BMC Evolutionary Biology BioMed Central Research article Open Access Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance Marina V Omelchenko1,2, Yuri I Wolf2, Elena K Gaidamakova1, Vera Y Matrosova1, Alexander Vasilenko1, Min Zhai1, Michael J Daly1, Eugene V Koonin2 and Kira S Makarova*2 Address: 1Department of Pathology, F.E. Hebert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814- 4799, USA and 2National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA Email: Marina V Omelchenko - [email protected]; Yuri I Wolf - [email protected]; Elena K Gaidamakova - [email protected]; Vera Y Matrosova - [email protected]; Alexander Vasilenko - [email protected]; Min Zhai - [email protected]; Michael J Daly - [email protected]; Eugene V Koonin - [email protected]; Kira S Makarova* - [email protected] * Corresponding author Published: 20 October 2005 Received: 23 August 2005 Accepted: 20 October 2005 BMC Evolutionary Biology 2005, 5:57 doi:10.1186/1471-2148-5-57 This article is available from: http://www.biomedcentral.com/1471-2148/5/57 © 2005 Omelchenko et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 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). Conclusion: 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. Page 1 of 22 (page number not for citation purposes) BMC Evolutionary Biology 2005, 5:57 http://www.biomedcentral.com/1471-2148/5/57 Background post-irradiation adjustment of metabolism of D. radio- Deinococcus spp. and Thermus spp. are believed to belong to durans might prevent production of reactive oxygen spe- a distinct branch of bacteria called the Deinococcus-Ther- cies (ROS) by decreasing the number of reactions mus group [1]. The common origin of these bacteria is involving oxygen [27,28], and high intracellular manga- supported by the fact that they consistently form a nese concentrations of Deinococcus spp. might help scav- strongly supported clade in phylogenetic trees of ribos- enge ROS generated during irradiation and post- omal RNAs and several conserved proteins including irradiation recovery [28,29]. However, these explanations ribosomal proteins, RNA polymerase subunits, RecA, and of radiation resistance have received little direct support others [1-7]. The Thermus genus currently consists of 14 from comparative-genomic analyses [7,27,28]. thermophilic species, whereas the Deinococcus genus includes at least eleven, mostly mesophilic species known Several evolutionary processes could potentially contrib- for their extreme resistance to γ-irradiation and other ute to the genome differentiation of TT and DR subse- agents causing DNA damage, particularly, desiccation quent to the divergence from the common ancestor: (i) [7,8]. Interestingly, two new species, D. frigens sp. nov., D. differential gene loss and gain, (ii) acquisition of genes via saxicola, have been isolated recently from Antarctic rock horizontal gene transfer (HGT) which may be followed by and soil samples [9]. D. geothermalis and D. murrayi, are loss of the ancestral orthologous gene (xenologous gene considered to be thermophilic (topt~45–50°C) [10]. displacement (XGD)), (iii) lineage-specific expansion of paralogous gene families by duplication and/or acquisi- T. thermophilus (TT) (strain HB27, ATCC BAA-163)and D. tion of paralogs via HGT; (IV) modification of amino acid radiodurans (DR) (strain R1, ATCC BAA-816) have similar composition that could affect protein stability. Here, we general physiology, both being catalase-positive, red-pig- experimentally characterize radiation and desiccation mented, non-sporulating, aerobic chemoorganohetero- resistance of TT in comparison to DR, and, assess the con- trophs [11]. However, the two organisms are dramatically tribution of different evolutionary processes to distinct different in terms of stress resistance: DR is one of the adaptations of TT and DR, using a variety of comparative- most resistant to radiation and desiccation among the genomic approaches and phylogenetic analysis. We iden- characterized organisms and, generally, can survive tify the unique feature of the gene repertoires of TT and diverse types of oxidative stress, whereas TT is a ther- DR that might contribute to these phenotypic differences, mophile that thrives under thermal stress conditions but which could be the subject of further experimental work. is relatively sensitive to radiation and other forms of oxi- In addition, we describe the results of a detailed analysis dative stress. Recently, the genomes of T. thermophilus of the proteins predicted to be involved in DNA repair and HB27 and HB8 [12,13] became available for comparison stress response functions, which are particularly relevant with the previously sequenced genome of D. raduodurans for adaptive evolution of resistance phenotypes. R1 [14]. Despite extensive research, genetic systems underlying both thermophilic adaptations and radiation resistance 1 remain poorly understood. Attempts have been made to 0 detect "thermophilic determinants" in the proteomes of -1 thermophiles using a comparative-genomic approach. -2 This resulted in the delineation of a set of proteins that -3 might be associated with the thermophilic phenotype, T. thermophilus -4 D. radiodurans although most of these are significantly enriched in ther- E. coli log survival -5 mophiles but not unique to these organisms [15-17]. Other distinctions between thermophilic and mesophilic -6 proteins might be due to differences in their structural -7 properties, such as different amino acid compositions, -8 loop lengths, number of salt bridges, strength of hydro- 0 2 4 6 8 10 12 14 16 18 20 22 24 26 phobic interaction, number of disulfide bonds, and other kGy features [18-25]. RadiationradioduransvidedFigure by 1 M. resistance (ATCCCashel, BAA-816) NIH)of T. thermophilus(60Co and irradiation) E. coli (ATCC (K-12 BAA-163),MG1655, pro- D. Various hypotheses also have been proposed to explain Radiation resistance of T. thermophilus (ATCC BAA-163), D. radiation resistance, some postulating the existence of radiodurans (ATCC BAA-816) and E. coli (K-12 MG1655, pro- specialized genetic systems, particularly those for DNA vided by M. Cashel, NIH) (60Co irradiation). Standard devia- repair and stress response [7,26]. Recently, however, alter- tions for the data points are shown. native possibilities have been advanced. For example, the Page 2 of 22 (page number not for citation purposes) BMC Evolutionary Biology 2005, 5:57 http://www.biomedcentral.com/1471-2148/5/57 We recently reported a trend of intracellular Mn/Fe con- centration ratios in bacterial IR resistance, where very high and very low Mn/Fe ratios correlated with very high and 1 very low resistances, respectively [29]. We have also 0 shown that growing D. radiodurans in conditions which -1 limited Mn(II) accumulation, significantly lowered the -2 cells' IR resistance [29]. These observations led to the hypothesis that the ratio of Mn to Fe in a cell might deter- -3 T. thermophilus mine the relative abundance of different ROS