title: An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi.
abstract: The hyperthermophilic euryarchaeon Pyrococcus abyssi and the related species Pyrococcus furiosus and Pyrococcus horikoshii, whose genomes have been completely sequenced, are presently used as model organisms in different laboratories to study archaeal DNA replication and gene expression and to develop genetic tools for hyperthermophiles. We have performed an extensive re-annotation of the genome of P. abyssi to obtain an integrated view of its phylogeny, molecular biology and physiology. Many new functions are predicted for both informational and operational proteins. Moreover, several candidate genes have been identified that might encode missing links in key metabolic pathways, some of which have unique biochemical features. The great majority of Pyrococcus proteins are typical archaeal proteins and their phylogenetic pattern agrees with its position near the root of the archaeal tree. However, proteins probably from bacterial origin, including some from mesophilic bacteria, are also present in the P. abyssi genome.
authors.affiliation: Institut Pasteur, 25,28 rue du Docteur Roux, 75724 Paris CEDEX 15, France.
authors.forename: Georges N
authors.initials: GN
authors.lastname: Cohen
authors.forename: Valérie
authors.initials: V
authors.lastname: Barbe
authors.forename: Didier
authors.initials: D
authors.lastname: Flament
authors.forename: Michael
authors.initials: M
authors.lastname: Galperin
authors.forename: Roland
authors.initials: R
authors.lastname: Heilig
authors.forename: Odile
authors.initials: O
authors.lastname: Lecompte
authors.forename: Olivier
authors.initials: O
authors.lastname: Poch
authors.forename: Daniel
authors.initials: D
authors.lastname: Prieur
authors.forename: Joël
authors.initials: J
authors.lastname: Quérellou
authors.forename: Raymond
authors.initials: R
authors.lastname: Ripp
authors.forename: Jean-Claude
authors.initials: JC
authors.lastname: Thierry
authors.forename: John
authors.initials: J
authors.lastname: Van der Oost
authors.forename: Jean
authors.initials: J
authors.lastname: Weissenbach
authors.forename: Yvan
authors.initials: Y
authors.lastname: Zivanovic
authors.forename: Patrick
authors.initials: P
authors.lastname: Forterre
mesh_terms: D000222:Adaptation, Physiological; D000596:Amino Acids / Q000096:biosynthesis; D019843:Archaeal Proteins / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D001692:Biological Transport; D050260:Carbohydrate Metabolism; D002455:Cell Division / Q000235:genetics; D020090:Chromosome Segregation; D004260:DNA Repair / Q000502:physiology; D004261:DNA Replication; D022761:Gene Transfer, Horizontal; D020745:Genome, Archaeal; D008969:Molecular Sequence Data; D010802:Phylogeny; D014176:Protein Biosynthesis; D019711:Pyrococcus / Q000166:cytology / Q000235:genetics* / Q000378:metabolism*; D011995:Recombination, Genetic; D014158:Transcription, Genetic
chemical_list: D000596:Amino Acids; D019843:Archaeal Proteins