Review
The Ku heterodimer: Function in DNA repair and beyond

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Abstract

Ku is an abundant, highly conserved DNA binding protein found in both prokaryotes and eukaryotes that plays essential roles in the maintenance of genome integrity. In eukaryotes, Ku is a heterodimer comprised of two subunits, Ku70 and Ku80, that is best characterized for its central role as the initial DNA end binding factor in the “classical” non-homologous end joining (C-NHEJ) pathway, the main DNA double-strand break (DSB) repair pathway in mammals. Ku binds double-stranded DNA ends with high affinity in a sequence-independent manner through a central ring formed by the intertwined strands of the Ku70 and Ku80 subunits. At the break, Ku directly and indirectly interacts with several C-NHEJ factors and processing enzymes, serving as the scaffold for the entire DNA repair complex. There is also evidence that Ku is involved in signaling to the DNA damage response (DDR) machinery to modulate the activation of cell cycle checkpoints and the activation of apoptosis. Interestingly, Ku is also associated with telomeres, where, paradoxically to its DNA end-joining functions, it protects the telomere ends from being recognized as DSBs, thereby preventing their recombination and degradation. Ku, together with the silent information regulator (Sir) complex is also required for transcriptional silencing through telomere position effect (TPE). How Ku associates with telomeres, whether it is through direct DNA binding, or through protein–protein interactions with other telomere bound factors remains to be determined. Ku is central to the protection of organisms through its participation in C-NHEJ to repair DSBs generated during V(D)J recombination, a process that is indispensable for the establishment of the immune response. Ku also functions to prevent tumorigenesis and senescence since Ku-deficient mice show increased cancer incidence and early onset of aging. Overall, Ku function is critical to the maintenance of genomic integrity and to proper cellular and organismal development.

Introduction

Ku was first identified in the early 1980s as an autoantigen targeted by autoantibodies in the serum of patients diagnosed with an autoimmune disease known as scleroderma polymyositis overlap syndrome [1]. The name Ku comes from the first two letters of the name of the original patient in whose serum it was identified. Autoantibodies directed against Ku were subsequently found in several other autoimmune diseases, including systemic lupus erythematosus, Sjorgren's syndrome, polymyositis and scleroderma [2], [3], [4]. Early studies using serum from Ku-positive patients identified Ku as an abundant, mostly nuclear protein [1], [5]. Subsequent reports showed that Ku had unusual DNA binding properties, binding avidly to the ends of double-stranded DNA molecules in a sequence-independent manner, and to a lesser extent, to other forms of DNA discontinuities such as hairpins gaps and nicks [5], [6], [7]. These unusual end-binding properties made Ku an appealing candidate for a role in DSB repair and V(D)J recombination, which was confirmed when the two Ku subunits (XRCC5, Ku80 and XRCC6, Ku70) were found to complement the DNA repair defect of several IR-sensitive cell lines [8], [9], [10], [11], [12], [13], [14]. It is now well established that while not essential to individual life in the short term, Ku function is critical to the maintenance of genomic integrity and to the proper cellular and organismal development. A better understanding of Ku's diverse roles at the cellular and organismal level have implications for the study and the treatment of other human diseases, such as immune system disorders, cancer and aging.

Section snippets

Ku structure

Ku is a highly abundant protein found in vivo as a stable heterodimer consisting of two subunits, Ku70 and Ku80 (70 and 80 kDa, respectively). Both Ku70 and Ku80 eukaryotic Ku subunits contain three domains (Fig. 1A): an N-terminal alpha helix/beta barrel von Willebrand A (vWA) domain; a central core domain required for DNA binding and dimerization; and a helical C-terminal domain.

The Ku70/80 crystal structure (Fig. 1B) shows that the two subunits dimerize through the central domain to form a

Non-homologous end joining

There are three main DSB repair pathways in eukaryotes (Fig. 2): the classical NHEJ (C-NHEJ), alternative NHEJ or microhomology-mediated end joining (A-NHEJ or MMEJ) and homologous recombination (HR)[42], [43], [44]. C-NHEJ and A-NHEJ have the potential to be active in all stages of the cell cycle, however HR, is only active in the S and G2 phases because it utilizes the complementarity of the sister chromatid to repair the DSB with high accuracy [43], [44]. C-NHEJ is capable of ligating any

Ku as a DNA damage signaling molecule

The DNA damage response (DDR) pathway (Fig. 3) is initiated by sensor proteins that form large complexes that accumulate in foci at the site of damage (reviewed in [131]). This complex formation promotes the activation of a phosphorylation cascade, and the modification of surrounding chromatin to allow DNA repair factors to access the break. These initial sensors include the MRN complex, 53BP1, BRCA1, as well as the serine/threonine (S/T) PIKK family members Ataxia Telangiectasia Mutated (ATM),

Ku at telomeres

Telomeres are the linear ends of chromosomes and therefore have the potential to be recognized as DSBs and processed by DSB repair pathways. Specific protein complexes, such as the shelterin complex in mammals and the Rap1 and the CST (Cdc13–Stn1–Ten1) complexes in yeast have evolved to bind and form protective caps on the DNA ends to prevent access by the DNA repair complexes (Fig. 4) [146], [147]. A role for Ku in the maintenance of telomeres in yeast has been long established. Foundational

Immune system disorders

The vertebrate immune system utilizes Ku and C-NHEJ to repair physiological DSBs generated to create immune system genetic diversity. Recombination of the V, D, and J segments of immunoglobulins in lymphoid cells and class switch recombination of the T-cell receptor genes in mature B cells allows for the recognition of a wide variety antigens, which results in an adaptive immune response [193]. Ku70 and Ku80 knockout mice display many immune system abnormalities including B cell developmental

Conclusion

Ku is a versatile, multifunctional protein that has integral roles in DNA repair, telomere maintenance and DNA damage signaling. The central importance of Ku to cellular homeostasis is best demonstrated by the knockout of Ku in mouse models, which results in a complex phenotype, highlighted by extreme immunodeficiency, susceptibility to cancer and accelerated aging. Interestingly, despite the identification of human diseases stemming from mutation in the majority of other important DSB and DDR

Acknowledgement

This work was supported by a Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant to C.S.P.

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