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Cr2007108.Pdf npg Michael R Lieber et al. Cell Research (2008) 18:125-133. npg125 © 2008 IBCB, SIBS, CAS All rights reserved 1001-0602/08 $ 30.00 REVIEW www.nature.com/cr Flexibility in the order of action and in the enzymology of the nuclease, polymerases, and ligase of vertebrate non- homologous DNA end joining: relevance to cancer, aging, and the immune system Michael R Lieber1, Haihui Lu1, Jiafeng Gu1, Klaus Schwarz2 1USC Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Rm 5428, Los Angeles, CA 90089-9176, USA; 2Institute for Clinical Transfusion Medicine & Immunogenetics, Institute for Transfusion Medicine, Univer- sity Hospital, Ulm, Germany Nonhomologous DNA end joining (NHEJ) is the primary pathway for repair of double-strand DNA breaks in hu- man cells and in multicellular eukaryotes. The causes of double-strand breaks often fragment the DNA at the site of damage, resulting in the loss of information there. NHEJ does not restore the lost information and may resect ad- ditional nucleotides during the repair process. The ability to repair a wide range of overhang and damage configura- tions reflects the flexibility of the nuclease, polymerases, and ligase of NHEJ. The flexibility of the individual com- ponents also explains the large number of ways in which NHEJ can repair any given pair of DNA ends. The loss of information locally at sites of NHEJ repair may contribute to cancer and aging, but the action by NHEJ ensures that entire segments of chromosomes are not lost. Keywords: nonhomologous DNA end joining (NHEJ), Ku, DNA-PKcs, Artemis, Cernunnos/XLF, ligase IV, XRCC4, poly- merase µ, polymerase λ Cell Research (2008) 18:125-133. doi: 10.1038/cr.2007.108; published online 18 December 2007 Introduction are ideally suited for the NHEJ process. Our view of NHEJ is that Ku binds initially at the This review is part of a series of reviews on DNA re- DSB site. Ku may bind at one side of the DSB or both pair, and other reviews in this issue provide an overview sides, depending on the length of the overhang relative of nonhomologous DNA end joining (NHEJ) and discuss to the nearest nucleosomes. DSBs within the DNA that is the earliest steps of NHEJ (see Weterings and Chen, this wrapped around a single nucleosome appear to be able to issue; and Shrivastav et al., this issue). In this review, diffuse off of the nucleosome surface sufficiently to per- we focus on the nucleolytic, polymerization, and ligation mit Ku binding [1]. Thereafter, Ku can recruit the nucle- steps of NHEJ. ase (Artemis:DNA-PKcs), polymerase (pol µ and pol λ), Most DNA repair pathways require nucleolytic resec- or ligase (XLF:XRCC4:DNA ligase IV) in any order to tion of the damaged DNA, DNA polymerization to pro- work on the ‘left’ or ‘right’ end at the DSB. In addition, vide new DNA to replace the resected DNA, and ligation the nuclease and the ligase activities can work on the ‘top’ to restore the integrity of the phosphodiester backbone. strand somewhat independently of their action on the ‘bot- NHEJ includes nuclease, polymerase, and ligase activites tom’ strand of each of the two DNA ends of the DSB [2, that demonstrate distinctive enzymatic flexibilities that 3]. The polymerase activities also have substantial flex- ibility, as we will discuss. The focus here is on vertebrate NHEJ (Figure 1). Yeast, plants, and invertebrates appear to differ in some Correspondence: Michael R Lieber Tel: +1-323-865-0568; Fax: +1-323-865-3019 aspects of NHEJ, because they do not have DNA-PKcs E-mail: [email protected] or Artemis; hence, the nuclease in some of these organ- www.cell-research.com | Cell Research npg Nonhomologous DNA end joining 126 isms may, in part, be provided by the RAD50:MRE11: tivates the serine/threonine kinase activity of DNA-PKcs. XRS2 complex [4]. In addition, homologous recombina- DNA-PKcs can phosphorylate itself in cis, but if two tion is, by far, the preferred pathway for repair of DSBs DNA-PKcs molecules are at the DSB – one at each end – in yeast. Because other aspects of NHEJ are discussed then this phosphorylation can also occur in trans [6]. In elsewhere in this series, the emphasis here will be on the addition, DNA-PKcs can phosphorylate Artemis [3]. The flexibility of vertebrate NHEJ and how that flexibility is Artemis:DNA-PKcs complex changes conformation as a optimal for the roles of NHEJ. result of these phosphorylation events, allowing Artemis to function as an endonuclease. Which precise phosphor- Nucleolytic resection by the Artemis: DNA-PKcs ylation sites in Artemis are most critical is not yet clear complex in NHEJ [7, 8]; one group maintains that the most critical sites are within DNA-PKcs itself [9]. However, a conformational The Ku:DNA complex at DSBs can recruit DNA- change within Artemis as a result of either its binding to PKcs with or without Artemis, though we suspect that DNA-PKcs or its phosphorylation by DNA-PKcs seems the Artemis:DNA-PKcs complex may be more common- likely, given that removal of the C-terminal half of Ar- ly recruited in these cases [3]. Ku can slide internally to temis, which is the site of most of the phosphorylation, permit DNA contact with the DNA-PKcs [5], and this ac- permits Artemis to function as an endonuclease, even Pathologic double-strand DNA break/repair Physiologic double-strand DNA break/repair 1. Ionizing radiation 1. V(D)J recombination breaks (RAG1,2) 2. Oxidative free radicals Cleavage phase 2. Class switch breaks (AID/UNG/APE) 3. Replication across a nick 4. Inadvertent enzyme action, particularly at fragile sites 5. Mechanical shearing (at anaphase bridges) 6. Topoisomerse failures 7. Chemotherapy radiomimetics G0 M G2 Homologous G1 Nonhomologous Joining phase recombination DNA end joining S (HR) (NHEJ) RAD50, MRE11, Nbs1 (MRN); Ku70/86, 469 kDa DNA-PKcs; RAD51 (B, C, D), XRCC2, XRCC4, DNA ligase IV, XLF, XRCC3, RAD52, RAD54 Artemis, pol µ & λ Intact chromosome Figure 1 Double-strand breaks and their repair. The causes of pathologic double-strand breaks (DSBs) include ionizing radia- tion (γ and X-rays) and free radicals. Physiologically programmed double-strand breaks are generated during the course of V(D)J recombination in pre-B (bone marrow) and pre-T cells (thymus) and during the course of class switch recombination in activated B cells (in the peripheral lymphoid tissues such as spleen, lymph nodes and Peyer’s patches). RAG1 and 2 (along with HMGB1) are involved in generating the breaks in V(D)J recombination. Activation-induced deaminase (AID), uracil glyco- sylase (UNG2), and perhaps abasic endonuclease (apurinic/apyrimidinic endonuclease) are involved in generating the breaks in class switch recombination. Homologous recombination can repair DSBs in late S or G2 of the cell cycle. Nonhomologous DNA end joining (NHEJ) can repair DSBs anytime. A subset of the proteins involved in homologous recombination is listed. The known proteins involved in NHEJ are listed. Cell Research | Vol 18 No 1 | January 2008 npg Michael R Lieber et al. 127 without DNA-PKcs for some DNA substrates [8]. These POL4 functions in NHEJ, although other polymerases issues of conformational change and of specific phos- also appear able to function when POL4 is absent [17]. phorylation sites merit continued detailed analysis. POL4 is the only Pol X family member in S. cerevisiae. Once activated, the Artemis:DNA-PKcs complex In humans, the closest homologues are pol µ or pol λ. demonstrates a degree of nucleolytic flexibility that is In mice lacking pol µ or pol λ, the junctions of V(D)J distinctive among structure-specific nucleases [10]. The recombination have more nucleolytic resection [13, 14]. Artemis:DNA-PKcs complex can cleave 5' overhangs Specifically, mice lacking pol µ have shorter Ig light- to a blunt or nearly blunt configuration and can cleave 3' chain V to J junctions, whereas mice lacking pol λ have overhangs back to a roughly 4 nt overhang. In the context shorter Ig heavy-chain D to J and V to DJ junctions. of V(D)J recombination (Figure 2), the RAG complex Because both pol µ and pol λ appear to be expressed creates hairpinned coding ends, and the Artemis: DNA- widely in somatic cells, it is not yet clear how there PKcs complex nicks these hairpins, thereby allowing the might be a division of labor between these two poly- resulting physiologic DNA ends to now be treated like merases. This division of labor may have its basis in double-strand breaks generated by any pathologic cause how stable either of them is at pairs of DNA ends with [3]. Among the 3' overhang structures that can be cut by 5' overhangs versus 3' overhangs [18]. When human pol activated Artemis:DNA-PKcs, 3' phosphoglycolate and µ was introduced into S. cerevisiae lacking POL4, the other 3' termini can be removed, activities relevant to a fill-in synthesis was different from that when pol λ was wide range of breaks created by ionizing radiation [11, introduced. Specifically, pol λ appeared better at fill-in of 12]. 5' overhangs, whereas pol µ appeared more stable at fill- The Artemis:DNA-PKcs complex is able to nick a in of 3' overhangs. Therefore, pol µ and pol λ may differ wider range of DNA structures than just overhangs. It can in their range of efficiency for fill-in synthesis at meta- nick regions of mismatched bases (e.g., 5 bp bubbles). It stable regions, such as at an unligated junction annealed can also nick the ssDNA within gaps of double-stranded together via a few hydrogen bonds.
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