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Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea

Yvan Zivanovic1, Jean Armengaud2, Arnaud Lagorce1, Christophe Leplat1, Philippe Guérin2, Murielle Dutertre1, Véronique Anthouard3, Patrick Forterre4, Patrick Wincker3 and Fabrice Confalonieri1*

Author Affiliations

1 Laboratoire de Génomique des Archae, Université Paris-Sud 11, CNRS, UMR8621, Bât400 F-91405 Orsay, France

2 CEA, DSV, IBEB Laboratoire de Biochimie des Systèmes Perturbés, Bagnols-sur-Cèze, F-30207, France

3 CEA, DSV, Institut de Génomique, Genoscope, rue Gaston Crémieux CP5706, F-91057 Evry Cedex, France

4 Laboratoire de Biologie moléculaire du gène chez les extrêmophiles, Université Paris-Sud 11, CNRS, UMR8621, Bât 409, F-91405 Orsay, France

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Genome Biology 2009, 10:R70  doi:10.1186/gb-2009-10-6-r70

Published: 26 June 2009

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.