**1. Introduction**

44 DNA Repair

Tell,G., Wilson,D.M., III, & Lee,C.H. (2010) Intrusion of a DNA repair protein in the RNome

Tyndall,C., Meister,J., & Bickle,T.A. (1994) The Escherichia coli prr region encodes a

van den,B.E., Omelchenko,M.V., Bekkelund,A., Leihne,V., Koonin,E.V., Dolja,V.V., &

van Noort,J., van der Heijden,T., Dutta,C.F., Firman,K., & Dekker,C. (2004) Initiation of

van,N.J., van Der,H.T., de,J.M., Wyman,C., Kanaar,R., & Dekker,C. (2003) The coiled-coil of

Weinfeld,M., Mani,R.S., Abdou,I., Aceytuno,R.D., & Glover,J.N. (2011) Tidying up loose

Wheeler,L.J., Ray,N.B., Ungermann,C., Hendricks,S.P., Bernard,M.A., Hanson,E.S., &

White,M.A., Eykelenboom,J.K., Lopez-Vernaza,M.A., Wilson,E., & Leach,D.R. (2008) Non-

Williams,G.J., Lees-Miller,S.P., & Tainer,J.A. (2010) Mre11-Rad50-Nbs1 conformations and

Williams,G.J., Williams,R.S., Williams,J.S., Moncalian,G., Arvai,A.S., Limbo,O., Guenther,G.,

Williams,R.S., Williams,J.S., & Tainer,J.A. (2007) Mre11-Rad50-Nbs1 is a keystone complex

Wool,I.G., Gluck,A., & Endo,Y. (1992) Ribotoxin recognition of ribosomal RNA and a proposal for the mechanism of translocation. *Trends Biochem.Sci.*, 17, 266-269. Yamagami,H. & Endo,H. (1969) Loss of lysis inhibition in filamentous Escherichia coli infected with wild-type bacteriophage T4. *Journal of Virology*, 3, 343-349. Youell,J. & Firman,K. (2008) EcoR124I: from plasmid-encoded restriction-modification system to nanodevice. *Microbiology and Molecular Biology Reviews*, 72, 365-77, table. Zhang,Y., Zhang,J., Hara,H., Kato,I., & Inouye,M. (2005) Insights into the mRNA cleavage mechanism by MazF, an mRNA interferase. *J Biol.Chem.*, 280, 3143-3150.

alleviation in Escherichia coli K12: an SOS function not repressed by lexA.

functional type IC DNA restriction system closely integrated with an anticodon

Falnes,P.O. (2008) Viral AlkB proteins repair RNA damage by oxidative

translocation by Type I restriction-modification enzymes is associated with a short

the human Rad50 DNA repair protein contains specific segments of increased

ends: the role of polynucleotide kinase/phosphatase in DNA strand break repair.

Mathews,C.K. (1996) T4 phage gene 32 protein as a candidate organizing factor for the deoxyribonucleoside triphosphate synthetase complex. *Journal of Biological* 

random segregation of sister chromosomes in Escherichia coli. *Nature*, 455, 1248-1250.

the control of sensing, signaling, and effector responses at DNA double-strand

Sildas,S., Hammel,M., Russell,P., & Tainer,J.A. (2011) ABC ATPase signature helices in Rad50 link nucleotide state to Mre11 interface for DNA repair.

connecting DNA repair machinery, double-strand break signaling, and the

world: is this the beginning of a new era? *Mol.Cell Biol.*, 30, 366-371. Thompson,D.M. & Parker,R. (2009) Stressing out over tRNA cleavage. *Cell*, 138, 215-219. Thoms,B. & Wackernagel,W. (1984) Genetic control of damage-inducible restriction

nuclease gene. *Journal of Molecular Biology*, 237, 266-274.

demethylation. *Nucleic Acids Res.*, 36, 5451-5461.

DNA extrusion. *Nucleic Acids Res.*, 32, 6540-6547.

flexibility. *Proc.Natl.Acad.Sci.U.S.A*, 100, 7581-7586.

*Mol.Gen.Genet.*, 197, 297-303.

*Trends Biochem.Sci.* 

*Chemistry*, 271, 11156-11162.

breaks. *DNA Repair (Amst)*, 9, 1299-1306.

chromatin template. *Biochem.Cell Biol.*, 85, 509-520.

*Nat.Struct.Mol.Biol.*, 18, 423-431.

Nucleotide excision repair (NER) represents a central cellular process for the removal of structurally and chemically diverse DNA lesions [Friedberg et al., 2006]. Mutations in genes involved in NER are associated with rare autosomal recessive syndromes such as xeroderma pigmentosum (XP), a condition characterized by sensitivity to UV light, neurological abnormalities, and a propensity to develop skin cancer (Cleaver, 2005). The observation that cells from XP subgroup E (XP-E cells XP2RO and XP3RO) are defective in recognizing damaged DNA and performing NER highlighted the physiological importance of the protein termed DNA damage-binding protein, or DDB [Chu & Chang, 1988]. The DDB protein, sometimes also referred to as UV-DDB due to its high affinity and specificity for UV-damaged DNA, contains two principal subunits, DDB1 and DDB2 [Grossman, 1976; Keeney et al., 1993; Takao et al., 1993]. The DDB protein complex also binds to non-UVdamaged DNA, like cisplatin-modified DNA, although with much lower affinity. Although the history of DDB spans more than two decades, the complete understanding of its physiological functions remains to be clarified. The activity of DDB has been repeatedly described in crude mammalian cell extracts by electrophoretic mobility shift assays or filterbinding assays performed by different laboratories since the first report of its discovery [Feldberg & Grossman, 1976]. Notably, micro-injections of DDB complexes into the nucleus of XP-E cells restored NER activity [Keeney et al., 1994], supporting the notion that DDB participates in chromatin NER. The *DDB1* gene from simian cells was the first *DDB* gene to be identified [Takao et al., 1993]. The human *DDB1* and *DDB2* genes were subsequently sequenced [Dualan et al., 1995; Lee et al., 1995]. Soon after, DNA sequencing from Linn's laboratory revealed that *DDB2* is mutated in XP-E cells which lack DDB activity [Nichols et al., 1996; Tang & Chu, 2002]. The predicted DDB2 protein sequence was shown to contain several functional domains, including WD40 repeats, post-translation modification sites (e.g. acetylation, phosphorylation, and ubiquitination), DDB1- and DNA-binding sites, as well as a DWD box. Notably, in a majority of XP-E cell lines, DDB2 was found to be altered at domains other than the one required for binding DNA. Thus, DDB appears to be regulated at several levels in UV-irradiated cells, including by transcriptional activation of DDB2 mRNA, post-translational modification, translocation to the nucleus, complex formation,

The Role of DDB2 in Regulating Cell Survival

and Apoptosis Following DNA Damage - A Mini-Review 47

Fig. 1. Overall structure of the DDB1-DDB2-DNA complex. Ribbon representation of the DDB-DNA6-4PP complex: DDB2; DDB1-BPA; DDB1-BPB; DDB1-BPC; DDB1-CTD. The DNA6- 4PP damaged and undamaged DNA strands are depicted in black and gray, respectively. DNA binding is carried out exclusively by the DDB2 subunit via its WD40 domain. The DDB1 structure consists of three WD40 β-propeller domains (BPA, BPB, and BPC) and a Cterminal helical domain (CTD, shown at the center). DDB2 binds to an interface between the DDB1 propellers BPA and BPC, where its helix-loop-helix motif inserts into a cavity formed by the two propellers. The structures reveal the molecular mechanism underlying highaffinity recognition of UV lesions (damaged DNA strand) that are refractory to detection by XPC. The structures also suggest a mechanism for the assembly of the DDB-CUL4 ubiquitin ligase in chromatin and provide a framework for understanding the ubiquitination of

three founding cullins that are conserved from yeast to humans. A large number of E3 ubiquitin-protein ligase complexes are part of the DCX proteins (short for DDB1-CUL4-Xbox). Components of the CUL4-DDB-ROC1 (also known as CUL4-DDB-RBX1) include CUL4A or CUL4B, DDB1, DDB2, and RBX1 (Chen et al., 2001; Groisman et al., 2003). Other CUL4-DDB-ROC1 complexes may also exist in which DDB2 is replaced by a subunit that targets an alternative substrate. These targeting subunits are generally known as DCAF proteins (short for DDB1- and CUL4-associated factor) or CDW (short for CUL4-DDB1 associated WD40-repeat; for reviews, see Lee & Zhou, 2007; Jackson & Xiong, 2009; Sugasawa, 2009). Many CUL4 complexes are involved in chromatin regulation and are frequently hijacked by viruses (reviewed by Jackson & Xiong, 2009). The DDB1-CUL4-ROC1 complex may ubiquitinate histones H2A, H3, and H4 at sites of UV-induced DNA damage (Wang et al., 2006; Kapetanaki et al., 2006; Guerrero-Santoro et al., 2008). The ubiquitination of histones may facilitate their removal from the nucleosome and promote assembly of NER components for subsequent DNA repair. Furthermore, the DDB1-CUL4-ROC1 complex

proteins proximal to damage sites. [For detail, see Scrima et al., 2008].

and proteolytic degradation of DDB2 protein through ubiquitination [for a recent review, see Sugasawa, 2010]. Notably, 60% of chromatin-bound DDB2 is degraded within 4 hrs of UV irradiation. After 48 hrs, DDB2 mRNA levels increase several fold above the level seen in non-irradiated cells [Nichols et al., 2000; Rapic-Otrin et al., 2002]. Interestingly, the majority of UV-induced DNA photoproducts in human cells are repaired by this time [Mitchell et al., 1985].
