Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti

• Published in: PLoS genetics 2009-03, Vol.5 (3), p.e1000434-e1000434
• Main Authors: de Groot, Arjan, Dulermo, Rémi, Ortet, Philippe, Blanchard, Laurence, Guérin, Philippe, Fernandez, Bernard, Vacherie, Benoit, Dossat, Carole, Jolivet, Edmond, Siguier, Patricia, Chandler, Michael, Barakat, Mohamed, Dedieu, Alain, Barbe, Valérie, Heulin, Thierry, Sommer, Suzanne, Achouak, Wafa, Armengaud, Jean
• Format: Article
• Language: English
• Subjects: Africa, Northern; Bacteria; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Bacteriology; Biochemistry, Molecular Biology; Biophysics/Protein Chemistry and Proteomics; Computational Biology/Comparative Sequence Analysis; Deinococcus; Deinococcus - chemistry; Deinococcus - genetics; Deinococcus - radiation effects; Desert Climate; DNA repair; Ecology/Environmental Microbiology; Evolutionary Biology/Microbial Evolution and Genomics; Gamma Rays; Genetic aspects; Genetics and Genomics/Comparative Genomics; Genetics and Genomics/Gene Discovery; Genetics and Genomics/Gene Expression; Genome, Bacterial; Genomics; Health aspects; Life Sciences; Microbiology; Microbiology and Parasitology; Microbiology/Environmental Microbiology; Molecular Biology/DNA Repair; Molecular Biology/Recombination; Molecular Sequence Data; Proteomics; Ultraviolet radiation; Ultraviolet Rays
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1000434

To better understand adaptation to harsh conditions encountered in hot arid deserts, we report the first complete genome sequence and proteome analysis of a bacterium, Deinococcus deserti VCD115, isolated from Sahara surface sand. Its genome consists of a 2.8-Mb chromosome and three large plasmids of 324 kb, 314 kb, and 396 kb. Accurate primary genome annotation of its 3,455 genes was guided by extensive proteome shotgun analysis. From the large corpus of MS/MS spectra recorded, 1,348 proteins were uncovered and semiquantified by spectral counting. Among the highly detected proteins are several orphans and Deinococcus-specific proteins of unknown function. The alliance of proteomics and genomics high-throughput techniques allowed identification of 15 unpredicted genes and, surprisingly, reversal of incorrectly predicted orientation of 11 genes. Reversal of orientation of two Deinococcus-specific radiation-induced genes, ddrC and ddrH, and identification in D. deserti of supplementary genes involved in manganese import extend our knowledge of the radiotolerance toolbox of Deinococcaceae. Additional genes involved in nutrient import and in DNA repair (i.e., two extra recA, three translesion DNA polymerases, a photolyase) were also identified and found to be expressed under standard growth conditions, and, for these DNA repair genes, after exposure of the cells to UV. The supplementary nutrient import and DNA repair genes are likely important for survival and adaptation of D. deserti to its nutrient-poor, dry, and UV-exposed extreme environment.