Do proteins predate DNA? Science, vol.286, pp.690-692, 1999. ,
Methyl-RNA: an evolutionary bridge between RNA and DNA?, Chem Biol, vol.7, issue.12, pp.207-216, 2000. ,
The evolution of the ribonucleotide reductases: much ado about oxygen, J Mol Evol, vol.55, issue.2, pp.180-196, 2002. ,
From RNA to DNA, why so many ribonucleotide reductases? Science, vol.260, pp.1773-1777, 1993. ,
Ribonucleotide reductases: divergent evolution of an ancient enzyme, J Mol Evol, vol.55, issue.2, pp.138-152, 2002. ,
RNRdb, a curated database of the universal enzyme family ribonucleotide reductase, reveals a high level of misannotation in sequences deposited to Genbank, BMC Genomics, vol.10, p.589, 2009. ,
Structural basis for allosteric substrate specificity regulation in anaerobic ribonucleotide reductases, Structure, vol.9, issue.8, pp.739-750, 2001. ,
Structural mechanism of allosteric substrate specificity regulation in a ribonucleotide reductase, Nat Struct Mol Biol, vol.11, issue.11, pp.1142-1149, 2004. ,
The crystal structure of class II ribonucleotide reductase reveals how an allosterically regulated monomer mimics a dimer, Nat Struct Biol, vol.9, issue.4, pp.293-300, 2002. ,
Structure of ribonucleotide reductase protein R1, Nature, vol.370, issue.6490, pp.533-539, 1994. ,
Mass spectrometric determination of the radical scission site in the anaerobic ribonucleotide reductase of Escherichia coli, Biochem Biophys Res Commun, vol.206, issue.2, pp.731-735, 1995. ,
Bacteriophage T4 anaerobic ribonucleotide reductase contains a stable glycyl radical at position 580, J Biol Chem, vol.271, issue.34, pp.20770-20775, 1996. ,
Ribonucleotide reductases, Annu Rev Biochem, vol.67, pp.71-98, 1998. ,
Ribonucleotide reductases, Annu Rev Biochem, vol.75, pp.681-706, 2006. ,
The ribonucleotide reductase family -Genetics and genomics, Ribonucleotide Reductase. Edited by: Andersson KK, pp.17-77, 2008. ,
Two genes differentially regulated in the cell cycle and by DNA-damaging agents encode alternative regulatory subunits of ribonucleotide reductase, Genes Dev, vol.4, issue.5, pp.740-751, 1990. ,
A ribonucleotide reductase gene involved in a p53, BMC Evolutionary Biology, vol.10, issue.6773, pp.42-49, 2000. ,
A manganese(IV)/iron(III) cofactor in Chlamydia trachomatis ribonucleotide reductase, Science, vol.316, issue.5828, pp.1188-1191, 2007. ,
High catalytic activity achieved with a mixed manganese-iron site in protein R2 of Chlamydia ribonucleotide reductase, FEBS Lett, vol.581, issue.18, pp.3351-3355, 2007. ,
The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea, Proc Natl Acad Sci, vol.102, issue.50, pp.18147-18152, 2005. ,
Psychromonas antarcticus gen. nov., sp. nov., A new aerotolerant anaerobic, halophilic psychrophile isolated from pond sediment of the McMurdo ice shelf, antarctica, Arch Microbiol, vol.169, issue.3, pp.231-238, 1998. ,
Leeuwenhoekiella blandensis sp. nov., a genome-sequenced marine member of the family Flavobacteriaceae, Int J Syst Evol Microbiol, vol.56, pp.1489-1493, 2006. ,
Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus, Nat Biotechnol, vol.25, issue.5, pp.569-575, 2007. ,
The genome sequence of the extreme thermophile Thermus thermophilus, Nat Biotechnol, vol.22, issue.5, pp.547-553, 2004. ,
Polaribacter gen. nov., with three new species, P. irgensii sp. nov., P. franzmannii sp. nov. and P. filamentus sp. nov., gas vacuolate polar marine bacteria of the Cytophaga-Flavobacterium-Bacteroides group and reclassification of 'Flectobacillus glomeratus' as Polaribacter glomeratus comb. nov, Int J Syst Bacteriol, vol.48, pp.223-235, 1998. ,
Living with two extremes: conclusions from the genome sequence of Natronomonas pharaonis, Genome Res, vol.15, issue.10, pp.1336-1343, 2005. ,
A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes, Genome Biol, vol.10, issue.6, p.65, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00397761
, Lateral Gene Transfer. In Evolutionary Genomics and Proteomics, pp.45-79, 2007.
Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups, Proc Natl Acad Sci, vol.106, issue.10, pp.3859-3864, 2009. ,
Evolution: revisiting the root of the eukaryote tree, Curr Biol, vol.19, issue.4, pp.165-167, 2009. ,
Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes, Nat Rev Genet, vol.5, issue.2, pp.123-135, 2004. ,
Psychroflexus torquis gen. nov., sp. nov., a psychrophilic species from Antarctic sea ice, and reclassification of Flavobacterium gondwanense (Dobson et al. 1993) as Psychroflexus gondwanense gen. nov., comb. nov. Microbiology, vol.144, pp.1601-1609, 1998. ,
, Genome analysis of the proteorhodopsincontaining marine bacterium Polaribacter sp. MED152 (Flavobacteria)
, Proc Natl Acad Sci, vol.105, issue.25, pp.8724-8729, 2008.
Dynamics of bacterial community composition and activity during a mesocosm diatom bloom, Appl Environ Microbiol, vol.66, issue.2, pp.578-587, 2000. ,
Microorganisms resistant to free-living amoebae, Clin Microbiol Rev, vol.17, issue.2, pp.413-433, 2004. ,
You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes, Trends Genet, vol.14, issue.8, pp.307-311, 1998. ,
Evolutionary analyses of the small subunit of glutamate synthase: gene order conservation, gene fusions, and prokaryote-to-eukaryote lateral gene transfers, Eukaryot Cell, vol.1, issue.2, pp.304-310, 2002. ,
Evolutionary origins of the eukaryotic shikimate pathway: gene fusions, horizontal gene transfer, and endosymbiotic replacements, Eukaryot Cell, vol.5, issue.9, pp.1517-1531, 2006. ,
Evolution of filamentous plant pathogens: gene exchange across eukaryotic kingdoms, Curr Biol, vol.16, issue.18, pp.1857-1864, 2006. ,
Euglena gracilis ribonucleotide reductase: the eukaryote class II enzyme and the possible antiquity of eukaryote B12 dependence, J Biol Chem, vol.281, issue.9, pp.5604-5611, 2006. ,
Nitratiruptor tergarcus gen. nov., sp. nov. and Nitratifractor salsuginis gen. nov., sp. nov., nitrate-reducing chemolithoautotrophs of the {varepsilon}-Proteobacteria isolated from a deep-sea hydrothermal system in the Mid-Okinawa Trough, Int J SystEvolMicrobiol, vol.55, pp.925-933, 2005. ,
, Cases in which Parsimony or Compatibility Methods will be Positively Misleading, vol.27, pp.401-410, 1978.
Ancient phylogenetic relationships, Theor Popul Biol, vol.61, issue.4, pp.391-408, 2002. ,
Thermotoga heats up lateral gene transfer, Curr Biol, vol.9, issue.19, pp.747-751, 1999. ,
Lateral gene transfer in eukaryotes, Cell Mol Life Sci, vol.62, issue.11, pp.1182-1197, 2005. ,
Gene transfer and diversification of microbial eukaryotes, Annu Rev Microbiol, vol.63, pp.177-193, 2009. ,
Elevation of Francisella philomiragia subsp. noatunensis Mikalsen et al. (2007) to Francisella noatunensis comb. nov. [syn. Francisella piscicida Ottem et al. (2008) syn. nov.] and characterization of Francisella noatunensis subsp. orientalis subsp. nov., two important fish pathogens, J Appl Microbiol, vol.106, issue.4, pp.1231-1243, 2009. ,
The evolution of ribonucleotide reduction, Trends Biochem Sci, vol.22, issue.3, pp.81-85, 1997. ,
Ribonucleotide reductases: the evolution of allosteric regulation, Arch Biochem Biophys, vol.397, issue.2, pp.149-155, 2002. ,
Respiratory chains in the last common ancestor of living organisms, J Mol Evol, vol.49, issue.4, pp.453-460, 1999. ,
Evolution of energetic metabolism: the respiration-early hypothesis, Trends Biochem Sci, vol.20, issue.11, pp.443-448, 1995. ,
The multiple evolutionary histories of dioxygen reductases: Implications for the origin and evolution of aerobic respiration, Mol Biol Evol, vol.26, issue.2, pp.285-297, 2009. ,
Earth's early atmosphere, Science, vol.259, issue.5097, pp.920-926, 1993. ,
Modern mRNA proofreading and repair: clues that the last universal common ancestor possessed an RNA genome?, Mol Biol Evol, vol.22, issue.6, pp.1444-1455, 2005. ,
Phylogenomics of sterol synthesis: insights into the origin, evolution, and diversity of a key eukaryotic feature, Genome Biol Evol, vol.1, pp.364-381, 2009. ,
General trends in trace element utilization revealed by comparative genomic analyses of Co, J Biol Chem, vol.285, issue.5, pp.3393-3405, 2010. ,
The slow road to the eukaryotic genome, BioEssays, vol.28, issue.1, pp.57-64, 2006. ,
Ribonucleotide reduction in Pseudomonas species: simultaneous presence of active enzymes from different classes, J Bacteriol, vol.181, issue.13, pp.3974-3980, 1999. ,
Two proteins mediate class II ribonucleotide reductase activity in Pseudomonas aeruginosa: expression and transcriptional analysis of the aerobic enzymes, J Biol Chem, vol.280, issue.17, pp.16571-16578, 2005. ,
Ribonucleotide reductase modularity: Atypical duplication of the ATP-cone domain in Pseudomonas aeruginosa, J Biol Chem, vol.281, issue.35, pp.25287-25296, 2006. ,
and analysis of the Irish potato famine pathogen Phytophthora infestans, BMC Evolutionary Biology, vol.10, issue.7262, pp.393-398, 2009. ,
Preservation of duplicate genes by complementary, degenerative mutations, Genetics, vol.151, issue.4, pp.1531-1545, 1999. ,
Evolution by gene duplication, 1970. ,
Adapting to environmental changes using specialized paralogs, Trends Genet, vol.24, issue.4, pp.154-158, 2008. ,
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data, Mol Biol Evol, vol.14, issue.7, pp.685-695, 1997. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00730410
ProbCons: Probabilistic consistency-based multiple sequence alignment, Genome Res, vol.15, issue.2, pp.330-340, 2005. ,
PROMALS3D: a tool for multiple protein sequence and structure alignments, Nucleic Acids Res, vol.36, issue.7, pp.2295-2300, 2008. ,
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, vol.22, issue.21, pp.2688-2690, 2006. ,
Phylogenetic Models of Rate Heterogeneity: A High Performance Computing Perspective, Proceedings of 20th IEEE/ACM International Parallel and Distributed Processing Symposium (IPDPS2006), High Performance Computational Biology Workshop, 2006. ,
A rapid bootstrap algorithm for the RAxML Web servers, Syst Biol, vol.57, issue.5, pp.758-771, 2008. ,
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood, Syst Biol, vol.52, issue.5, pp.696-704, 2003. ,
Phylogenetic mixture models for proteins, Philos Trans R Soc Lond B Biol Sci, vol.363, pp.3965-3976, 1512. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00365645
An improved general amino acid replacement matrix, Mol Biol Evol, vol.25, issue.7, pp.1307-1320, 2008. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00324106
Application of phylogenetic networks in evolutionary studies, Mol Biol Evol, vol.23, issue.2, pp.254-267, 2006. ,
Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative, Syst Biol, vol.55, issue.4, pp.539-552, 2006. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00136658
Dendroscope: An interactive viewer for large phylogenetic trees, BMC Bioinformatics, vol.8, p.460, 2007. ,
The radical site in chlamydial ribonucleotide reductase defines a new R2 subclass, Science, vol.305, issue.5681, pp.245-248, 2004. ,
SWISS-MODEL: An automated protein homology-modeling server, Nucleic Acids Res, vol.31, issue.13, pp.3381-3385, 2003. ,
Ribonucleotide reduction -horizontal transfer of a required function spans all three domains, BMC Evolutionary Biology, vol.10, p.383, 2010. ,
URL : https://hal.archives-ouvertes.fr/pasteur-02445883