title: Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea.
abstract: BACKGROUND
  Thermococcus gammatolerans was isolated from samples collected from hydrothermal chimneys. It is one of the most radioresistant organisms known amongst the Archaea. We report the determination and annotation of its complete genome sequence, its comparison with other Thermococcales genomes, and a proteomic analysis.
  
  
  RESULTS
  T. gammatolerans has a circular chromosome of 2.045 Mbp without any extra-chromosomal elements, coding for 2,157 proteins. A thorough comparative genomics analysis revealed important but unsuspected genome plasticity differences between sequenced Thermococcus and Pyrococcus species that could not be attributed to the presence of specific mobile elements. Two virus-related regions, tgv1 and tgv2, are the only mobile elements identified in this genome. A proteogenome analysis was performed by a shotgun liquid chromatography-tandem mass spectrometry approach, allowing the identification of 10,931 unique peptides corresponding to 951 proteins. This information concurrently validates the accuracy of the genome annotation. Semi-quantification of proteins by spectral count was done on exponential- and stationary-phase cells. Insights into general catabolism, hydrogenase complexes, detoxification systems, and the DNA repair toolbox of this archaeon are revealed through this genome and proteome analysis.
  
  
  CONCLUSIONS
  This work is the first archaeal proteome investigation done at the stage of primary genome annotation. This archaeon is shown to use a large variety of metabolic pathways even under a rich medium growth condition. This proteogenomic study also indicates that the high radiotolerance of T. gammatolerans is probably due to proteins that remain to be characterized rather than a larger arsenal of known DNA repair enzymes.
authors: Laboratoire de Génomique des Archae, Université Paris-Sud 11, CNRS, UMR8621, Bât400 F-91405 Orsay, France. yvan.zivanovic@igmors.u-psud.fr
authors: Yvan
authors: Y
authors: Zivanovic
authors: Jean
authors: J
authors: Armengaud
authors: Arnaud
authors: A
authors: Lagorce
authors: Christophe
authors: C
authors: Leplat
authors: Philippe
authors: P
authors: Guérin
authors: Murielle
authors: M
authors: Dutertre
authors: Véronique
authors: V
authors: Anthouard
authors: Patrick
authors: P
authors: Forterre
authors: Patrick
authors: P
authors: Wincker
authors: Fabrice
authors: F
authors: Confalonieri
mesh_terms: D019843:Archaeal Proteins / Q000378:metabolism; D001692:Biological Transport / Q000528:radiation effects; D002462:Cell Membrane / Q000201:enzymology / Q000528:radiation effects; D002875:Chromosomes / Q000378:metabolism; D018387:Codon, Initiator / Q000235:genetics; D004260:DNA Repair / Q000528:radiation effects; D004251:DNA Transposable Elements / Q000235:genetics; D005720:Gamma Rays; D020745:Genome, Archaeal / Q000235:genetics*; D006864:Hydrogenase / Q000378:metabolism; D013058:Mass Spectrometry; D050296:Microbial Viability / Q000528:radiation effects; D014176:Protein Biosynthesis / Q000235:genetics / Q000528:radiation effects; D011499:Protein Processing, Post-Translational / Q000528:radiation effects; D020543:Proteome / Q000235:genetics; D040901:Proteomics; D011836:Radiation Tolerance / Q000235:genetics* / Q000528:radiation effects; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D019712:Thermococcus / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism / Q000821:virology
chemical_list: D019843:Archaeal Proteins; D018387:Codon, Initiator; D004251:DNA Transposable Elements; D020543:Proteome; D006864:Hydrogenase