DOE Human Genome Program Contractor-Grantee Workshop VIII
February 27-March 2, 2000  Santa Fe, NM

120. Unusual Features of Radioresistant Bacterium Deinococcus radiodurans Genome Revealed by Comparative-Genomic Analysis

Kira S. Makarova^1,2, L. Aravind², Roman L. Tatusov², Eugene V. Koonin², and Michael J. Daly¹

¹Uniformed Services University of the Health Sciences, Bethesda, MD 20814-479 and ²The National Center for Biotechnology Information, The National Institutes of Health, Bethesda, MD 20814

makarova@ncbi.nlm.nih.gov

In-depth analysis of Deinococcus radiodurans genome reveals some unusual features, which may be relevant to its extreme radioresistance and desiccation resistance. Comparison of the Deinococcus gene products to the collection of Clusters of Orthologous Groups of proteins (COGs) allowed us to identify not only a set of genes which are shared with all or most bacteria, but some surprisingly missing genes, including those for several enzymes involved in repair and recombination. Using this information, we tentatively reconstructed the metabolic pathways, repair and recombination systems and stress response mechanisms of D. radiodurans. The comparative analysis helped in identifying phylogenetic affiliations of Deinococcus and sets of genes with unusual phylogenetic patterns, especially those that are shared with thermophilic archaea and bacteria, indicating a possible thermophilic ancestor for Deinococcus. We described several protein families that are specifically expanded in the genome of D. radiodurans, namely possible nuclease inhibitors, specific transcriptional regulators and desiccation-related proteins, which could contribute to the radioresistance and desiccation resistance of this bacterium. Some additional unique multidomain proteins, which could be involved in novel repair or stress-response-related mechanisms were detected. Investigation of short repeats in Deinococcus resulted in the identification of their mosaic nature and suggested that they could contribute to the recombinational proficiency of this organism.