. B. Arnvig, S. R. Martin, and I. A. Taylor, Structure of a Mycobacterium tuberculosis NusARNA complex, EMBO J, vol.24, issue.20, p.16193062, 2005.

J. A. Dunkle, K. Vinal, P. M. Desai, N. Zelinskaya, M. Savic et al., Molecular recognition and modification of the 30S ribosome by the aminoglycoside-resistance methyltransferase NpmA, Proc Natl Acad Sci, vol.111, issue.17, p.24717845, 2014.

T. H. Tahirov, K. S. Makarova, I. B. Rogozin, Y. I. Pavlov, and E. V. Koonin, Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol ? and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors, Biol Direct, vol.4, p.19296856, 2009.

L. A. Kelley, S. Mezulis, C. M. Yates, M. N. Wass, and M. Sternberg, The Phyre2 web portal for protein modeling, prediction and analysis, Nat Protoc, vol.10, issue.6, p.25950237, 2015.

M. Landau, I. Mayrose, Y. Rosenberg, F. Glaser, E. Martz et al., ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures, Nucleic Acids Res, vol.33, p.15980475, 2005.

Y. Shen, X. Tang, H. Yokoyama, E. Matsui, and I. Matsui, A 21-amino acid peptide from the cysteine cluster II of the family D DNA polymerase from Pyrococcus horikoshii stimulates its nuclease activity which is Mre11-like and prefers manganese ion as the cofactor, Nucleic Acids Res, vol.32, issue.1, p.14704353, 2004.

X. Tang, Y. Shen, E. Matsui, and I. Matsui, Domain topology of the DNA polymerase D complex from a hyperthermophilic archaeon Pyrococcus horikoshii. Biochemistry (Mosc), vol.43, pp.11818-11845, 2004.

P. J. Rothwell and G. Waksman, Structure and mechanism of DNA polymerases, Adv Protein Chem, vol.71, p.16230118, 2005.

S. Doublié and K. E. Zahn, Structural insights into eukaryotic DNA replication. Front Microbiol, vol.5, 2014.

J. Abellón-ruiz, K. J. Waldron, and B. A. Connolly, Archaeoglobus Fulgidus DNA Polymerase D: A Zinc-Binding Protein Inhibited by Hypoxanthine and Uracil, J Mol Biol, vol.17, issue.14, p.27320386, 2016.

T. T. Richardson, L. Gilroy, Y. Ishino, B. A. Connolly, and G. Henneke, Novel inhibition of archaeal family-D DNA polymerase by uracil, Nucleic Acids Res, vol.41, issue.7, p.23408858, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00834323

T. T. Richardson, X. Wu, B. J. Keith, P. Heslop, A. C. Jones et al., Unwinding of primer-templates by archaeal family-B DNA polymerases in response to template-strand uracil, Nucleic Acids Res, vol.41, issue.4, p.23303790, 2013.

N. C. Seeman, J. M. Rosenberg, and A. Rich, Sequence-specific recognition of double helical nucleic acids by proteins, Proc Natl Acad Sci, vol.73, issue.3, p.1062791, 1976.

S. Doublié, S. Tabor, A. M. Long, C. C. Richardson, and T. Ellenberger, Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution, Nature, vol.391, issue.6664, p.9440688, 1998.

S. Matsumiya, Y. Ishino, and K. Morikawa, Crystal structure of an archaeal DNA sliding clamp: Proliferating cell nuclear antigen from Pyrococcus furiosus, Protein Sci Publ Protein Soc, vol.10, issue.1, pp.17-23, 2001.

S. Matsumiya, S. Ishino, Y. Ishino, and K. Morikawa, Physical interaction between proliferating cell nuclear antigen and replication factor C from Pyrococcus furiosus, Genes Cells Devoted Mol Cell Mech, vol.7, issue.9, pp.911-933, 2002.

R. Mcnally, G. D. Bowman, E. R. Goedken, O. Donnell, M. Kuriyan et al., Analysis of the role of PCNA-DNA contacts during clamp loading, BMC Struct Biol, vol.10, p.20113510, 2010.

K. Tori, M. Kimizu, S. Ishino, and Y. Ishino, DNA polymerases BI and D from the hyperthermophilic archaeon Pyrococcus furiosus both bind to proliferating cell nuclear antigen with their C-terminal PIP-box motifs, J Bacteriol, vol.189, issue.15, p.17496095, 2007.

M. Castillo-lizardo, G. Henneke, and E. Viguera, Replication slippage of the thermophilic DNA polymerases B and D from the Euryarchaeota Pyrococcus abyssi. Front Microbiol, vol.5, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01111443

P. S. Salgado, M. Koivunen, E. V. Makeyev, D. H. Bamford, D. I. Stuart et al., The structure of an RNAi polymerase links RNA silencing and transcription, PLoS Biol, vol.4, issue.12, 2006.

K. D. Westover, D. A. Bushnell, and R. D. Kornberg, Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center, PLOS Biology, vol.53, issue.4, p.15537538, 2004.

R. Weinzierl, The Bridge Helix of RNA Polymerase Acts as a Central Nanomechanical Switchboard for Coordinating Catalysis and Substrate Movement

, Archaea, 2011.

S. Hamdan, P. D. Carr, S. E. Brown, D. L. Ollis, and N. E. Dixon, Structural basis for proofreading during replication of the Escherichia coli chromosome, Struct Lond Engl, vol.10, issue.4, pp.535-581, 1993.

L. Aravind and E. V. Koonin, Phosphoesterase domains associated with DNA polymerases of diverse origins, Nucleic Acids Res, vol.26, issue.16, p.9685491, 1998.

M. Lemor, Z. Kong, E. Henry, R. Brizard, S. Laurent et al., Differential Activities of DNA Polymerases in Processing Ribonucleotides during DNA Synthesis in Archaea, J Mol Biol, 2018.

Y. Suwa, J. Gu, A. G. Baranovskiy, N. D. Babayeva, Y. I. Pavlov et al., Crystal Structure of the Human Pol ? B Subunit in Complex with the C-terminal Domain of the Catalytic Subunit, J Biol Chem, vol.290, issue.23, p.25847248, 2015.

P. Schuck, M. A. Perugini, N. R. Gonzales, G. J. Howlett, and D. Schubert, Size-distribution analysis of proteins by analytical ultracentrifugation: strategies and application to model systems, Biophys J, vol.82, issue.2, p.11806949, 2002.

M. Jokela, A. Eskelinen, H. Pospiech, J. Rouvinen, and J. E. Syväoja, Characterization of the 3' exonuclease subunit DP1 of Methanococcus jannaschii replicative DNA polymerase D, Nucleic Acids Res, vol.32, issue.8, p.15121900, 2004.

P. Emsley and K. Cowtan, Coot: model-building tools for molecular graphics, Acta Crystallogr D Biol Crystallogr, vol.60, p.15572765, 2004.

P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, N. Echols et al., The Phenix software for automated determination of macromolecular structures. Methods San Diego Calif, vol.55, pp.94-106, 2011.