Non-homologous end-joining partners in a helical dance: structural studies of XLF–XRCC4 interactions

Wu, Qian; Ochi, Takashi; Matak-Vinković, Dijana; Robinson, Carol V.; Chirgadze, Dimitri Y.; Blundell, Tom L.

doi:10.1042/bst0391387

Cited by 65 publications

(70 citation statements)

References 30 publications

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“…We propose a speculative yet plausible explanation for this intriguing observation, based on our recent report on the Cernunnos-Xrcc4 complex structure (27). Crystals of Cernunnos-Xrcc4 complexes revealed that both homodimers associate with each other in long filaments through their head domains, helping to tether the broken DNA ends by creating a "DNA ligation synapse" (27)(28)(29)(30). The absence of Cernunnos would then result in DNA ligation synapse destabilization rather than a catalytic malfunction of the Xrcc4-Cernunnos-DNA ligase IV complex per se.…”

Section: Discussionmentioning

confidence: 99%

Cernunnos Deficiency Reduces Thymocyte Life Span and Alters the T Cell Repertoire in Mice and Humans

Vera

Rivera-Munoz

Abramowski

et al. 2013

Molecular and Cellular Biology

128

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f Cernunnos is a DNA repair factor of the nonhomologous end-joining machinery. Its deficiency in humans causes radiosensitive severe combined immune deficiency (SCID) with microcephaly, characterized in part by a profound lymphopenia. In contrast to the human condition, the immune system of Cernunnos knockout (KO) mice is not overwhelmingly affected. In particular, Cernunnos is dispensable during V(D)J recombination in lymphoid cells. Nevertheless, the viability of thymocytes is reduced in Cernunnos KO mice, owing to the chronic activation of a P53-dependent DNA damage response. This translates into a qualitative alteration of the T cell repertoire to one in which the most distal V␣ and J␣ segments are missing. This results in the contraction of discrete T cell populations, such as invariant natural killer T (iNKT) and mucosa-associated invariant T (MAIT) cells, in both humans and mice.T he immune system is the site of intense genome dynamics, in particular during the development and maturation of B and T lymphocytes in bone marrow and the thymus, when antigen receptor genes are rearranged through V(D)J recombination prior to their expression. DNA damages are also likely to occur during the several phases of intense proliferation which accompany the development of B and T cells.V(D)J recombination is the prototypical example of the generation of a programmed DNA double-strand break (DNA-dsb) during lymphoid development through the activity of recombination activating genes 1 and 2 (Rag1/2) on immunoglobulin (Ig) and T cell receptor (TCR) genes (see the work of Helmink and Sleckman [1] for a recent review). The resulting DNA-dsb is resolved by the nonhomologous end-joining (NHEJ) DNA repair pathway, composed of seven core components (see the work of Lieber [2] for a recent review). The Cernunnos-Xrcc4-DNA ligase IV complex ultimately reseals the DNA-dsb. Cernunnos, also known as Xrcc4-like factor (XLF), was the last NHEJ factor that was independently identified, through a survey of RS-SCID patients (3) and a yeast two-hybrid screen with Xrcc4 as a bait (4). Cernunnos and Xrcc4 adopt the same overall three-dimensional crystal structure (5, 6) and, together with DNA ligase IV, are parts of the same complex (4, 7). Cernunnos stimulates the DNA-joining activity of the Xrcc4-DNA ligase IV complex (8, 9). V(D)J recombination constitutes a central checkpoint in the development of the immune system, as its defect leads to abortive B and T cell maturation in vivo, resulting in severe combined immune deficiency (SCID) (10), but its first recognized function was the generation of a diverse antigenic repertoire through the combinatorial association of variable, diversity, and joining segments that encode the variable domains of both Ig and TCRs (11). Numerous examples show that a reduced V(D)J recombinase activity affects the extent of antigenic diversity of immune receptors in mice and humans. The resulting immune deregulation may then lead to autoimmunity, increased susceptibility to infections, or the development of vario...

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Section: Discussionmentioning

confidence: 99%

Cernunnos Deficiency Reduces Thymocyte Life Span and Alters the T Cell Repertoire in Mice and Humans

Vera

Rivera-Munoz

Abramowski

et al. 2013

Molecular and Cellular Biology

128

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“…Since its discovery in 2005, several functions have been described for XLF. It stimulates LIG4 activity, 21,22 and it can form long filaments with XRCC4 that keep the DNA ends together in a ligation synapse, 24,[48][49][50][51] and XLF is essential for gap-filling by polymerase (pol) l and polm during NHEJ. The latter function is interesting, as poll and polm belong to the same polX family of polymerases as For personal use only.…”

Section: Discussionmentioning

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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“…There, in ring-forming SAS-6, invariably exists a small amino acid residue, typically glycine or alanine. In contrast, in the spiral forming CeSAS-6 this position is occupied by a valine ( Figure 5); a valine is also found at the hinge position of XRCC4, which forms spirals similar to CeSAS-6 [32,[34][35][36]. The steric effect imposed by the valine in CeSAS-6 moves the coiled-coil helix relative to the N-terminal domain by approximately 40° compared to other SAS-6 variants [30], thereby driving successive CeSAS-6 dimers out of the horizontal plane and into a steep spiral of ~30 nm pitch.…”

Section: Sas-6 Spiralsmentioning

confidence: 93%

“…The SAS-6 N-terminal domain bears strong structural resemblance to similar domains of XRCC4 and XLF (Figure 2), proteins involved in DNA repair and non-homologous end joining. Further, similar to SAS-6, XRCC4 forms dimers via a coiled-coil domain, and it hetero-oligomerises with XLF via the globular N-terminal domains to form a spiral [32][33][34][35][36]. Most SAS-6 oligomers resolved to date are highly reminiscent of cartwheel rings, with a central hub derived from the N-terminal globular domains and the SAS-6 coiled coils comprising the cartwheel spokes [28,29,31].…”

Section: Introductionmentioning

confidence: 99%

Coupling Form and Function: How the Oligomerisation Symmetry of the SAS-6 Protein Contributes to the Architecture of Centriole Organelles

2017

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Centrioles make up the centrosome and basal bodies in animals and as such play important roles in cell division, signalling and motility. They possess characteristic 9-fold radial symmetry strongly influenced by the protein SAS-6. SAS-6 is essential for canonical centriole assembly as it forms the central core of the organelle, which is then surrounded by microtubules. SAS-6 self-assembles into an oligomer with elongated spokes that emanate towards the outer microtubule wall; in this manner, the symmetry of the SAS-6 oligomer influences centriole architecture and symmetry. Here, we summarise the form and symmetry of SAS-6 oligomers inferred from crystal structures and directly observed in vitro. We discuss how the strict 9-fold symmetry of centrioles may emerge, and how different forms of SAS-6 oligomers may be accommodated in the organelle architecture.

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Non-homologous end-joining partners in a helical dance: structural studies of XLF–XRCC4 interactions

Cited by 65 publications

References 30 publications

Cernunnos Deficiency Reduces Thymocyte Life Span and Alters the T Cell Repertoire in Mice and Humans

Cernunnos Deficiency Reduces Thymocyte Life Span and Alters the T Cell Repertoire in Mice and Humans

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

Coupling Form and Function: How the Oligomerisation Symmetry of the SAS-6 Protein Contributes to the Architecture of Centriole Organelles

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