Interactome analysis identifies a new paralogue of XRCC4 in non-homologous end joining DNA repair pathway

Xing, Mengtan; Yang, Meng; Huo, Wei; Feng, Feng; Wei, Leizhen; Jiang, Wenxia; Ning, Shaokai; Yan, Zhong; Li, Wen; Wang, Qingsong; Hou, Mei; Dong, Chunxia; Guo, Rong; Gao, Ge; Ji, Jianguo; Zha, Shan; Lan, Li; Liang, Huanhuan; Xu, Dongyi

doi:10.1038/ncomms7233

Cited by 153 publications

(217 citation statements)

References 40 publications

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“…In some cases, XLF and PAXX may work together to stabilize DNA ends. In reactions containing Ku, XRCC4·Lig4, and XLF, PAXX promoted the ligation of a blunt end to a 3' overhang (65). Interestingly, a more recent biochemical study showed that if Artemis and Pol m are included, PAXX does not stimulate NHEJ for 3' overhangs, but it does for 5' overhangs (73), indicating that the role of PAXX may be to stabilize substrates that cannot generate microhomology by end processing or nucleotide addition.…”

Section: Xlf and Paxx Stimulate Ligation By The Xrcc4·lig4 Complexmentioning

confidence: 99%

“…Like XLF, PAXX also forms homodimers, and its C-terminus has been found to associate with Ku (64,65) (Fig. 2D).…”

Section: Xlf and Paxx Stimulate Ligation By The Xrcc4·lig4 Complexmentioning

confidence: 99%

“…This interaction would presumably stabilize the juxtaposition of the DNA ends prior to covalent ligation, but this is still an area of active investigation. Another protein found to have structural similarity to XRCC4 is the 22 kDa protein PAXX (paralog of XRCC4 and XLF) (64,65). The C-terminus of PAXX (aa 199 -201) interacts with Ku, and similar to XLF mutants, PAXX mutants are more sensitive to ionizing radiation and DSB inducing agents ( Fig.…”

Section: The Ligase Complex Of Nhejmentioning

confidence: 99%

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Nonhomologous DNA end-joining for repair of DNA double-strand breaks

Pannunzio

Watanabe

Lieber

2018

Journal of Biological Chemistry

405

360

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Nonhomologous DNA end joining (NHEJ) is the predominant DSB repair pathway throughout the cell cycle and accounts for nearly all DSB repair outside of the S and G2 phases. NHEJ relies on Ku to thread onto DNA termini and thereby improve the affinity of the NHEJ enzymatic components consisting of polymerases (Pol m and Pol l), a nuclease (the Artemis·DNA-PKcs complex), and a ligase (XLF·XRCC4·Lig4 complex). Each of the enzymatic components is distinctive for its versatility in acting on diverse incompatible DNA end configurations coupled with a flexibility in loading order, resulting in many possible junctional outcomes from one DSB. DNA ends can either be directly ligated or, if the ends are incompatible, processed until a ligatable configuration is achieved that is often stabilized by up to 4 bp of terminal microhomology. Processing of DNA ends results in nucleotide loss or addition, explaining why DSBs repaired by NHEJ are rarely restored to their original DNA sequence. Thus, NHEJ is a single pathway with multiple enzymes at its disposal to repair DSBs, resulting in a diversity of repair outcomes.

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Section: Xlf and Paxx Stimulate Ligation By The Xrcc4·lig4 Complexmentioning

confidence: 99%

“…Like XLF, PAXX also forms homodimers, and its C-terminus has been found to associate with Ku (64,65) (Fig. 2D).…”

Section: Xlf and Paxx Stimulate Ligation By The Xrcc4·lig4 Complexmentioning

confidence: 99%

Section: The Ligase Complex Of Nhejmentioning

confidence: 99%

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Nonhomologous DNA end-joining for repair of DNA double-strand breaks

Pannunzio

Watanabe

Lieber

2018

Journal of Biological Chemistry

405

360

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“…S3A in the supplemental material). In addition, two laboratories recently have described another XRCC4/XLF-like factor, PAXX (25,26). PAXX interacts with DNA-bound Ku and can be targeted to sites of DNA damage.…”

Section: Xlfmentioning

confidence: 99%

XRCC4/XLF Interaction Is Variably Required for DNA Repair and Is Not Required for Ligase IV Stimulation

Roy

Melo

et al. 2015

Molecular and Cellular Biology

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fThe classic nonhomologous end-joining (c-NHEJ) pathway is largely responsible for repairing double-strand breaks (DSBs) in mammalian cells. XLF stimulates the XRCC4/DNA ligase IV complex by an unknown mechanism. XLF interacts with XRCC4 to form filaments of alternating XRCC4 and XLF dimers that bridge DNA ends in vitro, providing a mechanism by which XLF might stimulate ligation. Here, we characterize two XLF mutants that do not interact with XRCC4 and cannot form filaments or bridge DNA in vitro. One mutant is fully sufficient in stimulating ligation by XRCC4/Lig4 in vitro; the other is not. This separation-of-function mutant (which must function as an XLF homodimer) fully complements the c-NHEJ deficits of some XLF-deficient cell strains but not others, suggesting a variable requirement for XRCC4/XLF interaction in living cells. To determine whether the lack of XRCC4/XLF interaction (and potential bridging) can be compensated for by other factors, candidate repair factors were disrupted in XLF-or XRCC4-deficient cells. The loss of either ATM or the newly described XRCC4/XLF-like factor, PAXX, accentuates the requirement for XLF. However, in the case of ATM/XLF loss (but not PAXX/XLF loss), this reflects a greater requirement for XRCC4/XLF interaction.

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“…This factor directly interacts with Ku and promotes DNA ligation; however, the exact role of this protein in V(D)J recombination is not yet known. 10,11 The diversity of the antigen receptors created during V(D)J recombination has been estimated to be more than 10 12 . Part of the diversity arises from different combinations of the V, D, and J genes (2 3 10 ends are processed during V(D)J recombination.…”

Section: Introductionmentioning

confidence: 99%

XLF deficiency results in reduced N-nucleotide addition during V(D)J recombination

IJspeert

Rozmus

Schwarz

et al. 2016

Blood

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Key Points• XLF belongs to the NHEJ ligation complex and has a dual role in DNA doublestrand break repair and V(D)J recombination.• XLF is involved in Nnucleotide addition, and thereby contributes to junctional diversity of the antigen receptors.Repair of DNA double-strand breaks (DSBs) by the nonhomologous end-joining pathway (NHEJ) is important not only for repair of spontaneous breaks but also for breaks induced in developing lymphocytes during V(D)J (variable [V], diversity [D], and joining [J] genes) recombination of their antigen receptor loci to create a diverse repertoire. Mutations in the NHEJ factor XLF result in extreme sensitivity for ionizing radiation, microcephaly, and growth retardation comparable to mutations in LIG4 and XRCC4, which together form the NHEJ ligation complex. However, the effect on the immune system is variable (mild to severe immunodeficiency) and less prominent than that seen in deficiencies of NHEJ factors ARTEMIS and DNA-dependent protein kinase catalytic subunit, with defects in the hairpin opening step, which is crucial and unique for V(D)J recombination. Therefore, we aimed to study the role of XLF during V(D)J recombination. We obtained clinical data from 9 XLF-deficient patients and performed immune phenotyping and antigen receptor repertoire analysis of immunoglobulin (Ig) and T-cell receptor (TR) rearrangements, using next-generation sequencing in 6 patients. The results were compared with XRCC4 and LIG4 deficiency. Both Ig and TR rearrangements showed a significant decrease in the number of nontemplated (N) nucleotides inserted by terminal deoxynucleotidyl transferase, which resulted in a decrease of 2 to 3 amino acids in the CDR3. Such a reduction in the number of N-nucleotides has a great effect on the junctional diversity, and thereby on the total diversity of the Ig and TR repertoire. This shows that XLF has an important role during V(D)J recombination in creating diversity of the repertoire by stimulating N-nucleotide insertion. (Blood. 2016;128(5):650-659)

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Interactome analysis identifies a new paralogue of XRCC4 in non-homologous end joining DNA repair pathway

Cited by 153 publications

References 40 publications

Nonhomologous DNA end-joining for repair of DNA double-strand breaks

Nonhomologous DNA end-joining for repair of DNA double-strand breaks

XRCC4/XLF Interaction Is Variably Required for DNA Repair and Is Not Required for Ligase IV Stimulation

XLF deficiency results in reduced N-nucleotide addition during V(D)J recombination

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