O. Donnell, M. Langston, L. Stillman, and B. , Principles and concepts of DNA replication in bacteria, archaea, and eukarya. Cold Spring Harb Perspect, 2013.

C. Woese, O. Kandler, and M. Wheelis, Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya., Proceedings of the National Academy of Sciences, vol.87, issue.12, pp.4576-4585
DOI : 10.1073/pnas.87.12.4576

C. Brochier-armanet, B. Boussau, S. Gribaldo, and P. Forterre, Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota, Nature Reviews Microbiology, vol.52, issue.3, pp.245-52, 2008.
DOI : 10.1038/nrmicro1852

URL : https://hal.archives-ouvertes.fr/hal-00256781

H. Myllykallio, P. Lopez, P. Lopez-garcia, R. Heilig, W. Saurin et al., Bac? terial mode of replication with eukaryotic-like machinery in a hyperthermophilic ar? chaeon, pp.2212-2217, 2000.

M. Hawkins, S. Malla, M. Blythe, C. Nieduszynski, and T. Allers, Accelerated growth in the absence of DNA replication origins, Nature, vol.9, issue.7477, pp.544-551
DOI : 10.1038/nature12650

C. Norais, M. Hawkins, A. Hartman, J. Eisen, H. Myllykallio et al., Genetic and Physical Mapping of DNA Replication Origins in Haloferax volcanii, PLoS Genetics, vol.393, issue.5, p.77
DOI : 10.1371/journal.pgen.0030077.st001

URL : https://hal.archives-ouvertes.fr/hal-00195310

E. Pelve, W. Martens-habbena, D. Stahl, and R. Bernander, Mapping of active replica? tion origins in vivo in thaum-and euryarchaeal replicons, Mol, vol.90, issue.3, pp.538-50, 2013.

S. Maisnier-patin, L. Malandrin, N. Birkeland, and R. Bernander, Chromosome replication patterns in the hyperthermophilic euryarchaea Archaeoglobus fulgidus and Metha? nocaldococcus (Methanococcus) jannaschii, Mol, vol.45, issue.5, pp.1443-50, 2002.

B. Berquist and S. Dassarma, An Archaeal Chromosomal Autonomously Replicating Sequence Element from an Extreme Halophile, Halobacterium sp. Strain NRC-1, Journal of Bacteriology, vol.185, issue.20, pp.5959-66, 2003.
DOI : 10.1128/JB.185.20.5959-5966.2003

J. Coker, P. Dassarma, M. Capes, T. Wallace, K. Mcgarrity et al., Multiple Replication Origins of Halobacterium sp. Strain NRC-1: Properties of the Conserved orc7-Dependent oriC1, Journal of Bacteriology, vol.191, issue.16, pp.5253-61, 2009.
DOI : 10.1128/JB.00210-09

Z. Wu, H. Liu, J. Liu, X. Liu, and H. Xiang, Diversity and evolution of multiple orc/cdc6-adjacent replication origins in haloarchaea, BMC Genomics, vol.13, issue.1, p.478, 2012.
DOI : 10.1093/bioinformatics/btn578

A. Majernik and J. Chong, A conserved mechanism for replication origin recognition and binding in archaea, Biochemical Journal, vol.409, issue.2, pp.511-519, 2008.
DOI : 10.1042/BJ20070213

URL : https://hal.archives-ouvertes.fr/hal-00478756

M. Lundgren, A. Andersson, L. Chen, P. Nilsson, and R. Bernander, Three replication origins in Sulfolobus species: Synchronous initiation of chromosome replication and asynchronous termination, Proceedings of the National Academy of Sciences, vol.101, issue.18, pp.7046-51, 2004.
DOI : 10.1073/pnas.0400656101

R. Samson, Y. Xu, C. Gadelha, T. Stone, J. Faqiri et al., Specificity and func? tion of archaeal DNA replication initiator proteins, Cell Rep2013 Feb, vol.213, issue.2, pp.485-96

E. Pelve, A. Lindas, A. Knoppel, A. Mira, and R. Bernander, Four chromosome replica? tion origins in the archaeon Pyrobaculum calidifontis, Mol, vol.85, issue.5, pp.986-95, 2012.

N. Robinson and S. Bell, Extrachromosomal element capture and the evolution of multiple replication origins in archaeal chromosomes, Proceedings of the National Academy of Sciences, vol.104, issue.14, pp.5806-5817
DOI : 10.1073/pnas.0700206104

H. Luo, C. Zhang, and F. Gao, Ori-Finder 2, an integrated tool to predict replication ori? gins in the archaeal genomes, Frontiers in Microbiology, vol.5, pp.2014-2029

A. Andersson, E. Pelve, S. Lindeberg, M. Lundgren, P. Nilsson et al., Replication-biased genome organisation in the crenarchaeon Sulfolobus, BMC Genomics, vol.11, issue.1, p.454, 2010.
DOI : 10.1186/1471-2164-11-454

F. Matsunaga, P. Forterre, Y. Ishino, and H. Myllykallio, In vivo interactions of archaeal Cdc6/Orc1 and minichromosome maintenance proteins with the replication origin, Proceedings of the National Academy of Sciences, vol.98, issue.20, pp.11152-11159, 2001.
DOI : 10.1073/pnas.191387498

S. Capaldi and J. Berger, Biochemical characterization of Cdc6/Orc1 binding to the replication origin of the euryarchaeon Methanothermobacter thermoautotrophicus, Nucleic Acids Research, vol.32, issue.16, pp.4821-4853, 2004.
DOI : 10.1093/nar/gkh819

N. Robinson, I. Dionne, M. Lundgren, V. Marsh, R. Bernander et al., Identification of Two Origins of Replication in the Single Chromosome of the Archaeon Sulfolobus solfataricus, Cell, vol.116, issue.1, pp.25-38, 2004.
DOI : 10.1016/S0092-8674(03)01034-1

Z. Wu, J. Liu, H. Yang, H. Liu, and H. Xiang, Multiple replication origins with diverse con? trol mechanisms in Haloarcula hispanica. Nucleic Acids Res2014 Feb, pp.2282-94

W. Woods and M. Smith, Construction and analysis of a recombination-deficient (radA) mutant of Haloferax volcanii, Molecular Microbiology, vol.23, issue.4, pp.791-798
DOI : 10.1046/j.1365-2958.1997.2651626.x

R. Kolodner, C. Putnam, and M. K. , Maintenance of genome stability in Saccharo? myces cerevisiae, pp.552-559, 2002.

T. Abbas, M. Keaton, and A. Dutta, Genomic instability in cancer. Cold Spring Harb Per? spect Biol2013 Mar, p.12914

A. Jackson, R. Laskey, and N. Coleman, Replication proteins and human disease. Cold Spring Harb Perspect, 2014.
DOI : 10.1101/cshperspect.a013060

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3941220

S. Breuert, T. Allers, G. Spohn, and J. Soppa, Regulated Polyploidy in Halophilic Archaea, PLoS ONE, vol.178, issue.22, p.92, 2006.
DOI : 10.1371/journal.pone.0000092.t001

C. Cvetic and J. Walter, Eukaryotic origins of DNA replication: could you please be more specific? Semin Cell Dev Biol2005, pp.343-53

B. Michel and R. Bernander, Chromosome replication origins: Do we really need them?, BioEssays, vol.11, issue.6, pp.585-90, 2014.
DOI : 10.1002/bies.201400003

P. Pluchon, T. Fouqueau, C. Creze, S. Laurent, J. Briffotaux et al., An Extended Network of Genomic Maintenance in the Archaeon Pyrococcus abyssi Highlights Unexpected Associations between Eucaryotic Homologs, PLoS ONE, vol.63, issue.11, p.79707, 2013.
DOI : 10.1371/journal.pone.0079707.s003

URL : https://hal.archives-ouvertes.fr/hal-00911795

R. Lestini, Z. Duan, and T. Allers, The archaeal Xpf/Mus81/FANCM homolog Hef and the Holliday junction resolvase Hjc define alternative pathways that are essential for cell viability in Haloferax volcanii, DNA Repair, vol.9, issue.9, pp.994-1002, 2010.
DOI : 10.1016/j.dnarep.2010.06.012

R. Lestini, S. Laptenok, J. Kuhn, M. Hink, M. Schanne-klein et al., Intracel? lular dynamics of archaeal FANCM homologue Hef in response to halted DNA repli? cation. Nucleic Acids, pp.10358-70, 2013.

J. Enzlin and O. Scharer, The active site of the DNA repair endonuclease XPF-ERCC1 forms a highly conserved nuclease motif, The EMBO Journal, vol.21, issue.8, pp.2045-53
DOI : 10.1093/emboj/21.8.2045

J. Sgouros, P. Gaillard, and R. Wood, A relationship between a DNA-repair/recombination nuclease family and archaeal helicases, Trends in Biochemical Sciences, vol.24, issue.3, pp.95-102, 1999.
DOI : 10.1016/S0968-0004(99)01355-9

A. Ciccia, C. Ling, R. Coulthard, Z. Yan, Y. Xue et al., Identification of FAAP24, a Fanconi Anemia Core Complex Protein that Interacts with FANCM, Molecular Cell, vol.25, issue.3, pp.331-374
DOI : 10.1016/j.molcel.2007.01.003

A. Meetei, A. Medhurst, C. Ling, Y. Xue, T. Singh et al., A human ortholog of archaeal DNA repair protein Hef is defective in Fanconi anemia complementation group M, Nature Genetics, vol.7, issue.9, pp.958-63
DOI : 10.1073/pnas.1937626100

A. Ciccia, N. Mcdonald, and S. West, Structural and Functional Relationships of the XPF/MUS81 Family of Proteins, Annual Review of Biochemistry, vol.77, issue.1, pp.259-87, 2008.
DOI : 10.1146/annurev.biochem.77.070306.102408

K. Komori, R. Fujikane, H. Shinagawa, and Y. Ishino, Novel endonuclease in Archaea cleaving DNA with various branched structure, Genes & Genetic Systems, vol.77, issue.4, pp.227-268, 2002.
DOI : 10.1266/ggs.77.227

G. Mosedale, W. Niedzwiedz, A. Alpi, F. Perrina, J. Pereira-leal et al., The vertebrate Hef ortholog is a component of the Fanconi anemia tumor-suppressor pathway, Nature Structural & Molecular Biology, vol.11, issue.9, pp.763-71
DOI : 10.1093/emboj/cdf355

M. Newman, J. Murray-rust, J. Lally, R. J. Fadden, A. Knowles et al., Structure of an XPF endonuclease with and without DNA suggests a model for substrate rec? ognition, pp.895-905, 2005.

J. Roberts, S. Bell, and M. White, An archaeal XPF repair endonuclease dependent on a heterotrimeric PCNA, Molecular Microbiology, vol.277, issue.2, pp.361-71
DOI : 10.1046/j.1365-2958.2003.03444.x

L. Meslet-cladiere, C. Norais, J. Kuhn, J. Briffotaux, J. Sloostra et al., A Novel Proteomic Approach Identifies New Interaction Partners for Proliferating Cell Nuclear Antigen, Journal of Molecular Biology, vol.372, issue.5, pp.1137-1185, 2007.
DOI : 10.1016/j.jmb.2007.06.056

URL : https://hal.archives-ouvertes.fr/hal-00193755

R. Hutton, T. Craggs, M. White, and J. Penedo, PCNA and XPF cooperate to distort DNA substrates. Nucleic Acids Res2010 Mar, pp.1664-75

R. Hutton, J. Roberts, J. Penedo, and M. White, PCNA stimulates catalysis by struc? ture-specific nucleases using two distinct mechanisms: substrate targeting and cata? lytic step. Nucleic Acids, pp.6720-6727, 2008.

J. Roberts and M. White, DNA end-directed and processive nuclease activities of the archaeal XPF enzyme, Nucleic Acids Research, vol.33, issue.20, pp.6662-70, 2005.
DOI : 10.1093/nar/gki974

J. Roberts and M. White, An archaeal endonuclease displays key properties of both eu? karyal XPF-ERCC1 and Mus81, J Biol Chem2005 Feb, vol.18280, issue.7, pp.5924-5932

T. Nishino, K. Komori, Y. Ishino, and K. Morikawa, X-Ray and Biochemical Anatomy of an Archaeal XPF/Rad1/Mus81 Family Nuclease, Structure, vol.11, issue.4, pp.445-57
DOI : 10.1016/S0969-2126(03)00046-7

T. Nishino, K. Komori, Y. Ishino, and K. Morikawa, Structural and Functional Analyses of an Archaeal XPF/Rad1/Mus81 Nuclease: Asymmetric DNA Binding and Cleavage Mechanisms, Structure, vol.13, issue.8, pp.1183-92, 2005.
DOI : 10.1016/j.str.2005.04.024

T. Nishino, K. Komori, D. Tsuchiya, Y. Ishino, and K. Morikawa, Crystal Structure and Functional Implications of Pyrococcus furiosus Hef Helicase Domain Involved in Branched DNA Processing, Structure, vol.13, issue.1, pp.143-53
DOI : 10.1016/j.str.2004.11.008

K. Komori, M. Hidaka, T. Horiuchi, R. Fujikane, H. Shinagawa et al., Cooperation of the N-terminal Helicase and C-terminal endonuclease activities of Archaeal Hef pro? tein in processing stalled replication forks, J Biol, vol.279, issue.51, pp.53175-85, 2004.

C. Doe, F. Osman, J. Dixon, and M. Whitby, DNA repair by a Rad22-Mus81-dependent pathway that is independent of Rhp51, Nucleic Acids Research, vol.32, issue.18, pp.5570-81, 2004.
DOI : 10.1093/nar/gkh853

B. Froget, J. Blaisonneau, S. Lambert, and G. Baldacci, Cleavage of Stalled Forks by Fission Yeast Mus81/Eme1 in Absence of DNA Replication Checkpoint, Molecular Biology of the Cell, vol.19, issue.2, pp.445-56
DOI : 10.1091/mbc.E07-07-0728

M. Kai, M. Boddy, P. Russell, and T. Wang, Replication checkpoint kinase Cds1 regulates Mus81 to preserve genome integrity during replication stress, Genes & Development, vol.19, issue.8, pp.919-951, 2005.
DOI : 10.1101/gad.1304305

P. Matulova, V. Marini, R. Burgess, A. Sisakova, Y. Kwon et al., Coopera? tivity of Mus81.Mms4 with Rad54 in the resolution of recombination and replication intermediates, J Biol, vol.284, issue.12, pp.7733-7778, 2009.

L. Roseaulin, Y. Yamada, Y. Tsutsui, P. Russell, H. Iwasaki et al., Mus81 is es? sential for sister chromatid recombination at broken replication forks, pp.1378-87, 2008.

V. Kaliraman, J. Mullen, W. Fricke, S. Bastin-shanower, and S. Brill, Functional overlap between Sgs1-Top3 and the Mms4-Mus81 endonuclease, Genes & Development, vol.15, issue.20, pp.2730-2770, 2001.
DOI : 10.1101/gad.932201

X. Chen, R. Melchionna, C. Denis, P. Gaillard, A. Blasina et al., Human Mus81-Associated Endonuclease Cleaves Holliday Junctions In Vitro, Molecular Cell, vol.8, issue.5, pp.1117-1144
DOI : 10.1016/S1097-2765(01)00375-6

A. Ciccia, A. Constantinou, and S. West, Identification and Characterization of the Human Mus81-Eme1 Endonuclease, Journal of Biological Chemistry, vol.278, issue.27, pp.25172-25180
DOI : 10.1074/jbc.M302882200

A. Franchitto, L. Pirzio, E. Prosperi, O. Sapora, M. Bignami et al., Replication fork stalling in WRN-deficient cells is overcome by prompt activation of a MUS81-dependent pathway, The Journal of Cell Biology, vol.14, issue.2, pp.241-52, 2008.
DOI : 10.1073/pnas.95.15.8733

K. Hanada, M. Budzowska, S. Davies, E. Van-drunen, H. Onizawa et al., The structure-specific endonuclease Mus81 contributes to replication restart by generating double-strand DNA breaks, Nature Structural & Molecular Biology, vol.574, issue.11, pp.1096-104, 2007.
DOI : 10.1128/MCB.24.13.5776-5787.2004

T. Shimura, M. Torres, M. Martin, V. Rao, Y. Pommier et al., Bloom's Syndrome Helicase and Mus81 are Required to Induce Transient Double-strand DNA Breaks in Response to DNA Replication Stress, Journal of Molecular Biology, vol.375, issue.4, pp.1152-64, 2008.
DOI : 10.1016/j.jmb.2007.11.006

S. Ishino, T. Yamagami, M. Kitamura, N. Kodera, T. Mori et al., Multiple Interactions of the Intrinsically Disordered Region between the Helicase and Nuclease Domains of the Archaeal Hef Protein, Journal of Biological Chemistry, vol.289, issue.31, pp.21627-21666, 2014.
DOI : 10.1074/jbc.M114.554998

R. Fujikane, S. Ishino, Y. Ishino, and P. Forterre, Genetic analysis of DNA repair in the hyperthermophilic archaeon, Thermococcus kodakaraensis, Genes & Genetic Systems, vol.85, issue.4, pp.243-57, 2010.
DOI : 10.1266/ggs.85.243

C. Rouillon and M. White, The evolution and mechanisms of nucleotide excision repair proteins, Research in Microbiology, vol.162, issue.1, pp.19-26
DOI : 10.1016/j.resmic.2010.09.003

A. Bardwell, L. Bardwell, A. Tomkinson, and E. Friedberg, Specific cleavage of model recombination and repair intermediates by the yeast Rad1-Rad10 DNA endonu? clease, pp.2082-2087, 1994.

A. Sijbers, W. De-laat, R. Ariza, M. Biggerstaff, Y. Wei et al., Xeroder? ma pigmentosum group F caused by a defect in a structure-specific DNA repair en? donuclease, pp.811-833, 1996.

Z. Duan, Genetic Analysis of Two Structure-specific Endonucleases Hef and Fen1 in Archaeon Haloferax volcanii (PhD thesis): University of Nottingham, 2008.

O. Shimomura, F. Johnson, and Y. Saiga, Extraction, Purification and Properties of Aequorin, a Bioluminescent Protein from the Luminous Hydromedusan,Aequorea, Journal of Cellular and Comparative Physiology, vol.5, issue.3, pp.223-262
DOI : 10.1002/jcp.1030590302

M. Ormo, A. Cubitt, K. Kallio, L. Gross, R. Tsien et al., Crystal Structure of the Aequorea victoria Green Fluorescent Protein, Science, vol.273, issue.5280, pp.1392-1397, 1996.
DOI : 10.1126/science.273.5280.1392

R. Tsien, THE GREEN FLUORESCENT PROTEIN, Annual Review of Biochemistry, vol.67, issue.1, pp.509-553, 1998.
DOI : 10.1146/annurev.biochem.67.1.509

D. Chudakov, M. Matz, S. Lukyanov, and K. Lukyanov, Fluorescent Proteins and Their Applications in Imaging Living Cells and Tissues, Physiological Reviews, vol.90, issue.3, pp.1103-63
DOI : 10.1152/physrev.00038.2009

W. Vermeulen, Dynamics of mammalian NER proteins, DNA Repair, vol.10, issue.7, pp.760-71, 2011.
DOI : 10.1016/j.dnarep.2011.04.015

C. Reuter and J. Maupin-furlow, Analysis of Proteasome-Dependent Proteolysis in Haloferax volcanii Cells, Using Short-Lived Green Fluorescent Proteins, Applied and Environmental Microbiology, vol.70, issue.12, pp.7530-7538, 2004.
DOI : 10.1128/AEM.70.12.7530-7538.2004

C. Reuter, S. Uthandi, J. Puentes, and J. Maupin-furlow, Hydrophobic carboxy-termi? nal residues dramatically reduce protein levels in the haloarchaeon Haloferax volca? nii, pp.248-55, 2010.

A. Henche, A. Koerdt, A. Ghosh, and S. Albers, Influence of cell surface structures on crenarchaeal biofilm formation using a thermostable green fluorescent protein, Environmental Microbiology, vol.192, issue.3, pp.779-93, 2012.
DOI : 10.1111/j.1462-2920.2011.02638.x

A. Cubitt, L. Woollenweber, and R. Heim, Chapter 2: Understanding Structure???Function Relationships in the Aequorea victoria Green Fluorescent Protein, Methods Cell Bi?, vol.58, pp.19-30, 1999.
DOI : 10.1016/S0091-679X(08)61946-9

G. Patterson, S. Knobel, W. Sharif, S. Kain, and D. Piston, Use of the green fluores? cent protein and its mutants in quantitative fluorescence microscopy, Biophys, vol.73, issue.5, pp.2782-90, 1997.

P. Forterre, C. Elie, and M. Kohiyama, Aphidicolin inhibits growth and DNA synthesis in halophilic arachaebacteria, J, vol.159, issue.2, pp.800-802, 1984.

M. Digman, R. Dalal, A. Horwitz, and E. Gratton, Mapping the Number of Molecules and Brightness in the Laser Scanning Microscope, Biophysical Journal, vol.94, issue.6, pp.2320-2352, 2008.
DOI : 10.1529/biophysj.107.114645

S. Bakker, H. Van-de-vrugt, M. Rooimans, A. Oostra, J. Steltenpool et al., Fancm-deficient mice reveal unique features of Fanconi anemia complementation group M, Human Molecular Genetics, vol.18, issue.18, pp.3484-95, 2009.
DOI : 10.1093/hmg/ddp297

W. Crismani, C. Girard, N. Froger, M. Pradillo, J. Santos et al., FANCM Limits Meiotic Crossovers, Science, vol.336, issue.6088, pp.1588-90, 2012.
DOI : 10.1126/science.1220381

URL : https://hal.archives-ouvertes.fr/hal-01004174

A. Lorenz, F. Osman, W. Sun, S. Nandi, R. Steinacher et al., The Fission Yeast FANCM Ortholog Directs Non-Crossover Recombination During Meiosis, Science, vol.336, issue.6088, pp.1585-1593, 2012.
DOI : 10.1126/science.1220111

M. Wagner, M. Van-wolferen, A. Wagner, K. Lassak, B. Meyer et al., Versa? tile Genetic Tool Box for the Crenarchaeote Sulfolobus acidocaldarius, Front Micro?, vol.3, p.214, 2012.

C. Zhang, B. Tian, S. Li, X. Ao, K. Dalgaard et al., Genetic manipulation in Sul? folobus islandicus and functional analysis of DNA repair genes, Biochem Soc Trans2013 Feb, vol.141, issue.1, pp.405-415