Area of Interest

The primary goal of our research is to define the subset of proteins that mediate the ionizing radiation resistance of Deinococcus radiodurans R1. D. radiodurans, a non-sporeforming bacterium, has extraordinary tolerance for ionizing radiation. Exponential phase cultures of D. radiodurans R1 survive 500,000 Rad (5000 Gray) of γ radiation without loss of viability or evidence of mutation. In terms of DNA damage, 5000 Gy γ radiation introduces approximately 200 DNA double strand breaks, over 3000 single strand breaks, and greater than 1000 sites of base damage per genome. This organism does not passively protect its genome from the incident radiation. Instead all available evidence argues that D. radiodurans efficiently and accurately repairs DNA damage.

The D. radiodurans genome has been sequenced in its entirety, and encodes essentially the entire ensemble of DNA repair proteins found in E. coli. With the exception of alkylation transfer and photoreactivation, all of the major prokaryotic DNA repair pathways are represented. This observation is significant, not because it says anything about why D. radiodurans is radioresistant, but because it confirms something long suspected; D. radiodurans possesses unique mechanisms for dealing with ionizing radiation-induced DNA damage. Clearly, the collection of repair proteins identified in D. radiodurans, in and of itself, is not sufficient to confer radioresistance. If it were, E. coli would be as radioresistant. D. radiodurans must encode novel DNA repair proteins or, alternatively, it must use the DNA repair proteins it encodes much more efficiently than more radiosensitive prokaryotes. Either possibility suggests that there are unprecedented mechanisms facilitating this species recovery following exposure to ionizing radiation.

Of the 3187 open reading frames identified in D. radiodurans R1, only 1493 could be assigned a function based on similarity to other gene products found in the protein databases. Of the 1694 proteins of unknown function, 1002 are, at present, unique to D. radiodurans, showing no database match. The secret to understanding the radioresistance of D. radiodurans is presumably found among these proteins of unknown function. The challenge lies in unequivocally determining what proteins are responsible for radioresistance.

Currently, a combination of two approaches (random mutagenesis and DNA microarray-based analysis) is being employed to allow identification of gene products potentially involved in ionizing radiation resistance. Once identified, these gene products are characterized to establish how these proteins contribute to ionizing radiation resistance. In the long term, it is expected that this work will: a) enhance our understanding of D. radiodurans, and b) define novel protein families involved in DNA damage tolerance.

 

Selected Publications

Cox, M. M. and Battista, J. R. 2005. Deinococcus radiodurans — the consummate survivor, Nature Rev. Microbiol., 3:882-892

Zimmerman J.M., and Battista J.R., 2005 A ring-like nucleoid is not necessary for radioresistance in the Deinococcaceae. BMC Microbiol. 5:17

Schmid A.K., Howell H.A., Battista J.R., Peterson S.N., and Lidstrom M.E., 2005. Global Transcriptional and Proteomic Analysis of the Sig1 Heat Shock Regulon of Deinococcus radiodurans. J Bacteriol. 187:3339-3351.

Tanaka, M., Earl, A.M., Howell, H. A., Park, M-J., Eisen, J. A., Peterson, S. N., and Battista, J. R., 2004. Analysis of Deinococcus radiodurans' transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance. Genetics, 168: 21-33

Harris, D. R., Tanaka, M., Saveliev, S. V., Jolivet, Earl, A. M., Cox, M. M., and Battista, J. R., 2004. Preserving Genome Integrity: the DdrA protein of Deinococcus radiodurans R1, PLOS Biology, 2: 1629-1640 (e304)

Kim, M., Wolff, E., Huang, T., Garibyan, L., Earl, A. M., Battista, J. R., and Miller, J. H., 2004. Developing a genetic system in Deinococcus radiodurans for analyzing mutations. Genetics, 166:661-668