**2. Acknowledgements**

This work was performed under the auspices of the Tunisian National Center for Nuclear Sciences and Technology (CNSTN). Special thanks to Dr. Issay Narumi from Japan Atomic Energy Agency (JAEA) for previous discussions that improved an initial draft.

### **3. References**


Archaea (*e.g. Pyrococcus*, *Thermococcus*). A recent *in vitro* investigation (Beblo et al., 2011) led to a definitive refutation of the "desiccation adaptation hypothesis" (Mattimore and Battista, 1996) and to an implicit vindication of the "radiation adaptation hypothesis" (Sghaier et al., 2007). In brief, it was demonstrated that desiccation-tolerant as well as desiccation-intolerant (hyper-) thermophilic archaea survived comparably high doses of IR (Beblo et al., 2011). In so far as other mechanisms of IR resistance are concerned, it is not surprising that the *Deinococcus* lineage does not share with *Pyrococcus* its five transcripts (DR0423, *ddrA*; DR0070, *ddrB*; DR0003, *ddrC*; DR0326, *ddrD*; DRA0346, *pprA*), most likely evolving in response to IR and desiccation (Tanaka et al., 2004). This network of five transcripts is *Deinococcus* lineage-specific. Similarly, a putative DNA-repair gene cluster of five conserved hypothetical genes in *P. furiosus* (PF0639, PF0640, PF0641, PF0642, PF0643), specifically induced by exposure to IR and probably involved in translesion synthesis, seems to be unique to thermophilic archaea and bacteria (Williams et al., 2007). Does this mean that this putative cluster is important for thermophily? The answer is probably no. One could highlight the fact that the mechanism that protects the DNA against thermal degradation does not prevent the formation of DNA breaks during irradiation (Gerard et al., 2001). A corollary to all these analyses is the notion that there is a multiplicity of evolutionary and functional processes associated with IR resistance (Omelchenko et al., 2005; Makarova et al., 2007; Sghaier et al., 2007; Daly, 2010; Makarova and Daly, 2011; Slade and Radman, 2011). However, this integrative appraisal does not exclude the possibility of common processes among IRRP. Future analyses might consider more experimental and genomic data from a variety of IRRP in order to determine whether they possess a set of genes that would refute

either the concept of convergent evolution or the idea of a common ancestor.

Energy Agency (JAEA) for previous discussions that improved an initial draft.

This work was performed under the auspices of the Tunisian National Center for Nuclear Sciences and Technology (CNSTN). Special thanks to Dr. Issay Narumi from Japan Atomic

Albuquerque, L., Simoes, C., Nobre, M.F., Pino, N.M., Battista, J.R., Silva, M.T. et al. (2005)

prokaryotic double-strand break repair system. *Genome Res* 11: 1365-1374. Bagwell, C.E., Bhat, S., Hawkins, G.M., Smith, B.W., Biswas, T., Hoover, T.R. et al. (2008)

Battista, J.R., Park, M.J., and McLemore, A.E. (2001) Inactivation of two homologues of

Battista, J.R., Cox, M.M., Daly, M.J., Narumi, I., Radman, M., and Sommer, S. (2003) The structure of *D. radiodurans*. *Science* 302: 567-568; author reply 567-568.

*Deinococcus radiodurans* R1 to desiccation. *Cryobiology* 43: 133-139.

proposal of *Trueperaceae* fam. nov. *FEMS Microbiol Lett* 247: 161-169. Aravind, L., and Koonin, E.V. (2001) Prokaryotic homologs of the eukaryotic DNA-end-

*Truepera radiovictrix* gen. nov., sp. nov., a new radiation resistant species and the

binding protein Ku, novel domains in the Ku protein and prediction of a

Survival in nuclear waste, extreme resistance, and potential applications gleaned from the genome sequence of *Kineococcus radiotolerans* SRS30216. *PLoS One* 3: e3878.

proteins presumed to be involved in the desiccation tolerance of plants sensitizes

**2. Acknowledgements** 

**3. References** 


DNA Repair: Lessons from the Evolution of

851.

219-227.

99: 7917-7921.

Guinea. *Appl Environ Microbiol* 69: 644-648.

bacteria into eukaryota. *Mol Biol Evol* 20: 1098-1112.

common ancestor. *Nat Rev Microbiol* 1: 127-136.

and gamma irradiation. *Extremophiles* 9: 219-227.

radioresistance? *Science* 299: 254-256.

*Res* 34: D332-334.

*Res* 38: D346-354.

Ionizing-Radiation-Resistant Prokaryotes – Fact and Theory 153

Jain, R., Rivera, M.C., and Lake, J.A. (1999) Horizontal gene transfer among genomes: the

Jolivet, E., L'Haridon, S., Corre, E., Forterre, P., and Prieur, D. (2003a) *Thermococcus* 

Jolivet, E., Corre, E., L'Haridon, S., Forterre, P., and Prieur, D. (2004) *Thermococcus marinus*

Jolivet, E., Matsunaga, F., Ishino, Y., Forterre, P., Prieur, D., and Myllykallio, H. (2003b)

thermophilic archaebacterium, *Pyrococcus horikoshii* OT3. *DNA Res* 5: 55-76. Kim, J.I., and Cox, M.M. (2002) The RecA proteins of *Deinococcus radiodurans* and *Escherichia* 

Kimura, H., Asada, R., Masta, A., and Naganuma, T. (2003) Distribution of microorganisms

Klotz, M.G., and Loewen, P.C. (2003) The molecular evolution of catalatic hydroperoxidases:

Koonin, E.V. (2003) Comparative genomics, minimal gene-sets and the last universal

Kopylov, V.M., Bonch-Osmolovskaya, E.A., Svetlichnyi, V.A., Miroshnicheko, M.L., and

Levin-Zaidman, S., Englander, J., Shimoni, E., Sharma, A.K., Minton, K.W., and Minsky, A.

Liolios, K., Tavernarakis, N., Hugenholtz, P., and Kyrpides, N.C. (2006) The Genomes On

Liolios, K., Chen, I.M., Mavromatis, K., Tavernarakis, N., Hugenholtz, P., Markowitz, V.M.,

thermophilic archaebacteria and eubacteria. *Mikrobiologiya* 62: 90-95. Kottemann, M., Kish, A., Iloanusi, C., Bjork, S., and DiRuggiero, J. (2005) Physiological

DNA damage caused by ionizing radiation. *J Bacteriol* 185: 3958-3961. Kawarabayasi, Y., Sawada, M., Horikawa, H., Haikawa, Y., Hino, Y., Yamamoto, S. et al.

*gammatolerans* sp. nov., a hyperthermophilic archaeon from a deep-sea hydrothermal vent that resists ionizing radiation. *Int J Syst Evol Microbiol* 53: 847-

sp. nov. and *Thermococcus radiotolerans* sp. nov., two hyperthermophilic archaea from deep-sea hydrothermal vents that resist ionizing radiation. *Extremophiles* 8:

Physiological responses of the hyperthermophilic archaeon "*Pyrococcus abyssi*" to

(1998) Complete sequence and gene organization of the genome of a hyper-

*coli* promote DNA strand exchange via inverse pathways. *Proc Natl Acad Sci U S A*

in the subsurface of the manus basin hydrothermal vent field in Papua New

evidence for multiple lateral transfer of genes between prokaryota and from

Skobin, V.S. (1993) Gamma-irradiation resistance and UV sensitivity of extremely

responses of the halophilic archaeon *Halobacterium* sp. strain NRC1 to desiccation

(2003) Ringlike structure of the *Deinococcus radiodurans* genome: a key to

Line Database (GOLD) v.2: a monitor of genome projects worldwide. *Nucleic Acids* 

and Kyrpides, N.C. (2010) The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. *Nucleic Acids* 

complexity hypothesis. *Proc Natl Acad Sci U S A* 96: 3801-3806.


Daly, M.J., Gaidamakova, E.K., Matrosova, V.Y., Vasilenko, A., Zhai, M., Leapman, R.D. et

Daly, M.J., Gaidamakova, E.K., Matrosova, V.Y., Vasilenko, A., Zhai, M., Venkateswaran, A.

de Groot, A., Chapon, V., Servant, P., Christen, R., Saux, M.F., Sommer, S., and Heulin, T.

de Groot, A., Dulermo, R., Ortet, P., Blanchard, L., Guerin, P., Fernandez, B. et al. (2009)

Dean, C.J., Feldschreiber, P., and Lett, J.T. (1966) Repair of x-ray damage to the

DiRuggiero, J., Brown, J.R., Bogert, A.P., and Robb, F.T. (1999) DNA repair systems in

DiRuggiero, J., Santangelo, N., Nackerdien, Z., Ravel, J., and Robb, F.T. (1997) Repair of

hyperthermophilic archaeon *Pyrococcus furiosus*. *J Bacteriol* 179: 4643-4645. Earl, A.M., Mohundro, M.M., Mian, I.S., and Battista, J.R. (2002) The IrrE protein of

Ferreira, A.C., Nobre, M.F., Moore, E., Rainey, F.A., Battista, J.R., and da Costa, M.S. (1999)

Gutman, P.D., Fuchs, P., and Minton, K.W. (1994) Restoration of the DNA damage

Harris, D.R., Pollock, S.V., Wood, E.A., Goiffon, R.J., Klingele, A.J., Cabot, E.L. et al. (2009)

Hua, Y., Narumi, I., Gao, G., Tian, B., Satoh, K., Kitayama, S., and Shen, B. (2003) PprI: a

Ito, H., and Iizuka, H. (1971) Taxonomic studies on a radio-resistant *Pseudomonas*. Part XII. Studies on the microorganisms of cereal grain. *Agric Biol Chem* 35: 1566-1571. Ivanova, N., Rohde, C., Munk, C., Nolan, M., Lucas, S., Del Rio, T.G. et al. (2011) Complete

Galhardo, R.S., and Rosenberg, S.M. (2009) Extreme genome repair. *Cell* 136: 998-1000. Gerard, E., Jolivet, E., Prieur, D., and Forterre, P. (2001) DNA protection mechanisms are not

DNA polymerase I and Klenow fragment. *Mutat Res* 314: 87-97.

deoxyribonucleic acid in *Micrococcus radiodurans*. *Nature* 209: 49-52.

from the Sahara Desert. *Int J Syst Evol Microbiol* 55: 2441-2446.

bacterium *Deinococcus deserti*. *PLoS Genet* 5: e1000434.

and *Rubrobacter xylanophilus*. *Extremophiles* 3: 235-238.

and *P. furiosus*. *Mol Genet Genomics* 266: 72-78.

*Biochem Biophys Res Commun* 306: 354-360.

radioresistance. *PLoS Biol* 5: e92.

484.

6216-6224.

5240-5252.

91-99.

radiation resistance. *Science* 306: 1025-1028.

al. (2007) Protein oxidation implicated as the primary determinant of bacterial

et al. (2004) Accumulation of Mn(II) in *Deinococcus radiodurans* facilitates gamma-

(2005) *Deinococcus deserti* sp. nov., a gamma-radiation-tolerant bacterium isolated

Alliance of proteomics and genomics to unravel the specificities of Sahara

archaea: mementos from the last universal common ancestor? *J Mol Evol* 49: 474-

extensive ionizing-radiation DNA damage at 95 degrees C in the

*Deinococcus radiodurans* R1 is a novel regulator of *recA* expression. *J Bacteriol* 184:

Characterization and radiation resistance of new isolates of *Rubrobacter radiotolerans*

involved in the radioresistance of the hyperthermophilic archaea *Pyrococcus abyssi*

resistance of *Deinococcus radiodurans* DNA polymerase mutants by *Escherichia coli*

Directed evolution of ionizing radiation resistance in *Escherichia coli*. *J Bacteriol* 191:

general switch responsible for extreme radioresistance of *Deinococcus radiodurans*.

genome sequence of *Truepera radiovictrix* type strain (RQ-24). *Stand Genomic Sci* 4:


DNA Repair: Lessons from the Evolution of

172.

*Acids Res* 39: D38-51.

*Genomics* 9: 297.

*Research* 4: 111-118.

*Microbiol Mol Biol Rev* 75: 133-191.

radioresistance. *Genetics* 168: 21-33.

molecules. *Nat Rev Genet* 5: 366-375.

Ionizing-Radiation-Resistant Prokaryotes – Fact and Theory 155

Ouzounis, C.A., Kunin, V., Darzentas, N., and Goldovsky, L. (2006) A minimal estimate for

Pfeiffer, F., Schuster, S.C., Broicher, A., Falb, M., Palm, P., Rodewald, K. et al. (2008)

Phillips, R.W., Wiegel, J., Berry, C.J., Fliermans, C., Peacock, A.D., White, D.C., and

Polyanichko, A.M., Andrushchenko, V.V., Chikhirzhina, E.V., Vorob'ev, V.I., and Wieser, H.

Pukall R, Zeytun A, Lucas S, Lapidus A, Hammon N, Deshpande S, Nolan M, Cheng JF,

Repar, J., Cvjetan, S., Slade, D., Radman, M., Zahradka, D., and Zahradka, K. (2010) RecA

Sayers, E.W., Barrett, T., Benson, D.A., Bolton, E., Bryant, S.H., Canese, K. et al. (2011)

Sghaier, H., Ghedira, K., Benkahla, A., and Barkallah, I. (2008) Basal DNA repair machinery

Sghaier, H., Satoh, K., Ohba, H., and Narumi, I. (2010) Assessing the role of RecA protein in

Sghaier, H., Narumi, I., Satoh, K., Ohba, H., and Mitomo, H. (2007) Problems with the current deinococcal hypothesis: an alternative theory. *Theory Biosci* 126: 43-45. Slade, D., and Radman, M. (2011) Oxidative stress resistance in *Deinococcus radiodurans*.

Slade, D., Lindner, A.B., Paul, G., and Radman, M. (2009) Recombination and replication in DNA repair of heavily irradiated *Deinococcus radiodurans*. *Cell* 136: 1044-1055. Tanaka, M., Earl, A.M., Howell, H.A., Park, M.J., Eisen, J.A., Peterson, S.N., and Battista, J.R.

Thornton, J.W. (2004) Resurrecting ancient genes: experimental analysis of extinct

terrestrial perspective. *Res Microbiol* 157: 57-68.

compared to that of strain NRC-1. *Genomics* 91: 335-346.

positive bacterium. *Int J Syst Evol Microbiol* 52: 933-938.

circular dichroism studies. *Nucleic Acids Res* 32: 989-996.

*radiodurans*. *DNA Repair (Amst)* 9: 1151-1161.

the gene content of the last universal common ancestor--exobiology from a

Evolution in the laboratory: the genome of *Halobacterium salinarum* strain R1

Shimkets, L.J. (2002) *Kineococcus radiotolerans* sp. nov., a radiation-resistant, gram-

(2004) The effect of manganese(II) on DNA structure: electronic and vibrational

Pitluck S, Liolios K, Pagani I, Mikhailova N, Ivanova N, Mavromatis K, Pati A, Tapia R, Han C, Goodwin L, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Brambilla EM, Rohde M, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. (2011) Complete genome sequence of *Deinococcus maricopensis* type strain (LB-34). *Stand Genomic Sci* 4(2):163-

protein assures fidelity of DNA repair and genome stability in *Deinococcus* 

Database resources of the National Center for Biotechnology Information. *Nucleic* 

is subject to positive selection in ionizing-radiation-resistant bacteria. *BMC* 

the radioresistant bacterium *Deinococcus geothermalis*. *African Journal of Biochemistry* 

(2004) Analysis of *Deinococcus radiodurans*'s transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme


Lu, H., Gao, G., Xu, G., Fan, L., Yin, L., Shen, B., and Hua, Y. (2009) *Deinococcus radiodurans*

Maeder, D.L., Weiss, R.B., Dunn, D.M., Cherry, J.L., Gonzalez, J.M., DiRuggiero, J., and

Makarova, K.S., and Daly, M.J. (2011) Comparative Genomics of Stress Response Systems in

Makarova, K.S., Omelchenko, M.V., Gaidamakova, E.K., Matrosova, V.Y., Vasilenko, A.,

Markillie, L.M., Varnum, S.M., Hradecky, P., and Wong, K.K. (1999) Targeted mutagenesis

Mattimore, V., and Battista, J.R. (1996) Radioresistance of *Deinococcus radiodurans*: functions

Moseley, B.E., and Copland, H.J. (1975) Isolation and properties of a recombination-deficient

Moseley, B.E., and Copland, H.J. (1976) The rate of recombination repair and its relationship

Moseley, B.E.B. (1983) Photobiology and radiobiology of *Micrococcus* (*Deinococcus*)

Narumi, I., Satoh, K., Cui, S., Funayama, T., Kitayama, S., and Watanabe, H. (2004) PprA: a

Ng, W.V., Berquist, B.R., Coker, J.A., Capes, M., Wu, T.H., DasSarma, P., and DasSarma, S.

Ng, W.V., Kennedy, S.P., Mahairas, G.G., Berquist, B., Pan, M., Shukla, H.D. et al. (2000)

Nishimura, Y., Uchida, K., Tanaka, K., Ino, T., and Ito, H. (1994) Radiation sensitivities of *Acinetobacter* strains isolated from clinical sources. *J Basic Microbiol* 34: 357-360. Omelchenko, M.V., Wolf, Y.I., Gaidamakova, E.K., Matrosova, V.Y., Vasilenko, A., Zhai, M.

mutant of *Micrococcus radiodurans*. *J Bacteriol* 121: 422-428.

*radiodurans*. *Photochem Photobiol Rev* 7: 223-274.

radiation damage. *Mol Cell Proteomics* 8: 481-494.

Washington, DC: ASM Press, pp. 445-457.

resistance genes shrinks. *PLoS One* 2: e955.

desiccation. *J Bacteriol* 178: 633-637.

*Bacteriol* 181: 666-669.

*Microbiol* 93: 251-258.

*Microbiol* 54: 278-285.

reply 553-544.

12176-12181.

*BMC Evol Biol* 5: 57.

1305.

PprI switches on DNA damage response and cellular survival networks after

Robb, F.T. (1999) Divergence of the hyperthermophilic archaea *Pyrococcus furiosus* and *P. horikoshii* inferred from complete genomic sequences. *Genetics* 152: 1299-

*Deinococcus* Bacteria. In *Bacterial Stress Responses*. Storz, G., and Hengge, R. (eds).

Zhai, M. et al. (2007) *Deinococcus geothermalis*: the pool of extreme radiation

by duplication insertion in the radioresistant bacterium *Deinococcus radiodurans*: radiation sensitivities of catalase (*katA*) and superoxide dismutase (*sodA*) mutants. *J* 

necessary to survive ionizing radiation are also necessary to survive prolonged

to the radiation-induced delay in DNA synthesis in *Micrococcus radiodurans*. *J Gen* 

novel protein from *Deinococcus radiodurans* that stimulates DNA ligation. *Mol* 

(2008) Genome sequences of *Halobacterium* species. *Genomics* 91: 548-552; author

Genome sequence of *Halobacterium* species NRC-1. *Proc Natl Acad Sci U S A* 97:

et al. (2005) Comparative genomics of *Thermus thermophilus* and *Deinococcus radiodurans*: divergent routes of adaptation to thermophily and radiation resistance.


**8** 

*Japan* 

**Involvement of Non-Homologous** 

**End-Joining in Radiation-Induced** 

Keiji Suzuki, Motohiro Yamauchi, Masatoshi Suzuki,

*Nagasaki University Graduate School of Biomedical Sciences,* 

*Atomic Bomb Disease Institute, Department of Radiation Medical Sciences,* 

DNA double-strand breaks are the most detrimental form of DNA damage induced by either endogenous and exogenous sources. DNA double-strand breaks are generated in response to ionizing radiation, radiomimic drugs, and topoisomerase inhibitors. They also created during V(D)J and class switch recombination in lymphocytes, meiotic recombination in germ cells, and by retroviral integrations (Downs et al., 2007, Polo and Jackson, 2011). Since DNA double-strand breaks discontinue chromosome structure, they may result in cell death that are associated with radiosensitivity, immunodeficiency, neurodegeneration, and developmental defects (Jackson and Bartek, 2009, Mahaney et al., 2009, O'Driscoll and Jeggo, 2006, Weterings and Chen, 2007, Wyman and Kanaar, 2006). Thus, cells have evolved sophisticated mechanisms, by which DNA double-strand breaks are repaired. Two major pathways to repair DNA double-strand breaks are non-homologous end-joining and homologous and homologous recombination (Hartlerode and Scully, 2009, Mahaney et al., 2009, Weterings and Chen, 2007, Wyman and Kanaar, 2006). While rejoining of DNA breaks are indispensable for the survival of cells, DNA repair, by itself, may threaten the stability of the genome. (Burma et al., 2006, Pastink et al., 2001, Sonoda et al., 2006, van Gent et al., 2001). In particular, non-homologous end-joining, which is the primary DNA repair pathway functions in G1 phase, is error-prone (Hartlerode and Scully, 2009, Lieber, 2010). It causes loss or rearrangement of the genetic information through mis-rejoining of DNA double strand breaks. Processing of DNA broken ends by exonucleases and endonucleases also provide another chance to alter DNA sequences. Consequently, surviving cells can avoid lethal effects of DNA double-strand breaks but it results in a loss of heterozygosity as well as gross genome rearrangements that are associated with cancer predisposition. Although most genome rearrangements have been thought to be generated directly by the initial radiation exposure (Leonhardt et al., 1999), recent findings have demonstrated that the integrity of the genome is also endangered eventually, if the cells were survived exposure to DNA damaging agents. In this chapter, the results showing that delayed DNA double-strand breaks are induced several generations after the initial insult in the progenies of surviving cells are presented, and a role of non-homologous end-joining on delayed

**1. Introduction** 

**Genomic Instability** 

Yasuyoshi Oka and Shunichi Yamashita

