title: Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance.
abstract: BACKGROUND
  Thermus thermophilus and Deinococcus radiodurans belong to a distinct bacterial clade but have remarkably different phenotypes. T. thermophilus is a thermophile, which is relatively sensitive to ionizing radiation and desiccation, whereas D. radiodurans is a mesophile, which is highly radiation- and desiccation-resistant. Here we present an in-depth comparison of the genomes of these two related but differently adapted bacteria.
  
  
  RESULTS
  By reconstructing the evolution of Thermus and Deinococcus after the divergence from their common ancestor, we demonstrate a high level of post-divergence gene flux in both lineages. Various aspects of the adaptation to high temperature in Thermus can be attributed to horizontal gene transfer from archaea and thermophilic bacteria; many of the horizontally transferred genes are located on the single megaplasmid of Thermus. In addition, the Thermus lineage has lost a set of genes that are still present in Deinococcus and many other mesophilic bacteria but are not common among thermophiles. By contrast, Deinococcus seems to have acquired numerous genes related to stress response systems from various bacteria. A comparison of the distribution of orthologous genes among the four partitions of the Deinococcus genome and the two partitions of the Thermus genome reveals homology between the Thermus megaplasmid (pTT27) and Deinococcus megaplasmid (DR177).
  
  
  CONCLUSIONS
  After the radiation from their common ancestor, the Thermus and Deinococcus lineages have taken divergent paths toward their distinct lifestyles. In addition to extensive gene loss, Thermus seems to have acquired numerous genes from thermophiles, which likely was the decisive contribution to its thermophilic adaptation. By contrast, Deinococcus lost few genes but seems to have acquired many bacterial genes that apparently enhanced its ability to survive different kinds of environmental stresses. Notwithstanding the accumulation of horizontally transferred genes, we also show that the single megaplasmid of Thermus and the DR177 megaplasmid of Deinococcus are homologous and probably were inherited from the common ancestor of these bacteria.
authors.affiliation: Department of Pathology, F.E. Hebert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4799, USA. omelchen@ncbi.nlm.nih.gov
authors.forename: Marina V
authors.initials: MV
authors.lastname: Omelchenko
authors.forename: Yuri I
authors.initials: YI
authors.lastname: Wolf
authors.forename: Elena K
authors.initials: EK
authors.lastname: Gaidamakova
authors.forename: Vera Y
authors.initials: VY
authors.lastname: Matrosova
authors.forename: Alexander
authors.initials: A
authors.lastname: Vasilenko
authors.forename: Min
authors.initials: M
authors.lastname: Zhai
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Daly
authors.forename: Eugene V
authors.initials: EV
authors.lastname: Koonin
authors.forename: Kira S
authors.initials: KS
authors.lastname: Makarova
mesh_terms: D000064:Acclimatization; D001105:Archaea / Q000235:genetics; D004249:DNA Damage; D004260:DNA Repair; D034301:Deinococcus / Q000235:genetics*; D004926:Escherichia coli / Q000378:metabolism; D005720:Gamma Rays; D022761:Gene Transfer, Horizontal; D019766:Genes, Archaeal; D005798:Genes, Bacterial; D016678:Genome; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D006358:Hot Temperature; D007501:Iron / Q000737:chemistry; D008345:Manganese / Q000737:chemistry; D008957:Models, Genetic; D005810:Multigene Family; D010641:Phenotype; D010802:Phylogeny; D010957:Plasmids / Q000378:metabolism; D013696:Temperature; D016963:Thermus thermophilus / Q000235:genetics*
chemical_list: D008345:Manganese; D007501:Iron