C. Acquisti, J. Kleffe, and S. Collins, Oxygen content of transmembrane proteins over macroevolutionary time scales, Nature, vol.3, issue.7123, pp.47-52, 2007.
DOI : 10.1038/nature05450

R. Adamczak, A. Porollo, and J. Meller, Combining prediction of secondary structure and solvent accessibility in proteins, Proteins: Structure, Function, and Bioinformatics, vol.10, issue.3, pp.467-475, 2005.
DOI : 10.1002/prot.20441

R. Alves and M. Savageau, Evidence of selection for low cognate amino acid bias in amino acid biosynthetic enzymes, Molecular Microbiology, vol.18, issue.4, pp.1017-1034, 2005.
DOI : 10.1111/j.1365-2958.2005.04566.x

P. Baudouin-cornu, Y. Surdin-kerjan, P. Marliere, and D. Thomas, Molecular Evolution of Protein Atomic Composition, Science, vol.293, issue.5528, pp.297-300, 2001.
DOI : 10.1126/science.1061052

A. Bekker, H. Holland, P. Wang, D. Rumble, H. Stein et al., Dating the rise of atmospheric oxygen, Nature, vol.427, issue.6970, pp.117-120, 2004.
DOI : 10.1038/nature02260

G. Bernardi, B. Olofsson, J. Filipski, M. Zerial, J. Salinas et al., The mosaic genome of warm-blooded vertebrates, Science, vol.228, issue.4702, pp.953-958, 1985.
DOI : 10.1126/science.4001930

R. Berner, Atmospheric oxygen over Phanerozoic time, Proceedings of the National Academy of Sciences, vol.96, issue.20, pp.10955-10957, 1999.
DOI : 10.1073/pnas.96.20.10955

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC34224

J. Bragg and C. Hyder, Nitrogen versus carbon use in prokaryotic genomes and proteomes, Proceedings of the Royal Society B: Biological Sciences, vol.271, issue.Suppl_5, pp.374-377, 2004.
DOI : 10.1098/rsbl.2004.0193

J. Bragg, D. Thomas, and P. Baudouin-cornu, Variation among species in proteomic sulphur content is related to environmental conditions, Proceedings of the Royal Society B: Biological Sciences, vol.297, issue.1-2, pp.1293-1300, 2006.
DOI : 10.1016/S0378-1119(02)00871-5

J. Bragg and A. Wagner, Protein carbon content evolves in response to carbon availability and may influence the fate of duplicated genes, Proceedings of the Royal Society B: Biological Sciences, vol.22, issue.6, pp.1063-1070, 2007.
DOI : 10.1093/molbev/msi126

C. Chothia and A. Lesk, The relation between the divergence of sequence and structure in proteins, Embo J, vol.5, pp.823-826, 1986.

A. Coghlan and K. Wolfe, Relationship of codon bias to mRNA concentration and protein length inSaccharomyces cerevisiae, Yeast, vol.276, issue.12, pp.1131-1145, 2000.
DOI : 10.1002/1097-0061(20000915)16:12<1131::AID-YEA609>3.0.CO;2-F

E. Couturier and E. Rocha, Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes, Molecular Microbiology, vol.52, issue.5, pp.1506-1518, 2006.
DOI : 10.1111/j.1365-2958.2006.05046.x

V. Daubin and G. Perriere, G+C3 Structuring Along the Genome: A Common Feature in Prokaryotes, Molecular Biology and Evolution, vol.20, issue.4, pp.471-483, 2003.
DOI : 10.1093/molbev/msg022

URL : https://hal.archives-ouvertes.fr/hal-00427485

M. Davies and R. Truscott, Photo-oxidation of proteins and its role in cataractogenesis, Journal of Photochemistry and Photobiology B: Biology, vol.63, issue.1-3, pp.114-125, 2001.
DOI : 10.1016/S1011-1344(01)00208-1

R. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004.
DOI : 10.1093/nar/gkh340

J. Felsenstein, Phylogenies and the Comparative Method, The American Naturalist, vol.125, issue.1, pp.1-15, 1985.
DOI : 10.1086/284325

S. Fukuchi, K. Yoshimune, M. Wakayama, M. Moriguchi, and K. Nishikawa, Unique Amino Acid Composition of Proteins in Halophilic Bacteria, Journal of Molecular Biology, vol.327, issue.2, pp.347-357, 2003.
DOI : 10.1016/S0022-2836(03)00150-5

C. Goldblatt, T. Lenton, and A. Watson, Bistability of atmospheric oxygen and the Great Oxidation, Nature, vol.361, issue.7112, pp.683-686, 2006.
DOI : 10.1038/nature05169

S. Gould and R. Lewontin, The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme, Proceedings of the Royal Society B: Biological Sciences, vol.205, issue.1161, pp.581-598, 1979.
DOI : 10.1098/rspb.1979.0086

S. Guindon and O. Gascuel, A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood, Systematic Biology, vol.52, issue.5, pp.696-704, 2003.
DOI : 10.1080/10635150390235520

S. Hedges, J. Blair, M. Venturi, and J. Shoe, A molecular timescale of eukaryote evolution and the rise of complex multicellular life, BMC Evol Biol, vol.4, issue.2, 2004.

F. Hillmann, R. Fischer, F. Saint-prix, L. Girbal, and H. Bahl, PerR acts as a switch for oxygen tolerance in the strict anaerobe Clostridium acetobutylicum, Molecular Microbiology, vol.130, issue.4, pp.848-860, 2008.
DOI : 10.1111/j.1365-2958.2006.05079.x

K. Howe, A. Bateman, and R. Durbin, QuickTree: building huge Neighbour-Joining trees of protein sequences, Bioinformatics, vol.18, issue.11, pp.1546-1547, 2002.
DOI : 10.1093/bioinformatics/18.11.1546

W. Humphrey, A. Dalke, and K. Schulten, VMD: Visual molecular dynamics, Journal of Molecular Graphics, vol.14, issue.1, pp.33-38, 1996.
DOI : 10.1016/0263-7855(96)00018-5

L. Hurst, E. Feil, and E. Rocha, Protein evolution: Causes of trends in amino-acid gain and loss, Nature, vol.433, issue.7105, pp.11-12, 2006.
DOI : 10.1038/nature05137

J. Imlay, How oxygen damages microbes: Oxygen tolerance and obligate anaerobiosis, Adv Microb Physiol, vol.46, pp.111-153, 2002.
DOI : 10.1016/S0065-2911(02)46003-1

J. Imlay, Iron-sulphur clusters and the problem with oxygen, Molecular Microbiology, vol.136, issue.4, pp.1073-1082, 2006.
DOI : 10.1128/JB.183.15.4562-4570.2001

J. Imlay, How obligatory is anaerobiosis?, Molecular Microbiology, vol.266, issue.4, pp.801-804, 2008.
DOI : 10.1046/j.1365-2958.1998.00941.x

D. Kreil and C. Ouzounis, Identification of thermophilic species by the amino acid compositions deduced from their genomes, Nucleic Acids Research, vol.29, issue.7, pp.1608-1615, 2001.
DOI : 10.1093/nar/29.7.1608

E. Krissinel, On the relationship between sequence and structure similarities in proteomics, Bioinformatics, vol.23, issue.6, pp.717-723, 2007.
DOI : 10.1093/bioinformatics/btm006

A. Krogh, B. Larsson, G. Von-heijne, and E. Sonnhammer, Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen, Journal of Molecular Biology, vol.305, issue.3, pp.567-580, 2001.
DOI : 10.1006/jmbi.2000.4315

R. Levine, J. Moskovitz, and E. Stadtman, Oxidation of Methionine in Proteins: Roles in Antioxidant Defense and Cellular Regulation, IUBMB Life, vol.50, issue.4, pp.301-307, 2000.
DOI : 10.1080/15216540051081056

J. Lobry, Influence of genomic G + C content on average amino-acid composition of proteins from 59 bacterial species, Gene, vol.205, issue.1-2, pp.309-316, 1997.
DOI : 10.1016/S0378-1119(97)00403-4

URL : https://hal.archives-ouvertes.fr/hal-00434967

D. Mazel and P. Marliere, Adaptive eradication of methionine and cysteine from cyanobacterial light-harvesting proteins, Nature, vol.341, issue.6239, pp.245-248, 1989.
DOI : 10.1038/341245a0

J. Mccord, B. Keele, . Jr, and I. Fridovich, An Enzyme-Based Theory of Obligate Anaerobiosis: The Physiological Function of Superoxide Dismutase, Proceedings of the National Academy of Sciences, vol.68, issue.5, pp.1024-1027, 1971.
DOI : 10.1073/pnas.68.5.1024

C. Medigue, E. Krin, and G. Pascal, Coping with cold: The genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125, Genome Research, vol.15, issue.10, pp.1325-1335, 2005.
DOI : 10.1101/gr.4126905

B. Moosmann and C. Behl, Mitochondrially encoded cysteine predicts animal lifespan, Aging Cell, vol.32, issue.1, pp.32-46, 2008.
DOI : 10.1111/j.1474-9726.2007.00349.x

URL : http://doi.org/10.1111/j.1474-9726.2007.00349.x

H. Musto, H. Rodriguez-maseda, and G. Bernardi, Compositional properties of nuclear genes from Plasmodium falciparum, Gene, vol.152, issue.1, pp.127-132, 1995.
DOI : 10.1016/0378-1119(94)00708-Z

A. Muto and S. Osawa, The guanine and cytosine content of genomic DNA and bacterial evolution., Proceedings of the National Academy of Sciences, vol.84, issue.1, pp.166-169, 1987.
DOI : 10.1073/pnas.84.1.166

H. Naya, H. Romero, A. Zavala, B. Alvarez, and H. Musto, Aerobiosis Increases the Genomic Guanine Plus Cytosine Content (GC%) in Prokaryotes, Journal of Molecular Evolution, vol.55, issue.3, pp.260-264, 2002.
DOI : 10.1007/s00239-002-2323-3

E. Paradis and C. J. , Analysis of Comparative Data Using Generalized Estimating Equations, Journal of Theoretical Biology, vol.218, issue.2, pp.175-185, 2002.
DOI : 10.1006/jtbi.2002.3066

E. Paradis, C. J. Strimmer, and K. , APE: Analyses of Phylogenetics and Evolution in R language, Bioinformatics, vol.20, issue.2, pp.289-290, 2004.
DOI : 10.1093/bioinformatics/btg412

S. Park and J. Imlay, High Levels of Intracellular Cysteine Promote Oxidative DNA Damage by Driving the Fenton Reaction, Journal of Bacteriology, vol.185, issue.6, pp.1942-1950, 2003.
DOI : 10.1128/JB.185.6.1942-1950.2003

J. Posey and F. Gherardini, Lack of a Role for Iron in the Lyme Disease Pathogen, Science, vol.288, issue.5471, pp.1651-1653, 2000.
DOI : 10.1126/science.288.5471.1651

R. Development and C. Team, R: a language and environment for statistical computing. Vienna (Austria): R Foundation for Statistical Computing, 2007.

E. Rocha, Codon usage bias from tRNA's point of view: Redundancy, specialization, and efficient decoding for translation optimization, Genome Research, vol.14, issue.11, pp.2279-2286, 2004.
DOI : 10.1101/gr.2896904

M. Roseman, Hydrophilicity of polar amino acid side-chains is markedly reduced by flanking peptide bonds, Journal of Molecular Biology, vol.200, issue.3, pp.513-522, 1988.
DOI : 10.1016/0022-2836(88)90540-2

R. Sasidharan and C. Chothia, The selection of acceptable protein mutations, Proceedings of the National Academy of Sciences, vol.104, issue.24, pp.10080-10085, 2007.
DOI : 10.1073/pnas.0703737104

H. Schmidt, K. Strimmer, M. Vingron, V. Haeseler, and A. , TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing, Bioinformatics, vol.18, issue.3, pp.502-504, 2002.
DOI : 10.1093/bioinformatics/18.3.502

P. Sharp and W. Li, The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications, Nucleic Acids Research, vol.15, issue.3, pp.1281-1295, 1987.
DOI : 10.1093/nar/15.3.1281

G. Singer and D. Hickey, Nucleotide Bias Causes a Genomewide Bias in the Amino Acid Composition of Proteins, Molecular Biology and Evolution, vol.17, issue.11, pp.1581-1588, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026257

E. Stadtman, Protein oxidation and aging, Free Radical Research, vol.75, issue.12, pp.1250-1258, 2006.
DOI : 10.1016/0014-5793(95)01494-2

G. Storz and J. Imlay, Oxidative stress, Current Opinion in Microbiology, vol.2, issue.2, pp.188-194, 1999.
DOI : 10.1016/S1369-5274(99)80033-2

N. Sueoka, ON THE GENETIC BASIS OF VARIATION AND HETEROGENEITY OF DNA BASE COMPOSITION, Proceedings of the National Academy of Sciences, vol.48, issue.4, pp.582-591, 1962.
DOI : 10.1073/pnas.48.4.582

N. Sueoka, Directional mutation pressure and neutral molecular evolution., Proceedings of the National Academy of Sciences, vol.85, issue.8, pp.2653-2657, 1988.
DOI : 10.1073/pnas.85.8.2653

J. Swire, Selection on Synthesis Cost Affects Interprotein Amino Acid Usage in All Three Domains of Life, Journal of Molecular Evolution, vol.54, issue.5, pp.558-571, 2007.
DOI : 10.1007/s00239-006-0206-8

G. Talavera and J. Castresana, Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments, Systematic Biology, vol.56, issue.4, pp.564-577, 2007.
DOI : 10.1080/10635150701472164

F. Tekaia and E. Yeramian, Evolution of proteomes: fundamental signatures and global trends in amino acid compositions, BMC Genomics, vol.7, 1941.
URL : https://hal.archives-ouvertes.fr/pasteur-00134561

K. Towe, Evolution of Protein Amino Acids, Science, vol.300, issue.5624, pp.1370-1371, 2003.
DOI : 10.1126/science.300.5624.1370d

W. Venables and B. Ripley, Modern applied statistics with S, 4th, 2002.

J. Zeilstra-ryalls and S. Kaplan, Oxygen intervention in the regulation of gene expression: the photosynthetic bacterial paradigm, Cellular and Molecular Life Sciences (CMLS), vol.61, issue.4, pp.417-436, 2004.
DOI : 10.1007/s00018-003-3242-1

K. Zeldovich, I. Berezovsky, and E. Shakhnovich, Protein and DNA Sequence Determinants of Thermophilic Adaptation, PLoS Computational Biology, vol.342, issue.1, p.5, 2007.
DOI : 10.1371/journal.pcbi.0030005.st005