M. Alam and D. Oesterhelt, Morphology, function and isolation of halobacterial flagella, J Mol Biol, vol.176, issue.4, pp.459-475, 1984.

W. Marwan, M. Alam, and D. Oesterhelt, Rotation and switching of the flagellar motor assembly in Halobacterium halobium, J Bacteriol, vol.173, issue.6, pp.1971-1977, 1991.

R. M. Macnab, The bacterial flagellum: reversible rotary propellor and type III export apparatus, J Bacteriol, vol.181, issue.23, pp.7149-7153, 1999.

S. L. Bardy, S. Y. Ng, and K. F. Jarrell, Prokaryotic motility structures. Microbiology, vol.149, pp.295-304, 2003.

S. Y. Ng, B. Chaban, and K. F. Jarrell, Archaeal flagella, bacterial flagella and type IV pili: a comparison of genes and posttranslational modifications, J Mol Microbiol Biotechnol, vol.11, issue.3-5, pp.167-191, 2006.

N. A. Thomas, S. L. Bardy, and K. F. Jarrell, The archaeal flagellum: a different kind of prokaryotic motility structure, FEMS Microbiol Rev, vol.25, issue.2, pp.147-174, 2001.

D. M. Faguy, S. F. Koval, and K. F. Jarrell, Physical characterization of the flagella and flagellins from Methanospirillum hungatei, J Bacteriol, vol.176, issue.24, pp.7491-7498, 1994.

A. L. Metlina, Bacterial and archaeal flagella as prokaryotic motility organelles, Biochemistry (Mosc), vol.69, issue.11, pp.1203-1212, 2004.

D. Cruden, R. Sparling, and A. J. Markovetz, Isolation and Ultrastructure of the Flagella of Methanococcus thermolithotrophicus and Methanospirillum hungatei

, Appl Environ Microbiol, vol.55, issue.6, pp.1414-1419, 1989.

S. Cohen-krausz and S. Trachtenberg, The structure of the archeabacterial flagellar filament of the extreme halophile Halobacterium salinarum R1M1 and its relation to eubacterial flagellar filaments and type IV pili, J Mol Biol, vol.321, issue.3, pp.383-395, 2002.

S. Trachtenberg and S. Cohen-krausz, The archaeabacterial flagellar filament: a bacterial propeller with a pilus-like structure, J Mol Microbiol Biotechnol, vol.11, issue.3-5, pp.208-220, 2006.

S. L. Bardy and K. F. Jarrell, FlaK of the archaeon Methanococcus maripaludis possesses preflagellin peptidase activity, FEMS Microbiol Lett, vol.208, issue.1, pp.53-59, 2002.

S. L. Bardy and K. F. Jarrell, Cleavage of preflagellins by an aspartic acid signal peptidase is essential for flagellation in the archaeon Methanococcus voltae, Mol Microbiol, vol.50, issue.4, pp.1339-1347, 2003.

S. V. Albers, Z. Szabo, and A. J. Driessen, Archaeal homolog of bacterial type IV prepilin signal peptidases with broad substrate specificity, J Bacteriol, vol.185, issue.13, pp.3918-3925, 2003.

F. Wieland, G. Paul, and M. Sumper, Halobacterial flagellins are sulfated glycoproteins, J Biol Chem, vol.260, issue.28, pp.15180-15185, 1985.

J. S. Mattick, Type IV pili and twitching motility, Annu Rev Microbiol, vol.56, pp.289-314, 2002.

N. A. Thomas, C. T. Pawson, and K. F. Jarrell, Insertional inactivation of the flaH gene in the archaeon Methanococcus voltae results in non-flagellated cells

, Mol Genet Genomics, vol.265, issue.4, pp.596-603, 2001.

J. Rudolph and D. Oesterhelt, Deletion analysis of the che operon in the archaeon Halobacterium salinarium, J Mol Biol, vol.258, issue.4, pp.548-554, 1996.

H. Szurmant and G. W. Ordal, Diversity in chemotaxis mechanisms among the bacteria and archaea, Microbiol Mol Biol Rev, vol.68, issue.2, pp.301-319, 2004.

J. A. Eisen, A phylogenomic study of the MutS family of proteins, Nucleic Acids Res, vol.26, issue.18, pp.4291-4300, 1998.

G. M. Garrity, Bergey's Manual of Systematic Bacteriology, Garrity GM, 2001.

J. E. Galagan, C. Nusbaum, A. Roy, M. G. Endrizzi, P. Macdonald et al., The genome of M. acetivorans reveals extensive metabolic and physiological diversity, Genome Res, vol.12, issue.4, pp.532-542, 2002.

D. M. Faguy, D. P. Bayley, A. S. Kostyukova, N. A. Thomas, and K. F. Jarrell, Isolation and characterization of flagella and flagellin proteins from the Thermoacidophilic archaea Thermoplasma volcanium and Sulfolobus shibatae, J Bacteriol, vol.178, issue.3, pp.902-905, 1996.

P. Redder and R. A. Garrett, Mutations and rearrangements in the genome of Sulfolobus solfataricus P2, J Bacteriol, vol.188, issue.12, pp.4198-4206, 2006.

S. V. Albers and A. J. Driessen, Analysis of ATPases of putative secretion operons in the thermoacidophilic archaeon Sulfolobus solfataricus, Microbiology, pp.763-773, 2005.

P. J. Planet, S. C. Kachlany, R. Desalle, and D. H. Figurski, Phylogeny of genes for secretion NTPases: identification of the widespread tadA subfamily and development of a diagnostic key for gene classification, Proc Natl Acad Sci, vol.98, issue.5, pp.2503-2508, 2001.

C. R. Peabody, Y. J. Chung, M. R. Yen, D. Vidal-ingigliardi, A. P. Pugsley et al., Type II protein secretion and its relationship to bacterial type IV pili and archaeal flagella, Microbiology, vol.149, pp.3051-3072, 2003.

S. V. Albers, Z. Szabo, and A. J. Driessen, Protein secretion in the Archaea: multiple paths towards a unique cell surface, Nat Rev Microbiol, vol.4, issue.7, pp.537-547, 2006.

S. Gribaldo and C. Brochier-armanet, The origin and evolution of Archaea: a state of the art, Philos Trans R Soc Lond B Biol Sci, vol.361, pp.1007-1022, 1470.
URL : https://hal.archives-ouvertes.fr/hal-00697930

C. Brochier, P. Forterre, and S. Gribaldo, An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences, BMC Evol Biol, vol.5, issue.1, p.36, 2005.
URL : https://hal.archives-ouvertes.fr/hal-02372559

T. Cavalier-smith, The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification, Int J Syst Evol Microbiol, vol.52, pp.7-76, 2002.

A. Labes and P. Schonheit, Sugar utilization in the hyperthermophilic, sulfate-reducing archaeon Archaeoglobus fulgidus strain 7324: starch degradation to acetate and CO2 via a modified Embden-Meyerhof pathway and acetyl-CoA synthetase (ADP-forming), Arch Microbiol, vol.176, issue.5, pp.329-338, 2001.

J. R. Leadbetter and J. A. Breznak, Physiological ecology of Methanobrevibacter cuticularis sp. nov. and Methanobrevibacter curvatus sp

, Appl Environ Microbiol, vol.62, issue.10, pp.3620-3631, 1996.

M. L. Miroshnichenko, G. M. Gongadze, F. A. Rainey, A. S. Kostyukova, A. M. Lysenko et al., Thermococcus gorgonarius sp. nov. and Thermococcus pacificus sp. nov.: heterotrophic extremely thermophilic archaea from New Zealand submarine hot vents, vol.48, pp.23-29, 1998.

R. L. Weiss, Attachment of bacteria to sulfur in extreme environments, J Gen Microbiol, vol.77, pp.501-507, 1973.

D. Prangishvili, S. V. Albers, I. Holz, H. P. Arnold, K. Stedman et al., Conjugation in archaea: frequent occurrence of conjugative plasmids in Sulfolobus. Plasmid, vol.40, pp.190-202, 1998.

I. Rosenshine, R. Tchelet, and M. Mevarech, The mechanism of DNA transfer in the mating system of an archaebacterium, Science, vol.245, issue.4924, pp.1387-1389, 1989.

K. M. Stedman, Q. She, H. Phan, I. Holz, H. Singh et al., pING family of conjugative plasmids from the extremely thermophilic archaeon Sulfolobus islandicus: insights into recombination and conjugation in Crenarchaeota, J Bacteriol, vol.182, issue.24, pp.7014-7020, 2000.

S. F. Altschul, T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang et al., Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res, vol.25, issue.17, pp.3389-3402, 1997.

J. D. Thompson, D. G. Higgins, and T. J. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res, vol.22, issue.22, pp.4673-4680, 1994.

R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, vol.32, issue.5, pp.1792-1797, 2004.

O. Poirot, E. O'toole, and C. Notredame, Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments, Nucleic Acids Res, vol.31, issue.13, pp.3503-3506, 2003.

H. Philippe, MUST, a computer package of Management Utilities for Sequences and Trees, Nucleic Acids Res, vol.21, issue.22, pp.5264-5272, 1993.

S. Guindon and O. Gascuel, A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood, Syst Biol, vol.52, issue.5, pp.696-704, 2003.

S. Guindon, F. Lethiec, P. Duroux, and O. Gascuel, PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference, Nucleic Acids Res, vol.33, pp.557-566, 2005.
URL : https://hal.archives-ouvertes.fr/lirmm-00105317

D. T. Jones, W. R. Taylor, and J. M. Thornton, The rapid generation of mutation data matrices from protein sequences, Comput Appl Biosci, vol.8, issue.3, pp.275-282, 1992.

J. P. Huelsenbeck and F. Ronquist, MRBAYES: Bayesian inference of phylogenetic trees, Bioinformatics, vol.17, issue.8, pp.754-755, 2001.