Genome of the Extremely Radiation-Resistant Bacterium Deinococcus radiodurans Viewed from the Perspective of Comparative Genomics

Abstract

The bacterium Deinococcus radiodurans shows remarkable resistance to a range of damage caused by ionizing radiation, desiccation, UV radiation, oxidizing agents, and electrophilic mutagens. D. radiodurans is best known for its extreme resistance to ionizing radiation; not only can it grow continuously in the presence of chronic radiation (6 kilorads/h), but also it can survive acute exposures to gamma radiation exceeding 1,500 kilorads without dying 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 processes, the mechanisms underlying these extraordinary repair capabilities remain poorly understood. In this work we present an extensive comparative sequence analysis of the Deinococcus genome. Deinococcus is the first representative 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 Thermus and Deinococcus, supports the hypothesis that it is an ancient group with no clear affinities to any of the other known bacterial lineages. Distinctive features of the Deinococcus genome as well as features shared with other free-living bacteria were revealed by comparison of its proteome to the collection of clusters of orthologous groups of proteins. Analysis of paralogs in Deinococcus has revealed several unique protein families. In addition, specific expansions of several other families including phosphatases, proteases, acyltransferases, and Nudix family pyrophosphohydrolases were detected. Genes that potentially affect DNA repair and recombination and stress responses were investigated in detail. Some proteins appear to have been horizontally transferred from eukaryotes and are not present in other bacteria. For example, three proteins homologous to plant desiccation resistance proteins were identified, and these are particularly interesting because of the correlation between desiccation and radiation resistance. Compared to other 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 contribute to the multiple DNA repair-dependent phenotypes of this organism

A novel carotenoid 1,2-hydratase (CruF) from two species of the non-photosynthetic bacterium Deinococcus

“…CrtC-type carotenoid 1,2-hydratases have been found in photosynthetic bacteria (Armstrong et al, 1989;Frigaard et al, 2004;Kovács et al, 2003;Ouchane et al, 1997), primarily involved in the biosynthesis of spirilloxanthin, spheroidene, chlorobactene and its derivatives. However, no homologue of the CrtC-type carotenoid 1,2-hydratase has been detected in the D. radiodurans genome (Makarova et al, 2001;White et al, 1999). We identified the gene candidates of carotenoid 1,2-hydratase, dr0091 and dgeo2309, predicted in the gene neighbourhood of crtO from D. radiodurans R1 and D. geothermalis DSM 11300, respectively.…”

Down-regulation of radioresistance by LexA2 in Deinococcus radiodurans

“…On the basis of this finding we suggested that the co-protease activity rather than the recombination activity of RecA contributed to the extraordinary radiation resistance of D. radiodurans (Satoh et al, 2002). Bioinformatic analysis of the D. radiodurans genome sequence showed that the genome encodes a second, diverged copy of LexA1, LexA2 (DRA0074), which retains the same arrangement of the helix-turn-helix DNA-binding domain and the autocleavage domain (Makarova et al, 2001). Sheng et al (2004) suggested that the product of gene dra0074 is involved in metabolic pathways other than the DNA repair response elicited by irradiation.…”

Deinococcus deserti sp. nov., a gamma-radiation-tolerant bacterium isolated from the Sahara Desert

“…It can survive doses of radiation that do not exist naturally on Earth. Therefore, it is likely that this radiation tolerance is related to the bacterial response to natural non-radioactive DNA-damaging conditions such as desiccation (Makarova et al, 2001). At the time of writing, eight recognized species belong to the genus Deinococcus (Ferreira et al, 1997;Rainey et al, 1997;Suresh et al, 2004).…”