A. J. Schoeffler and J. M. Berger, Topos: harnessing and constraining energy to govern chromosome topology, Q. Rev. Biophys, vol.41, pp.41-101, 2008.

J. C. Wang, Untangling the Double Helix, 2009.

P. Forterre, Introduction and historical perspective, Topos and Cancer, pp.1-52, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00662588

, Nucleic Acids Research, vol.42, issue.13, 2014.

A. Bergerat, B. De-massy, D. Gadelle, P. C. Varoutas, A. Nicolas et al., An atypical topoisomerases II from Archaea with implications for meiotic recombination, Nature, vol.386, pp.414-417, 1997.

D. Gadelle, J. Filée, C. Buhler, and P. Forterre, Phylogenomics of type II Topos, Bioessays, vol.25, pp.232-242, 2003.

K. D. Corbett and J. M. Berger, Structure, molecular mechanisms, and evolutionary relationships in Topos, Annu. Rev. Biophys. Biomol. Struct, vol.33, pp.95-118, 2004.

P. Forterre and D. Gadelle, Phylogenomics of Topos: their origin and putative roles in the emergence of modern organisms, Nucleic Acids Res, vol.37, pp.679-692, 2009.

A. J. Schoeffler and J. M. Berger, Recent advances in understanding structure-function relationships in the type II topoisomerases mechanism, Biochem. Soc. Trans, vol.33, pp.1465-1470, 2005.

K. D. Corbett, P. Benedetti, and J. M. Berger, Holoenzyme assembly and ATP-mediated conformational dynamics of topoisomerases VI, Nat. Struct. Mol. Biol, vol.14, pp.611-619, 2007.

M. Graille, L. Cladì-ere, D. Durand, F. Lecointe, D. Gadelle et al., Crystal structure of an intact type II Topos: insights into DNA transfer mechanisms, Structure, vol.16, pp.360-370, 2008.

I. Laponogov, M. K. Sohi, D. A. Veselkov, X. Pan, R. Sawhney et al., Structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases, Nat. Struct. Mol. Biol, vol.16, pp.667-669, 2009.

R. Dutta and M. Inouye, GHKL, an emergent ATPase/kinase superfamily, Trends Biochem. Sci, vol.25, pp.24-28, 2000.

C. R. Woese, O. Kandler, and M. L. Wheelis, Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya, Proc. Natl. Acad. Sci. U.S.A, vol.87, pp.4576-4579, 1990.

O. Lecompte, R. Ripp, J. Thierry, D. Moras, and O. Poch, Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale, Nucleic Acids Res, vol.30, pp.5382-5390, 2002.

P. Forterre, S. Gribaldo, D. Gadelle, and M. Serre, Origin and evolution of Topos, Biochimie, vol.89, pp.427-446, 2007.

A. Bergerat, D. Gadelle, and P. Forterre, Purification of a Topos II from the hyperthermophilic archaeon Sulfolobus shibatae. A thermostable enzyme with both bacterial and eucaryal features, J. Biol. Chem, vol.269, pp.663-690, 1994.

C. Brochier-armanet, S. Gribaldo, and P. Forterre, A Topos IB in Thaumarchaeota testifies for the presence of this enzyme in the last common ancestor of Archaea and Eucarya, Biol. Direct, vol.3, p.54, 2008.

K. Sugimoto-shirasu, N. J. Stacey, J. Corsar, K. Roberts, and M. C. Mccann, Topos VI is essential for endoreduplication in Arabidopsis, Curr. Biol, vol.12, pp.1782-1786, 2002.

J. Filée, P. Forterre, T. Sen-lin, and J. Laurent, 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, The origin of DNA genomes and DNA replication proteins, Curr. Opin. Microbiol, vol.5, pp.525-532, 2002.

F. Plewniak, L. Bianchetti, Y. Brelivet, A. Carles, F. Chalmel et al., PipeAlign: A new toolkit for protein family analysis, Nucleic Acids Res, vol.31, pp.3829-3832, 2003.

D. T. Jones, Protein secondary structure prediction based on position-specific scoring matrices, J. Mol. Biol, vol.292, pp.195-202, 1999.

R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, vol.32, pp.1792-1797, 2004.

M. Gouy, S. Guindon, and O. Gascuel, SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building, Mol. Biol. Evol, vol.27, pp.221-224, 2010.
DOI : 10.1093/molbev/msp259

URL : https://hal.archives-ouvertes.fr/lirmm-00511794

A. Criscuolo and S. Gribaldo, BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments, BMC Evol. Biol, vol.10, p.210, 2010.

F. Abascal, R. Zardoya, and D. Posada, ProtTest: selection of best-fit models of protein evolution, Bioinformatics, vol.21, pp.2104-2105, 2005.
DOI : 10.1093/bioinformatics/bti263

URL : https://academic.oup.com/bioinformatics/article-pdf/21/9/2104/16840971/bti263.pdf

A. Stamatakis, RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, vol.22, pp.2688-2690, 2006.
DOI : 10.1093/bioinformatics/btl446

URL : https://academic.oup.com/bioinformatics/article-pdf/22/21/2688/16851699/btl446.pdf

F. Ronquist, M. Teslenko, P. Van-der-mark, D. L. Ayres, A. Darling et al., MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space, Syst. Biol, vol.61, pp.539-542, 2012.

L. A. Kelley and M. J. Sternberg, Protein structure prediction on the Web: a case study using the Phyre server, Nat. Protoc, vol.4, pp.363-371, 2009.
DOI : 10.1038/nprot.2009.2

URL : http://spiral.imperial.ac.uk/bitstream/10044/1/18157/2/Nature%20Protocols_4_3_2009.pdf

K. Arnold, L. Bordoli, J. Kopp, and T. Schwede, The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling, Bioinformatics, vol.22, pp.195-201, 2006.
DOI : 10.1093/bioinformatics/bti770

URL : https://academic.oup.com/bioinformatics/article-pdf/22/2/195/16851678/bti770.pdf

M. Krupovic, P. Forterre, and D. H. Bamford, Comparative analysis of the mosaic genomes of tailed archaeal viruses and proviruses suggests common themes for virion architecture and assembly with tailed viruses of bacteria, J. Mol. Biol, vol.397, pp.144-160, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00506375

J. Krumsiek, R. Arnold, and T. Rattei, Gepard: a rapid and sensitive tool for creating dotplots on genome scale, Bioinformatics, vol.23, pp.1026-1028, 2007.
DOI : 10.1093/bioinformatics/btm039

URL : https://academic.oup.com/bioinformatics/article-pdf/23/8/1026/501356/btm039.pdf

A. Bizard, F. Garnier, and M. Nadal, TopR2, the second reverse gyrase of Sulfolobus solfataricus, exhibits unusual properties, J. Mol. Biol, vol.408, pp.839-849, 2011.
DOI : 10.1016/j.jmb.2011.03.030

URL : https://hal.archives-ouvertes.fr/hal-00592361

S. F. Altschul, T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res, vol.25, pp.3389-3402, 1997.
DOI : 10.1093/nar/25.17.3389

URL : https://academic.oup.com/nar/article-pdf/25/17/3389/3639509/25-17-3389.pdf

M. Krupovic, S. Gribaldo, D. H. Bamford, and P. Forterre, The evolutionary history of archaeal MCM helicases: a case study of vertical evolution combined with hitchhiking of mobile genetic elements, Mol. Biol. Evol, vol.27, pp.2716-2732, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00555513

N. Soler, E. Marguet, D. Cortez, N. Desnoues, J. Keller et al., Two novel families of plasmids from hyperthermophilic archaea encoding new families of replication proteins, Nucleic Acids Res, vol.38, pp.5088-5104, 2010.

P. Forterre, Darwin's goldmine is still open: variation and selection run the world, Front. Cell Infect. Microbiol, vol.2, p.106, 2012.
DOI : 10.3389/fcimb.2012.00106

URL : https://www.frontiersin.org/articles/10.3389/fcimb.2012.00106/pdf

K. Raymann, P. Forterre, C. Brochier-armanet, and S. Gribaldo, Global phylogenomic analysis disentangles the complex evolutionary history of DNA replication in Archaea, Genome Biol. Evol, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00957432

R. A. Wozniak and M. K. Waldor, Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow, Nat. Rev. Microbiol, vol.8, pp.552-563, 2010.
DOI : 10.1038/nrmicro2382

G. Lipps, The replication protein of the Sulfolobus islandicus plasmid pRN1, Biochem. Soc. Trans, vol.32, pp.240-244, 2004.

M. Krupovic, M. Gonnet, W. B. Hania, P. Forterre, and G. Erauso, Insights into dynamics of mobile genetic elements in hyperthermophilic environments from five new Thermococcus plasmids, PLoS One, vol.8, p.49044, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00748527

S. Gill, M. Krupovic, N. Desnoues, P. Béguin, 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.
DOI : 10.1093/nar/gkt1385

URL : https://hal.archives-ouvertes.fr/hal-01332620

S. G. Gornik, K. L. Ford, T. D. Mulhern, A. Bacic, G. I. Mcfadden et al., Loss of nucleosomal DNA condensation coincides with appearance of a novel nuclear protein in dinoflagellates, Curr. Biol, vol.22, pp.2303-2312, 2012.

J. Filée and P. Forterre, Viral proteins functioning in organelles: a cryptic origin?, Trends Microbiol, vol.13, pp.510-513, 2005.

S. Lal, S. Romano, L. Chiarini, A. Signorini, and S. Tabacchioni, The Paenibacillus polymyxa species is abundant among hydrogen-producing facultative anaerobic bacteria in Lake Averno sediment, Arch. Microbiol, vol.194, pp.345-351, 2012.

R. Huber, P. Rossnagel, C. R. Woese, R. Rachel, T. A. Langworthy et al., Formation of ammonium from nitrate during chemolithoautotrophic growth of the extremely thermophilic bacterium ammonifex degensii gen. nov. sp. nov, Syst. Appl. Microbiol, vol.19, pp.40-49, 1996.

R. A. Lewin, A classification of flexibacteria, J. Gen. Microbiol, vol.58, pp.189-206, 1969.

C. Buhler, D. Gadelle, P. Forterre, J. C. Wang, and A. Bergerat, Reconstitution of DNA topoisomerase VI of the thermophilic archaeon Sulfolobus shibatae from subunits separately overexpressed in Escherichia coli, Nucleic Acids Res, vol.26, pp.5157-62, 1998.

A. K. Mcclendon, A. C. Rodriguez, and N. Osheroff, Human topoisomerase IIalpha rapidly relaxes positively supercoiled DNA: implications for enzyme action ahead of replication forks, J. Biol. Chem, vol.280, pp.39-337, 2005.

, Nucleic Acids Research, vol.42, issue.13, p.8591, 2014.

A. Aubry, L. M. Fisher, V. Jarlier, and E. Cambau, First functional characterization of a singly expressed bacterial type II topoisomerase: the enzyme from Mycobacterium tuberculosis, Biochem. Biophys. Res. Commun, vol.348, pp.158-65, 2006.

S. Matrat, S. Petrella, E. Cambau, W. Sougakoff, V. Jarlier et al., Expression and purification of an active form of the Mycobacterium leprae DNA gyrase and its inhibition by quinolones, Antimicrob. Agents Chemother, vol.51, pp.643-651, 2007.

M. Gellert, K. Mizuuchi, M. H. O'dea, T. Itoh, and J. I. Tomizawa, Nalidixic acid resistance: a second genetic character involved in DNA gyrase activity, Proc. Natl. Acad. Sci. U.S.A, vol.74, pp.4772-4776, 1977.

A. Sugino, C. L. Peebles, K. N. Kreuzer, and N. R. Cozzarelli, Mechanism of action of nalidixic acid: purification of Escherichia coli nalA gene product and its relationship to DNA gyrase and a novel nicking-closing enzyme, Proc. Natl. Acad. Sci. U.S.A, vol.74, pp.4767-71, 1977.

A. D. Bates, J. M. Berger, and A. Maxwell, The ancestral role of ATP hydrolysis in type II topoisomerases: prevention of DNA double-strand breaks, Nucleic Acids Res, vol.39, pp.6327-6339, 2011.

V. Kirik, A. Schrader, J. F. Uhrig, and M. Hulskamp, MIDGET unravels functions of the Arabidopsis topoisomerase VI complex in DNA endoreduplication, chromatin condensation, and transcriptional silencing, Plant Cell, vol.19, pp.3100-3110, 2007.

R. Hayama and K. J. Marians, Physical and functional interaction between the condensin MukB and the decatenase topoisomerase IV in Escherichia coli, Proc. Natl. Acad. Sci. U.S.A, vol.107, pp.18826-18831, 2010.

K. Chikamori, A. G. Grozav, T. Kozuki, D. Grabowski, R. Ganapathi et al., DNA topoisomerase II enzymes as molecular targets for cancer chemotherapy, Curr. Cancer Drug Targets, vol.10, pp.758-71, 2010.

B. Taneja, A. Patel, A. Slesarev, and A. Mondragónmondrag´mondragón, Structure of the N-terminal fragment of topoisomerases V reveals a new family of topoisomerases, EMBO J, vol.25, pp.398-408, 2006.

P. Forterre, Topos V: a new fold of mysterious origin, Trends Biotechnol, vol.24, pp.245-247, 2006.

P. Forterre, The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells, Biochimie, vol.87, pp.793-803, 2005.

E. V. Koonin and V. V. Dolja, A virocentric perspective on the evolution of life, Curr. Opin. Virol, vol.3, pp.546-557, 2013.

M. Krupovic, Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses, Curr. Opin. Virol, vol.3, pp.578-586, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-01977403

S. Nelson-sathi, T. Dagan, G. Landan, A. Janssen, M. Steel et al., Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea, Proc. Natl. Acad. Sci. U.S.A, vol.109, pp.537-557, 2012.

S. Kolkenbrock, B. Naumann, M. Hippler, and S. Fetzner, A novel replicative enzyme encoded by the linear Arthrobacter plasmid pAL1, J. Bacteriol, vol.192, pp.4935-4943, 2010.

Z. Li, H. Hiasa, U. Kumar, and R. J. Digate, The traE gene of plasmid RP4 encodes a homologue of Escherichia coli Topos III, J. Biol. Chem, vol.272, pp.582-601, 1997.

S. Lee, G. E. Siaw, S. Willcox, J. D. Griffith, and T. Hsieh, Synthesis and dissolution of hemicatenanes by type IA Topos, Proc. Natl. Acad. Sci. U.S.A, vol.110, pp.3587-94, 2013.

B. Niu, C. Rueckert, J. Blom, Q. Wang, and R. Borriss, The genome of the plant growth-promoting rhizobacterium Paenibacillus polymyxa M-1 contains nine sites dedicated to nonribosomal synthesis of lipopeptides and polyketides, J. Bacteriol, vol.193, pp.5862-5863, 2011.

M. W. Vetting, S. S. Hegde, M. Wang, G. A. Jacoby, D. C. Hooper et al., Structure of QnrB1, a plasmid-mediated fluoroquinolone resistance factor, J. Biol. Chem, vol.286, pp.25265-25273, 2011.