Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics

The bacterium Deinococcus radiodurans shows remarkable resistance to a rang e of damage caused by ionizing radiation, desiccation, UV radiation, oxidiz ing agents, and electrophilic mutagens. D. radiodurans is best known for it s extreme resistance to ionizing radiation; not only can ii grow continuous ly in the presence of chronic radiation (6 kilorads/h), but also it can sur vive acute exposures to gamma radiation exceeding 1,500 kilorads without dy ing or undergoing induced mutation. These characteristics were the impetus for sequencing the genome of D. radiodurans and the ongoing development of its use for bioremediation of radioactive wastes. Although it is known that these multiple resistance phenotypes stem from efficient DNA repair proces ses, the mechanisms underlying these extraordinary repair capabilities rema in poorly understood. In this work we present an extensive comparative sequ ence analysis of the Deinococcus genome. Deinococcus is the first represent ative with a completely sequenced genome from a distinct bacterial lineage of extremophiles, the Thermus-Deinococcus group. Phylogenetic tree analysis , combined with the identification of several synapomorphies between Thermu s and Deinococcus, supports the hypothesis that it is an ancient group with no clear affinities to any of the other known bacterial lineages. Distinct ive features of the Deinococcus genome as well as features shared with othe r free-living bacteria were revealed by comparison of its proteome to the c ollection of clusters of orthologous groups of proteins. Analysis of paralo gs in Deinococcus has revealed several unique protein families. In addition , specific expansions of several other families including phosphatases, pro teases, acyltransferases, and Nudix family pyrophosphohydrolases were detec ted. Genes that potentially affect DNA repair and recombination and stress responses were investigated in detail. Some proteins appear to have been ho rizontally transferred from eukaryotes and are not present in other bacteri a. For example, three proteins homologous to plant desiccation resistance p roteins were identified and these are particularly interesting because of t he correlation between desiccation and radiation resistance. Compared to ot her bacteria, the D. radiodurans genome is enriched in repetitive sequences , namely, IS-like transposons and small intergenic repeats. In combination these observations suggest that several different biological mechanisms con tribute to the multiple DNA repair-dependent phenotypes of this organism.