P. R. Alefounder, J. Mccarthy, and S. J. Ferguson, The basis of the control of nitrate reduction by oxygen in Paracoccus denitrificans, FEMS Microbiol Lett, vol.12, pp.321-326, 1981.

J. Alric, Y. Pierre, D. Picot, J. Lavergne, and F. Rappaport, Spectral and redox characterization of the heme c i of the cytochrome b 6 f complex, Proc Natl Acad Sci U S A, vol.102, pp.15860-15865, 2005.

T. M. Bandeiras, The cytochrome ba complex from the thermoacidophilic crenarchaeote Acidianus ambivalens is an analog of bc(1) complexes, Biochim Biophys Acta, vol.1787, pp.37-45, 2009.

F. Baymann, The redox protein construction kit: pre-LUCA evolution of energy conserving enzymes, Phil Trans R Soc Lond B, vol.358, pp.267-274, 2003.
URL : https://hal.archives-ouvertes.fr/hal-00343715

F. Baymann, F. Giusti, D. Picot, and W. Nitschke, The c i /b H -moiety in the cytochrome b 6 f complex studied by EPR. A pair of strongly interacting hemes, Proc Natl Acad Sci U S A, vol.104, pp.519-524, 2007.

H. Bö-nisch, S. L. Schmidt, G. Schä-fer, and R. Ladenstein, The structure of the soluble domain of an archaeal Rieske iron-sulfur protein at 1.1 A resolution, J Mol Biol, vol.319, pp.791-805, 2003.

F. C. Boogerd, H. W. Van-verseveld, and A. H. Stouthamer, Electron transport to nitrous oxide in Paracoccus enitrificans, FEBS Lett, vol.113, pp.279-284, 1980.

J. M. Bonete, R. M. Martinez-espinosa, C. Pire, B. Zafrilla, and D. J. Richardson, Nitrogen metabolism in haloarchaea, Saline Syst, vol.4, p.9, 2008.

Y. Boucher, Lateral gene transfer and the origin of prokaryotic groups, Annu Rev Genet, vol.37, pp.283-328, 2003.

C. Brochier-armanet, P. Forterre, and S. Gribaldo, Phylogeny and evolution of the Archaea: one hundred genomes later, Curr Opin Microbiol, vol.14, pp.274-281, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00598326

M. Brugna, Redox components of cytochrome bc-type enzymes in acidophilic prokaryotes. II. The Rieske protein of phylogenetically distant acidophilic organisms, J Biol Chem, vol.274, pp.16766-16772, 1999.

J. L. Cape, The respiratory substrate rhodoquinol induces Q-cycle bypass reactions in the yeast cytochrome bc 1 complex: mechanistic and physiological implications, J Biol Chem, vol.280, pp.34654-34660, 2005.

J. L. Cape, M. K. Bowman, and D. M. Kramer, Understanding the cytochrome bc complexes by what they do not do. The Q-cycle at 30, Trends Biochem Sci, vol.11, pp.46-55, 2006.

J. Castresana, M. Lü-bben, and M. Saraste, New archaebacterial genes coding for redox proteins: implications for the evolution of aerobic metabolism, J Mol Biol, vol.250, pp.202-210, 1995.

K. S. Cheah, Properties of electron transport particles from Halobacterium culirubrum. The respiratory chain system, Biochim Biophys Acta, vol.180, pp.320-333, 1969.

K. S. Cheah, The membrane-bound ascorbate oxidase system of Halobacterium halobium, Biochim Biophys Acta, vol.205, pp.148-160, 1970.

K. S. Cheah, Properties of the membrane-bound respiratory chain system of Halobacterium salinarum, Biochim Biophys Acta, vol.216, pp.43-53, 1970.

M. D. Collins and D. Jones, Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications, Microbiol Rev, vol.45, pp.316-354, 1981.

E. Denke, Alteration of the midpoint potential and catalytic activity of the rieske iron-sulfur protein by changes of amino acids forming hydrogen bonds to the iron-sulfur cluster, J Biol Chem, vol.273, pp.9085-9093, 1998.

M. De-rosa and A. Gambacorta, The lipids of archaebacteria, Prog Lipid Res, vol.27, pp.153-175, 1988.

A. L. Ducluzeau, E. Chenu, L. Capowiez, and F. Baymann, The Rieske/ cytochrome b complex of Heliobacteria, Biochim Biophys Acta, vol.1777, pp.1140-1146, 2008.

A. Ducluzeau, Was nitric oxide the first deep electron sink?, Trends in Biochem Sci, vol.34, pp.9-15, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00680459

S. Duval, A. Ducluzeau, W. Nitschke, and B. Schoepp-cothenet, Enzyme phylogenies as markers for the oxidation state of the environment: the case of the respiratory arsenate reductase and related enzymes, BMC Evol Biol, vol.8, p.206, 2008.

S. Duval, J. M. Santini, W. Nitschke, R. Hille, and B. Schoepp-cothenet, The small subunit AroB of arsenite oxidase: lessons on the [2Fe2S] Rieske protein superfamily, J Biol Chem, vol.285, pp.20442-20451, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00677536

J. Felsenstein, An alternating least squares approach to inferring phylogenies from pairwise distances, Syst Biol, vol.46, pp.101-112, 1997.

N. Galtier, M. Gouy, and C. Gautier, SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny, Comput Appl Biosci, vol.12, pp.543-548, 1996.
URL : https://hal.archives-ouvertes.fr/hal-00435028

M. Guiral, New insights into the respiratory chains of the chemolithoautotrophic and hyperthermophilic bacterium Aquifex aeolicus, J Prot Res, vol.8, pp.1717-1730, 2009.

C. Gruber, Halobacterium noricense sp. nov., an archaeal isolate from a bore core of an alpine Permian salt deposit, classification of Halobacterium sp. NRC-1 as a strain of H. salinarum and emended description of H. salinarum, Extremophiles, vol.8, pp.431-439, 2004.

C. Hallberg-gradin and A. Colmjö, Four different b-type cytochromes in the halophilic Archaebacterium Halobacterium halobium, Arch Biochem Biophys, vol.272, pp.130-136, 1989.

G. Hauska, Composition and structure of cytochrome bc1 and b 6 f complexes, Enz Plant Physiol, vol.19, pp.496-507, 1986.

T. Henninger, A novel Rieske iron-sulfur protein from the hyperthermophilic crenarchaeon Pyrobaculum aerophilum: sequencing of the gene, expression in E. coli and characterization of the protein, J Bioenerg Biomembr, vol.31, pp.119-128, 1999.

A. Hiller, T. Henninger, G. Schä-fer, and C. L. Schmidt, New genes encoding subunits of a cytochrome bc1-analogous complex in the respiratory chain of the hyperthermoacidophilic crenarchaeon Sulfolobus acidocaldarius, J Bioenerg Biomembr, vol.35, pp.121-131, 2003.

M. Itoh, K. Matsuura, and T. Satoh, Involvement of cytochrome bc 1 complex in the electron transfer pathway for N 2 O reduction in a photodenitrifier, Rhodobacter sphaeroides f. s. denitrificans, FEBS Lett, vol.251, pp.104-108, 1989.

T. Iwasaki, K. Matsuura, and T. Oshima, Resolution of the aerobic respiratory system of the thermoacidophilic Archaeon, Sulfolobus sp. Strain7, J Biol Chem, vol.270, pp.30881-30892, 1995.

T. Iwasaki, A. Kounosu, T. Uzawa, R. I. Samoilova, and S. A. Dikanov, Orientation-selected 15N-HYSCORE detection of weakly coupled nitrogens around the archaeal Rieske [2Fe-2S] center, J Am Chem Soc, vol.126, pp.13902-13903, 2004.

P. Joliot and A. Joliot, Proton pumping and electron transfer in the cytochrome b/f complex of algae, Biochim Biophys Acta, vol.849, pp.211-222, 1986.

S. Kelly, B. Wickstead, and K. Gull, Archaeal phylogenies provide evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin of the eukaryotes, Proc Biol Sci, vol.278, pp.1009-1018, 2011.

S. P. Kennedy, W. V. Ng, S. L. Salzberg, L. Hood, and S. Dassarma, Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence, Gen Res, vol.11, pp.1641-1650, 2001.

L. Komorowski, W. Verheyen, and G. Schä, The Archaeal respiratory supercomplex SoxM from S. acidocaldarius combines features of quinol and cytochrome c oxidases, J Biol Chem, vol.383, pp.1791-1799, 2002.

D. M. Kramer, B. Schoepp, U. Liebl, and W. Nitschke, Cyclic electron transfer in Heliobacillus mobilis involving a menaquinol-oxidizing cytochrome bc complex and an RCI-type reaction center, Biochemistry, vol.36, pp.4203-4211, 1997.

D. M. Kramer, W. Nitschke, and J. W. Cooles, The cytochrome bc1 and related bc complexes: Rieske/cytochrome b complexes as the functional core of a central electron/proton transfer complex, The purple photosynthetic bacteria, pp.451-473, 2009.

G. Kurisu, H. Zhang, J. L. Smith, and W. A. Cramer, Structure of the cytochrome b 6 f complex of oxygenic photosynthesis: tuning the cavity, Science, vol.302, pp.1009-1014, 2003.

N. Lane, J. F. Allen, and W. Martin, How did LUCA make a living? Chemiosmosis in the origin of life, BioEssays, vol.32, pp.271-280, 2010.

M. A. Larkin, Clustal W and Clustal X version 2.0, Bioinformatics, vol.23, pp.2947-2948, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00206210

E. Lebrun, Arsenite oxidase, an ancient bioenergetic enzyme, Mol Biol Evol, vol.20, pp.686-693, 2003.
URL : https://hal.archives-ouvertes.fr/hal-00113712

E. Lebrun, The Rieske protein: a case study on the pitfalls of multiple sequence alignments and phylogenetic reconstruction, Mol Biol Evol, vol.23, pp.1180-1191, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00132690

U. Liebl, S. Pezennec, A. Riedel, E. Kellner, and W. Nitschke, The Rieske FeS center from the gram-positive bacterium PS3 and its interaction with the menaquinone pool studied by EPR, J Biol Chem, vol.267, pp.14068-14072, 1992.

M. Lü-bben, A second terminal oxidase in Sulfolobus acidocaldarius, Eur J Biochem, vol.224, pp.151-159, 1994.

R. M. Martinez-espinosa, Look on the positive side! The orientation, identification and bioenergetics of "Archaeal" membrane-bound nitrate reductases, FEMS Microbiol Lett, vol.276, pp.129-139, 2007.

P. Mitchell, Aspects of the chemiosmotic hypothesis, Biochem J, vol.116, pp.5-6, 1970.

P. Mitchell, Chemiosmotic coupling in energy transduction: a logical development of biochemical knowledge, J Bioenerg, vol.3, pp.5-24, 1972.

E. F. Mongodin, The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea, Proc Natl Acad Sci U S A, vol.102, pp.18147-18152, 2005.

W. Nitschke and M. J. Russell, Hydrothermal focusing of chemical and chemiosmotic energy, supported by delivery of catalytic Fe, Ni, Mo/ W, Co, S and Se, forced life to emerge, J Mol Evol, vol.69, pp.481-496, 2009.

W. Nitschke, R. Van-lis, B. Schoepp-cothenet, and F. Baymann, The "green" phylogenetic clade of Rieske/cytb complexes, Photosynth Res, vol.104, pp.347-355, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00677682

T. Nü-bel, C. Klughammer, R. Hube, G. Hauska, and M. Schü, Sulfide:quinone oxidoreductase in membranes of the hyperthermophilic bacterium Aquifex aeolicus (VF5), Arch Microbiol, vol.173, pp.233-244, 2000.

T. Nunoura, Y. Sako, T. Wakagi, and A. Uchida, Regulation of the aerobic respiratory chain in the facultatively aerobic and hyperthermophilic archaeaon Pyrobaculum oguniense, Microbiology, vol.149, pp.673-688, 2003.

P. R. Rich, Electron and proton transfers through quinones and cytochrome bc complexes, Biochim Biophys Acta, vol.768, pp.53-79, 1984.

B. Scharf, R. Wittenberg, and M. Engelhard, Electron transfer proteins from the haloalkaliphilic Archaeon Natronobacterium pharaonis: possible components of the respiratory chain include cytochrome bc and a terminal oxidase cytochrome ba 3, Biochemistry, vol.36, pp.4471-4479, 1997.

B. Schoepp-cothenet, Menaquinone as a pool quinone in a purple bacterium, Proc Natl Acad Sci U S A, vol.106, pp.8549-8554, 2009.

T. Schrö-ter, Mutational analysis of residues forming hydrogen bonds in the Rieske [2Fe-2S] cluster of the cytochrome bc 1 complex in Paracoccus denitrificans, Eur J Biochem, vol.255, pp.100-106, 1998.

M. Schü-tz, Early evolution of cytochrome bc-complexes, J Mol Biol, vol.300, pp.663-676, 2000.

M. Schü-tz, The naphthoquinol oxidizing cytochrome bc 1 complex of the hyperthermophilic knallgasbacterium Aquifex aeolicus: properties and phylogenetic relationships, Biochemistry, vol.42, pp.10800-10808, 2003.

J. P. Shapleigh and W. J. Payne, Nitric oxide-dependant proton translocation in various denitrifiers, J Bact, vol.163, pp.837-840, 1985.

N. Sone and Y. Fujiwara, Effects of aeration during growth of Bacillus stearothermophilus on proton pumping activity and change of terminal oxidases, J Biochem, vol.110, pp.1016-1021, 1991.

N. Sone, G. Sawa, T. Sone, and S. Noguchi, Thermophilic bacilli have split cytochrome b genes for cytochrome b 6 and subunit IV. First cloning of cytochrome b from a Gram-positive bacterium (Bacillus stearothermophilus), J Biol Chem, vol.270, pp.10612-10617, 1995.

N. Sone, A novel hydrophobic diheme c-type cytochrome. Purification from Corynebacterium glutamicum and analysis of the QcrCBA operon encoding three subunit proteins of a putative cytochrome reductase complex, Biochim Biophys Acta, vol.1503, pp.279-290, 2001.

N. Sone, QcrCAB operon of a nocardia-form actinomycete Rhodococcus rhodochrous encodes cytochrome reductase complex with diheme cytochrome cc subunit, Biochim Biophys Acta, vol.1557, pp.125-131, 2003.

K. Sreeramulu, C. L. Schmidt, G. Schä-fer, A. , and S. , Studies on the electron transport chain of the Euryarchaeon Halobacterium salinarum: indications for a type II NADH dehydrogenase and a complex III analog, J Bioenerg Biomemb, vol.30, pp.447-453, 1998.

D. Stroebel, Y. Choquet, J. L. Popot, and D. Picot, An atypical haem in the cytochrome b(6)f complex, Nature, vol.426, pp.413-418, 2003.

H. Suharti, . Ha, and S. De-vries, NO reductase from Bacillus azotoformans is a bifunctional enzyme accepting electrons from menaquinol and a specific endogenous membrane-bound cytochrome c 551, Biochemistry, vol.43, pp.13487-13495, 1984.

M. Swierczek, An electronic bus bar lies in the core of cytochrome bc 1, Science, vol.329, pp.451-454, 2010.

T. Tanaka, M. Inoue, J. Sakamoto, and N. Sone, Intra-and inter-complex cross-linking of subunits in the quinol oxidase super-complex from thermophilic Bacillus PS3, J Biochem, vol.119, pp.482-486, 1996.

R. Thauer, A. Kaster, H. Seedorf, W. Buckel, and R. Hedderich, Methanogenic archaea: ecologically relevant differences in energy conservation, Nat Rev, vol.6, pp.579-591, 2008.

R. Van-lis, A. Ducluzeau, W. Nitschke, and B. Schoepp-cothenet, The nitrogen cycle in the archaean: an intricate interplay of enzymatic and abiotic reactions, Nitrogen cycling in bacteria: molecular analysis, pp.1-12, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01602042

M. Wainø, B. J. Tindall, and K. Ingvorsen, Halorhabdus utahensis gen. nov., sp. nov., an aerobic, extremely halophilic member of the Archaea from Great Salt Lake, Int J Sys Evol Biol, vol.50, pp.183-190, 2000.

W. R. Widger, W. A. Cramer, R. G. Herrmann, and A. Trebst, Sequence homology and structural similarity between cytochrome b of mitochondrial complex III and the chloroplast b6-f complex: position of cytochrome b hemes in the membrane, Proc Natl Acad Sci U S A, vol.81, pp.674-678, 1984.

D. Xia, Crystal structure of the cytochrome bc 1 complex from bovine heart mitochondria, Science, vol.277, pp.60-66, 1984.

P. Yarza, The all-species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains, Syst Appl Microbiol, vol.31, pp.241-250, 2008.

K. Yoshimatsu, T. Iwasaki, and T. Fujiwara, Sequence and electron paramagnetic resonance analyses of nitrate reductase NarGH from a denitrifying halophilic euryarchaeote Haloarcula marismortui, FEBS Lett, vol.516, pp.145-150, 2002.

K. Yoshimatsu, O. Araya, and T. Fujiwara, Haloarcula marismortui cytochrome b-561 is encoded by the narC gene in the dissimilatory nitrate reductase operon, Extremophiles, vol.11, pp.41-47, 2007.

J. Yu, L. Brun, and N. , Studies of the cytochrome subunits of menaquinone:cytochrome c reductase (bc-complex) of Bacillus subtilis. Evidence for the covalent attachment of heme to the cytochrome b subunit, J Biol Chem, vol.273, pp.8860-8866, 1988.

Z. Zhang, Electron transfer by domain movement in cytochrome bc 1, Nature, vol.392, pp.677-684, 1998.