In mammalian cells, DNA double-strand breaks (DSBs) are repaired by two main pathways, non-homologous end joining (NHEJ) and homologous recombination (HR) (
1–
3). Current models predict that NHEJ involves the sequential recruitment of proteins to the DSB in order to juxtapose free double-stranded DNA (dsDNA) ends (synapsis) and seal the phosphodiester backbone (ligation). The core NHEJ apparatus includes the catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs), the Ku70/Ku80 heterodimer (Ku) and the XRCC4-DNA ligase IV complex [reviewed in (
2,
4)]. Ku, which has a high affinity for ends of dsDNA, likely binds to the DSB first, followed by the recruitment of DNA-PKcs. The interaction of DNA-PKcs with DNA-end-bound Ku leads to the formation of the DNA-dependent protein kinase holoenzyme, DNA-PK, which is a serine/threonine protein kinase with an
in vitro substrate preference for serine or threonine residues followed by glutamine (SQ or TQ motifs) (
5,
6). Subsequently, the XRCC4-DNA ligase IV complex is recruited via Ku–DNA-PKcs, Ku–DNA ligase IV, and DNA-PKcs–XRCC4 protein–protein interactions [reviewed in (
2)]. In addition to the core NHEJ apparatus, additional factors may be required to repair a subset of DSBs, such as those with complex termini. Such factors include Artemis (
7), polynucleotide kinase (
8), Werner's Syndrome helicase (WRN) (
9,
10), DNA polymerase μ (
11) and DNA polymerase λ (
12).
Several studies have shown that the protein kinase activity of DNA-PKcs is essential for NHEJ (
13–
17); however, the precise role of DNA-PK kinase activity within NHEJ has not been determined. DNA-PKcs is a member of the phosphatidyl inositol 3 kinase-like family of protein kinases (PIKKs) [reviewed in (
2)]. Similar to other PIKKs, the
in vitro protein kinase activity of DNA-PK is inhibited by wortmannin and LY294002 (
18,
19), both of which radiosensitize cells and inhibit the repair of DSBs
in vivo (
17,
20,
21). In addition, both DNA-PKcs-deficient cells and DNA-PKcs-deficient cells complemented with kinase-dead DNA-PKcs are severely compromised in their ability to repair DSBs (
13,
14). Consistent with the requirement of DNA-PK kinase activity for NHEJ
in vivo, Mg-ATP is required for DNA-PK-dependent end joining in crude extracts from human cells (
22).
In vitro, DNA-PK undergoes autophosphorylation that correlates with loss of protein kinase activity (
23–
25). Some
in vitro studies have shown that autophosphorylation promotes dissociation of phosphorylated DNA-PKcs from DNA-bound Ku (
24,
25), whereas others have failed to see phosphorylation-induced dissociation (
26–
28).
In vitro studies have shown that DNA-PK can protect dsDNA ends from exonuclease digestion and that prior incubation of DNA-PK with ATP prevents dsDNA protection from exonucleases in a wortmannin-inhibitable manner (
28). Moreover, ATP and the protein kinase activity of DNA-PK were found to be required to make DNA ends accessible to T4 DNA ligase-mediated end joining (
28).
In vivo studies also suggest that DNA-PK kinase activity is intimately involved in regulating the accessibility of DNA ends to other proteins. For example, rates of HR were lower in DNA-PKcs-proficient cells that had been treated with the specific DNA-PK inhibitor IC86621 than in cells that lacked DNA-PKcs (
29), suggesting that in the absence of DNA-PK kinase activity, the DNA ends are not accessible to alternate DNA repair processes. Together, these data are all consistent with a requirement for autophosphorylation of DNA-PKcs for remodeling of DNA-end-bound DNA-PK prior to ligation (
28,
30).
We identified previously seven
in vitro autophosphorylation sites in DNA-PKcs, six of which are located in the central region of the protein, between amino acids 2609 and 2647 (
31). Three of these sites (threonines 2609, 2638 and 2647) were independently identified by other investigators (
32,
33). Four of the identified sites (threonines 2609, 2638 and 2647, and serine 2612) were phosphorylated
in vivo in okadaic-acid-treated cells (
31), and DNA-PKcs phosphorylated on threonine 2609 localized to sites of DNA damage
in vivo (
32). Cells expressing DNA-PKcs containing single mutations at any of the identified phosphorylation sites were not radiosensitive (
30,
32). In contrast, cells expressing DNA-PKcs containing six serine/threonine to alanine autophosphorylation site mutations (T2609A, S2612A, S2620A, S2624, T2638A and T2647A; referred to here as A6) were more radiosensitive than cells that lacked DNA-PKcs and had a severely impaired ability to repair coding and signal ends in
in vivo extrachromosomal V(D)J recombination assays (
30,
32). Surprisingly, the protein kinase activity of the purified DNA-PKcs A6 mutant protein was indistinguishable from wild-type (wt) DNA-PKcs, including the ability to undergo autophosphorylation-induced inactivation
in vitro (
30). Cells expressing DNA-PKcs containing six serine/threonine to aspartate mutations as a phosphorylation site mimic (referred to here as D6), were less radiosensitive than cells lacking DNA-PKcs or cells containing the A6 mutant DNA-PKcs, but were significantly more radiosensitive than cells expressing wt DNA-PKcs (
30). Also, D6 cells had <10% of the ability of wt cells to rejoin coding ends in extrachromosomal V(D)J recombination assays (
30). This suggests that the D6 mutant is significantly compromised with respect to DSB repair and that aspartate is a poor mimic for phosphorylation at these sites. Together these studies suggest a model in which autophosphorylation of DNA-PKcs is required to facilitate DNA end joining, likely by remodeling the DNA-PK holoenzyme, thereby making the DNA ends accessible for ligation.
To characterize the role of DNA-PKcs autophosphorylation in NHEJ, we have examined the repair of DSB in vivo. We found that similar to DNA-PKcs-deficient cells, both A6 and D6 cells were defective in the repair of ionizing radiation (IR)-induced DSBs compared to cells expressing wt DNA-PK. We next sought to rationalize this DSB repair defect based on the biochemical properties of the various purified DNA-PKcs proteins. We confirmed that the phosphorylation mutant forms of DNA-PKcs are catalytically active, and that each mutant form, like wt, undergoes ATP-dependent autophosphorylation and inactivation. However, autophosphorylation mutant forms of DNA-PKcs were defective with respect to the ability to support T4 DNA ligase-mediated DNA end joining. These results demonstrate that DNA-PKcs autophosphorylation on this small cluster of residues mediates the accessibility to DNA-PK-bound DNA ends without otherwise altering the biochemical properties of the protein kinase. We speculate that a remodeling deficiency of DNA-PK holoenzymes containing DNA-PKcs phosphorylation site mutants is responsible for both the radiosensitivity and the defective repair of IR-induced DSBs in vivo observed in the DNA-PK mutant cells.