Publications

2014

 

Probst AJ, Weinmaier T, Raymann K, Perras A, Emerson JB, Rattei T, Wanner G, Klingl A, Berg IA, Yoshinaga M, Viehweger B, Hinrichs K, Thomas BC, Meck S, Auerbach AK, Heise M, Schintlmeister A, Schmidt M, Wagner M, Gribaldo S, Banfield JF, and Moissl-Eichinger C (2014) Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface. Nature Communications (in press).

 

Appolaire A, Asunción Durá M, Ferruit M, Andrieu JP, Godfroy A, Gribaldo S, and Franzetti B (2014) The TET2 and TET3 aminopeptidases from Pyrococcus horikoshii form a hetero-subunit peptidasome with enhanced peptide destruction properties. Molecular Microbiology doi: 10.1111/mmi.12775.

 

Borrel G, Parisot N, Harris HMB, Peyretaillade E, Gaci N, Tottey W, Bardot O, Raymann K, Gribaldo S, Peyret P, O’Toole PW and Brugère JF (2014) Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine. BMC Genomics. 15:679. doi: 10.1186/1471-2164-15-679.

 

Muszkieta L, Aimanianda V, Mellado E, Gribaldo S, Alcàzar-Fuoli L, Szewczyk E, Prevost MC, Latgé JP. (2014) Deciphering the role of the chitin synthase families 1 and 2 in the in vivo and in vitro growth of Aspergillus fumigatus by multiple gene targeting deletion. Cell Microbiol. Jun 20. doi: 10.1111/cmi.12326.

 

Poole AM and Gribaldo S (2014) Eukaryotic origins: when and how was the mitochondrion acquired? Cold Spring Harbor Perspectives in Biology. In press.

 

Raymann K, Forterre P, Brochier-Armanet C, Gribaldo S (2014) Global phylogenomic analysis disentangles the complex evolutionary history of DNA replication in archaea. Genome Biol Evol. 6(1):192-212.

 

Borrel G, Gaci N, Peyret P, O'Toole PW, Gribaldo S, and Brugère JF (2014) Unique Characteristics of the Pyrrolysine System in the 7th Order of Methanogens: Implications for the Evolution of a Genetic Code Expansion Cassette. Archaea. Article ID 374146

 

2013

 

Borrel G, O'Toole P, Peyret P, Brugère JF, and Gribaldo S (2013) Phylogenomic data support a seventh order of methylotrophic methanogens and provide insights into the evolution of methanogenesis. Genome Biol Evol. 5(10):1769-80

 

Borrel G, Harris H, Parisot N, Gaci N, Tottey W, Mihajlovski A, Deane A, Gribaldo S, Bardot O, Peyretaillade E, Peyret P, O'Toole P, and Brugère JF. (2013) Genome sequence of "Candidatus Methanomassiliicoccus intestinalis" Issoire-Mx1, a third Thermoplasmatales-related methanogenic archaea from human feces. ASM Genome Announcements 11;1(4)

 

Gomez-Valero L, Neou Bonora M, Gribaldo S, Buchrieser C (2013) Interdomain horizontal gene transfer shaped the genomes of Legionella pneumophila and Legionella Longbeacheae. In “Lateral Gene Transfer in Evolution” Ed. Springer. In press.

 

Raymann K, Bobay LM, Doak TG, Lynch M, Gribaldo S (2013) A genomic survey of Reb homologs suggests widespread occurrence of R-bodies in proteobacteria. G3 (Bethesda) 3(3):505-16.

 

2012

 

Borrel G, Harris HM, Tottey W, Mihajlovski A, Parisot N, Peyretaillade E, Peyret P, Gribaldo S, O'Toole PW, Brugère JF (2012) Genome sequence of "Candidatus Methanomethylophilus alvus" Mx1201, a methanogenic archaeon from the human gut belonging to a seventh order of methanogens. J Bacteriol. 194(24):6944-5.

 

Gribaldo S, Brochier-Armanet C (2012) Time for order in microbial systematics. Trends in Microbiology 20(5):209-10

 

Brochier-Armanet C, Gribaldo S, Forterre P (2011) Evolution: Spotlight on the Thaumarchaeota. ISME J. 6(2):227-30 REVIEW

 

2011

 

Moriscot C, Gribaldo S, Jault JM, Krupovic M, Arnaud J, Jamin M, Schoehn G, Forterre P, Weissenhorn W, Renesto P. (2011) Crenarchaeal CdvA forms double-helical filaments containing DNA and interacts with ESCRT-III-like CdvB. PLoS One. 6(7):e21921.

 

Halter D, Cordi B, Gribaldo S, Gallien S, Goulhen-Chollet F, Heinrich-Salmeron A, Carapito C, Pagnout C, Montaut D, Seby F, Van Dorsselaer A, Schaeffer C, Bertin PN, Bauda P, Arsène-Ploetze F. (2011) Taxonomic and functional prokaryote diversity in mildly arsenic contaminated sediments. Res Microbiolol. 162(9):877-87.

 

Criscuolo A and Gribaldo S (2011) Large-scale phylogenomic analyses indicate a deep origin of primary plastids within Cyanobacteria. Mol Biol Evol. 28(11):3019-32.

 

Gribaldo S, Forterre P, Brochier-Armanet C (2011) Editorial: Archaea and the tree of life. Res Microbiol. 162(1):1-4.

 

Brochier-Armanet C, Forterre P, Gribaldo S (2011) Phylogeny and evolution of the Archaea: one hundred genomes later. Curr Opin Microbiol. 14(3):274-81.

 

Krupovic M, Spang A, Gribaldo S, Forterre P, Schleper C (2011) A thaumarchaeal provirus testifies for an ancient association of tailed viruses with archaea. Biochem Soc Trans 39(1):82-8.

 

Desmond E, Brochier-Armanet C, Forterre P, and Gribaldo S (2011) On the last eukaryotic common ancestor and early eukaryotic evolution: reconstructing the history of mitochondrial ribosomes. Res Microbiol. 162(1):53-70.

 

Gastebois A, Blanc Potard A, Gribaldo S, Beau R, Latgé JP and Mouyna I (2011) Phylogenetic and functional analysis of Aspergillus fumigatus MGTC, a fungal protein homologous to a bacterial virulence factor. Applied and Environmental Microbiology. 77(13):4700-3.

 

Gaget V, Gribaldo S, Tandeau de Marsac N (2011) A rpoB signature sequence provides unique resolution for the molecular typing of cyanobacteria. Int J Syst Evol Microbiol. 61:170-83.

 

2010

 

Gribaldo S, Poole AM, Daubin V, Forterre P, Brochier-Armanet C (2010) The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse? Nat Rev Microbiol  8(10):743-52.

 

Lundin D, Gribaldo S, Torrents E, Sjoberg BM, Poole AM (2010) Ribonucleotide reduction – horizontal transfer of a required function spans all three domains. BMC Evol Biol 10(1):383.

 

Cortez D, Quevillon-Cheruel S, Gribaldo S, Desnoues N, Sezonov G, Forterre P, Serre MC (2010) Evidence for a Xer/dif system for chromosome resolution in Archaea. PLoS Genetics. 6(10):e1001166.

 

Criscuolo A and Gribaldo S (2010) BMGE (Block Mapping and Gathering with Entropy): a New Software for   Selection of Phylogenetic Informative Regions from Multiple Sequence Alignments. BMC Evol Biol. 13;10:210.

 

Sime-Ngando T, Lucas S, Robin A, Pause Tucker K, Colombet J, Bettarel Y, Desmond E, Gribaldo S, Forterre P, Breitbart M  and Prangishvili D (2010) Diversity of virus-host systems in hypersaline Lake Retba, Senegal. Environ Microbiol. 13(8):1956-72

 

Krupovic M, Gribaldo S, Bamford DH, Forterre P (2010) The evolutionary history of archaeal MCM helicases: a case study of vertical evolution combined with hitchhiking of mobile genetic elements. Mol Biol Evol. 27(12):2716-32.

 

Jambou R, Martinelli A, Pinto J, Gribaldo S, Legrand E, Niang M, Kim N, Pharath L, Volnay B, Ekala MT, Bouchier C, Fandeur T, Berzosa P, Benito A, Ferreira ID, Ferreira C, Vieira PP, Alecrim MG, Mercereau-Puijalon O, Cravo P (2010) Geographic structuring of the Plasmodium falciparum sarco(endo)plasmic reticulum Ca2+ ATPase (PfSERCA) gene diversity. PLoS One. 25;5(2):e9424.

 

Forterre P, Gribaldo S (2010) Bacteria with a eukaryotic touch: a glimpse of ancient evolution? Proc Natl Acad Sci U S A. 107(29):12739-40. RESEARCH HIGHLIGHT

 

2009

 

Gribaldo S and Brochier C (2009) Phylogeny of prokaryotes: does it exist and why should we care? Res Microbiol.160 (7) :513-21.

 

Fondi M, Emiliani G, Liò P, Gribaldo S, and Fani R (2009) The evolution of histidine biosynthesis in Archaea: insights into the his genes structure and organization in LUCA. J. Mol. Evol. 69(5):512-26

 

Desmond E and Gribaldo S (2009) Phylogenomics of sterol synthesis: insights into the origin, evolution and diversity of a key eukaryotic feature. Genome Biol Evol. 2009:364-81.

 

Gribaldo S*, Talla E, Brochier-Armanet C* (2009) Evolution of the haem copper oxidases superfamily: a rooting tale. Trends Biochem Sci. 34(8):375-81.

 

Cortez D, Forterre P, Gribaldo S (2009) A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes. Genome Biol. 10(6):R65.

 

Emiliani G, Fondi M, Fani R, Gribaldo S (2009) A horizontal gene transfer at the origin of phenylpropanoid metabolism: a key adaptation of plants to land. Biology Direct. 16;4(1):7.

 

Forterre P, Gribaldo S, Brochier-Armanet C (2009) Happy together: genomic insights into the unique Nanoarchaeum/Ignicoccus association. J Biol. 2009 8(1):7.

 

2008

 

Brochier-Armanet C, Gribaldo S, and Forterre P (2008) A DNA Topoisomerase IB in Thaumarchaeota testifies for the presence of this enzyme in the last common ancestor of Archaea and Eucarya. Biology Direct 3:54.

 

Brochier-Armanet C, Talla E, Gribaldo S (2008) The multiple evolutionary histories of dioxygen reductases: implications for the origin and evolution of aerobic respiration. Mol Biol Evol. 26(2):285-97.

 

Frangeul L, Quillardet P, Castets AM, Humbert JF, Matthijs HC, Cortez D, Tolonen A, Zhang CC, Gribaldo S, Kehr JC, Zilliges Y, Ziemert N, Becker S, Talla E, Latifi A, Billault A, Lepelletier A, Dittmann E, Bouchier C, Tandeau de Marsac N (2008) Highly plastic genome of Microcystis aeruginosa PCC7806, a ubiquitous toxic freshwater cyanobacterium. BMC Genomics 5;9(1):274.

 

Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P (2008) Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat Rev Microbiol. 6(3):245-52.

 

2007

 

Desmond E, Brochier-Armanet C, Gribaldo S (2007) Phylogenomics of the archaeal flagellum: rare horizontal gene transfer in a unique motility structure. BMC Evol Biol. 2;7:106.

 

Yandoko EN, Gribaldo S, Finance C, Le Faou A, Rihn BH (2007) Molecular characterization of African orthobunyaviruses. J Gen Virol. 88(Pt 6):1761-6.

 

Forterre P, Gribaldo S, Gadelle D, Serre MC (2007) Origin and evolution of DNA topoisomerases. Biochimie. 89(4):427-46.

 

Forterre P and Gribaldo S (2007) The origin of modern terrestrial life. Human Frontiers Science Program Journal 1; 3:156-168.

 

2006

 

Forterre P, Gribaldo S, Brochier C (2006) Natural history of the archaeal domain. In Archaea - physiology, molecular biology and evolution. Eds R Garrett and HP Klenk. Ed. Blackwell Publishing, Oxford.

 

Forterre P, Zivanovic Y, Gribaldo S (2006). Structure and evolution of archaeal genomes. In Archaea : molecular cell biology. Ed R Cavicchioli. Ed. AMCB press.

 

Gribaldo S and Brochier C (2006) The origin and evolution of the Archaea : a state of the art. Proc Royal Acad Sci. 361(1470):1007-22.

 

2005

 

Brochier C, Gribaldo S, Forterre P (2005) An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences. BMC Evolutionary Biology 5(1):36.

 

Brochier C, Gribaldo S, Zivanovic Y, Confalonieri F, Forterre P (2005) Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales? Genome Biol 6(5):R42.

 

Gribaldo S and Forterre P (2005). Looking for “most primitive” life forms: pitfalls and progresses. In Lectures in Astrobiology - Vol I. Part 2: From Prebiotic Chemistry to the Origin of Life on Earth. Eds. Gargaud, M., Barbier, B., Martin, H. and Reisse, J. Ed. Springer-Verlag.

 

2004

 

Brochier C, Forterre P, Gribaldo S (2004) Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox. Genome Biol  5(3):R17.

 

Gribaldo S and Philippe H (2004) Pitfalls in tree reconstruction and the phylogeny of eukaryotes. In Organelles, Genomes and Eukaryote Phylogeny. Eds RP Hirt and DS Horner. CRC press Raton Fl.

 

2003

 

Armengaud J, Fernandez B, Chaumont V, Rollin-Genetet F, Finet S, Marchetti C, Myllykallio H, Vidaud C, Pellequer JL, Gribaldo S, Forterre P, Gans P (2003) Identification, purification and characterization of a eukaryotic-like phosphopanthetheine adenylyltransferase (coenzyme A biosynthetic pathway) in the hyperthermophilic archaeon Pyrococcus abyssi. J. Biol. Chem. 33: 31078-31087.

 

Gribaldo S, Casane D, Lopez P, Philippe H (2003) Functional divergence prediction from evolutionary analysis: a case study of vertebrate haemoglobin. Mol. Biol. Evol. 11: 1754-1759.

 

Bapteste E and Gribaldo S (2003) The genome reduction hypothesis and the phylogeny of eukaryotes. Trends in Genetics 19: 696-700.

 

Philippe H, Casane D, Gribaldo S, Lopez P, Meunier J (2003) Heterotachy and functional shift in protein evolution. IUBMB Life 55: 257-265.

 

2002

 

Cammarano P, Gribaldo S, and Johann A (2002) Updating carbamoylphosphate synthase (CPS) phylogenies. Occurrence and phylogenetic identity of archaeal CPS genes. J. Mol. Evol. 55 (2): 153-160.

 

Gribaldo S and H Philippe (2002) Ancient phylogenetic relationships. Theor. Popul. Biol. 61: 391-408.

 

2000

 

Bocchetta M, Gribaldo S, Sanangelantoni A, and P. Cammarano (2000) Phylogenetic depth of the bacterial genera Aquifex and Thermotoga inferred from analysis of ribosomal protein, elongation factor and RNA polymerase subunit sequences. J. Mol. Evol. 50 (4): 366-380.

 

1999

 

Gribaldo S, Lumia V, Creti R, Conway de Macario E, Sanangelantoni A, and P. Cammarano (1999) Discontinuous occurrence of the hsp70(dnaK) gene among Archaea and sequence features of Hsp70 suggests a novel outlook on the evolution of  this protein. J. Bacteriol. 181(2): 434-443.

 

1998

 

Gribaldo S, and P.Cammarano (1998) The root of the universal tree of life inferred from anciently duplicated genes encoding components of the protein-targeting machinery. J. Mol. Evol. 47(5): 508-516.

 

1997

 

Gribaldo S, Cookson B, Saunders N, Marples R, and J. Stanley (1997) Rapid identification by specific PCR of coagulase-negative staphylococcal species important in hospital infection. J. Med. Microbiol. 46(1): 45-53.

 

1996

 

Agodi A, Stefani S, Corsaro C, Campanile F, Gribaldo S and G. Sichel (1996) Study of a melanic pigment of Proteus mirabilisRes. Microbiol. 147(3): 167-174.

 

 

Science for the general public

 

Articles

 

Gribaldo S and Brochier-Armanet C (2013) LUCA, ancêtre de tous les êtres vivants. Les Dossiers de La Recherche N.2 pg 29-31.

 

Brochier-Armanet C, Gribaldo S (2012) Les defis de la systématique face au monde microbien. Biofutur (328):49-52

 

Gribaldo S, Forterre P, Brochier-Armanet C (2008) Les Archaea, évolution et diversité du troisième domaine du vivant. Bulletin de La Société Française de Microbiologie 23(3): 137-145.

 

Forterre P, Gribaldo S, Brochier C (2005) Luca: the last universal common ancestor Med Sci (Paris) 21(10):860-5.

 

Books

 

Gribaldo S, Maurel MC, Vannier J (2007) Les Débuts de la vie. Editions Le Pommier.

 

Mis à jour le 24/10/2014

Contact

Unité de Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE)

Bâtiment Fernbach 3eme étage

Institut Pasteur, 25 rue Dr. Roux

75724 Paris cedex 15 France

 

Secrétaire:

Ana Cova

ana.cova-rodrigues@pasteur.fr

01-45-68-88-30

01-45-68-88-34

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