Comparison of the Genomes of Deinococcal Species Using Oligonucleotide Microarrays
![]() |
Jung, Sun-Wook
(Radiation Research Division for Biotechnology, Korea Atomic Energy Research Institute)
Joe, Min-Ho (Radiation Research Division for Biotechnology, Korea Atomic Energy Research Institute) Im, Seong-Hun (Radiation Research Division for Biotechnology, Korea Atomic Energy Research Institute) Kim, Dong-Ho (Radiation Research Division for Biotechnology, Korea Atomic Energy Research Institute) Lim, Sang-Yong (Radiation Research Division for Biotechnology, Korea Atomic Energy Research Institute) |
1 | Narumi, I., K. Satoh, S. Cui, T. Funayama, S. Kitayama, and H. Watanabe. 2004. PprA: A novel protein from Deinococcus radiodurans that stimulates DNA ligation. Mol. Microbiol. 54: 278-285. DOI ScienceOn |
2 | Nishida, H. and I. Narumi. 2002. Disruption analysis of DR1420 and/or DR1758 in the extremely radioresistant bacterium Deinococcus radiodurans. Microbiology 148: 2911-2914. |
3 | Norais, C., S. Chitteni-Pattu, E. A. Wood, R. B. Inman, and M. M. Cox. 2009. DdrB protein, an alternative Deinococcus radiodurans SSB induced by ionizing radiation. J. Biol. Chem. 284: 21402-21411. DOI ScienceOn |
4 | Kitayama, S., Harsojo, and A. Matsuyama. 1980. Sensitization of Micrococcus radiophilus to gamma-rays by postirradiation incubation with chloramphenicol or at nonpermissive temperature. J. Radiat. Res. 21: 257-262. DOI ScienceOn |
5 | Lloyd, R. G. and C. Buckman. 1991. Genetic analysis of the recG locus of Escherichia coli K-12 and of its role in recombination and DNA repair. J. Bacteriol. 173: 1004-1011. |
6 | Makarova, K. S., L. Aravind, M. J. Daly, and E. V. Koonin. 2000. Specific expansion of protein families in the radioresistant bacterium Deinococcus radiodurans. Genetica 108: 25-34. DOI ScienceOn |
7 | Makarova, K. S., L. Aravind, Y. I. Wolf, R. L. Tatusov, K. W. Minton, E. V. Koonin, and M. J. Daly. 2001. Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol. Mol. Biol. Rev. 65: 44-79. DOI ScienceOn |
8 | Kalin, S. and J. Mrazek. 2001. Predicted highly expressed and putative alien genes of Deinococcus radiodurans and implication for resistance to ionizing radiation damage. Proc. Natl. Acad. Sci. USA 98: 5240-5245. DOI ScienceOn |
9 | Gutierrez-Preciado, A., R. A. Jensen, C. Yanofsky, and E. Merino. 2005. New insights into regulation of the tryptophan biosynthetic operon in Gram-positive bacteria. Trends Genet. 21: 432-436. DOI ScienceOn |
10 | Hua, Y., I. Narumi, G. Gao, B. Tain, and K. Satoh. 2003. PprI: A general switch responsible for extreme radioresistance of Deinococcus radiodurans. Biochem. Biophys. Res. Commun. 306: 354-360. DOI ScienceOn |
11 | Fukiya, S., H. Mizoguchi, T. Tobe, and H. Mori. 2004. Extensive genomic diversity in pathogenic Escherichia coli and Shigella strains revealed by comparative genomic hybridization microarray. J. Bacteriol. 186: 3911-3921. DOI ScienceOn |
12 | Bentchkou, E., P. Servant, G. Coste, and S. Sommer. 2010. A major role of the RecFOR pathway in DNA double-strandbreak repair through ESDSA in Deinococcus radiodurans. PLoS Genet. 6: e1000774. DOI ScienceOn |
13 | Goshal, D., M. V. Omelchenko, E. K. Gaidamakova, V. Y. Matrosova, A. Vasilenko, A. Venkateswaran, et al. 2005. How radiation kills cells: Survival of Denicoccus radiodurans and Shewanella oneidensis under oxidative stress. FEMS Microbiol. Rev. 29: 361-375. |
14 | Groot, A. D., R. Dulermo, P. Ortet, L. Blanchard, P. Guerin, B. Fernandez, et al. 2009. Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti. PLoS Genet. 5: e1000434. DOI ScienceOn |
15 |
Fuhrer, T., L. Chen, U. Sauer, and D. Vitkup. 2007. Computational prediction and experimental verification of the gene encoding the |
16 | Cox, M. M. and J. R. Batistta. 2005. Deinococcus radiodurans - the consummate survivor. Nature 6: 882-892. |
17 | Earl, A. M., M. M. Mohundro, I. S. Mian, and J. R. Batistta. 2002. The IrrE protein of Deinococcus radiodurans R1 is a novel regulator of recA expression. J. Bacteriol. 184: 6216-6224. DOI ScienceOn |
18 | Eggington, J. M., N. Haruta, E. A. Wood, and M. M. Cox. 2004. The single-stranded DNA-binding protein of Deinococcus radiodurans. BMC Microbiol. 4: 2. DOI ScienceOn |
19 | Eppinger, M., C. Baar, G. Raddatz, D. H. Huson, and S. Schuster. 2004. Comparative analysis of four Campylobacteriales. Nature 2: 872-885. |
20 | Anderson, A. W., H. C. Nordan, R. F. Cain, G. Parrish, and D. Duggan. 1956. Studies on a radio-resistant Micrococcus. I. Isolation, morphology, cultural characteristics, and resistance to gamma radiation. Food Technol. 10: 575-578. |
21 | Rocha, E. P. C., E. Cornet, and B. Michel. 2005. Comparative and evolutionary analysis of the bacterial homologous recombination system. PLoS Genet. 1: e15. DOI |
22 | Blasius, M., S. Sommer, and U. Hubcher. 2008. Deinococcus radiodurans: What belongs to the survival kit? Crit. Rev. Biochem. Mol. Biol. 43: 221-238. DOI ScienceOn |
23 |
Wu, Y., W. Chen, Y. Zhao, H. Xu, and Y. Hua. 2009. Involvement of RecG in |
24 | Yang, Y. H., S. Dudoit, P. Luu, D. M. Lin, V. Peng, J. Ngal, and T. P. Speed. 2002. Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30: e15. DOI ScienceOn |
25 | Zharadka, K., D. Slade, A. Balione, S. Sommer, D. Averbeck, M. Petranovic, A. B. Lindner, and M. Radman. 2006. Reassembly of shattered chromosomes in Deinococcus radiodurans. Nature 443: 569-573. |
26 | White, O., J. A. Eisen, J. F. Heideberg, E. K. Hickey, J. D. Peterson, R. J. Dodson, et al. 1999. Genome sequence of the radioresistant bacterium Deinococcus radioduran R1. Science 286: 1571-1577. DOI |
27 | Tanaka, M., A. M. Earl, H. A. Howell, M. J. Park, J. A. Eisen, S. N. Peterson, and J. R. Battista. 2004. Analysis of Deinococcus radiodurans's transcriptional response to ionizing radiation and desiccation reveals novel protein that contributes to extreme radioresistance. Genetics 168: 21-33. DOI ScienceOn |
28 | Udupa, K. S., P. A. O'Cain, V. Mattimore, and J. R. Battista. 1994. Novel ionizing radiation-sensitive mutants of Deinococcus radiodurans. J. Bacteriol. 24: 7439-7446. |
29 | Venkateswaren, A., S. C. Mcfarlan, D. Ghosal, K. W. Minton, A. Vasilenko, K. S. Makarova, L. P. Wackett, and M. J. Daly. 2000. Physiologic determinants of radation resistance in Deinococcus radiodurans. Appl. Environ. Microbiol. 66: 2620-2626. DOI ScienceOn |
30 | Rodin, S., A. F. Andersson, V. Wirta, L. Ericsson, M. Ljungstrom, B. Bjorkholm, H. Lindmark, and L. Engstrand. 2008. Performance of a 70-mer oligonucleotide microarray for genotyping of Campylobacter jejuni. BMC Microbiol. 8: 73. DOI ScienceOn |
31 | Slade, D., A. B. Lindner, G. Paul, and M. Radman. 2009. Recombination and replication in DNA repair of heavily irradiated Deinococcus radiodurans. Cell 136: 1044-1055. DOI ScienceOn |
32 | Makarova, K. S., M. V. Omenchenko, E. K. Gaidamakova, V. Y. Matrosova, A. Vasilenko, M. et al. 2007. Deinococcus geothermalis: The pool of extreme radiation resistance genes shrinks. PLoS ONE 9: e955. |
33 |
Prell, J., A. Bourdes, R. Karunakaran, M. Lopez-Gomez, and P. Poole. 2009. Pathway of |
34 | Omelchenko, M. V., Y. I. Wolf, E. Gaidamakova, V. T. MAtrosova, A. Vasilenko, M. Zhai, M. J. Daly, E. V. Koonin, and K. S. Makarova. 2005. Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: Divergent routes of adaptation to thermophily and radiation resistance. BMC Evol. Biol. 5: 57. DOI ScienceOn |
35 | Parker, C. T., B. Quinones, W. G. Miller, S. T. Horn, and R. E. Mandrell. 2006. Comparative genome analysis of Campylobacter jejuni strains reveals diversity due to genomic elements similar to those present in C. jejuni strain RM1221. J. Clin. Microbiol. 44: 4125-4135. DOI ScienceOn |
![]() |