Non-homologous end-joining factor 1 explained

Non-homologous end-joining factor 1 (NHEJ1), also known as Cernunnos or XRCC4-like factor (XLF), is a protein that in humans is encoded by the NHEJ1 gene.^[1] XLF was originally discovered as the protein mutated in five patients with growth retardation, microcephaly, and immunodeficiency.^[2] The protein is required for the non-homologous end joining (NHEJ) pathway of DNA repair. Patients with XLF mutations also have immunodeficiency due to a defect in V(D)J recombination, which uses NHEJ to generate diversity in the antibody repertoire of the immune system. XLF interacts with DNA ligase IV and XRCC4 and is thought to be involved in the end-bridging or ligation steps of NHEJ. The yeast (Saccharomyces cerevisiae) homolog of XLF is Nej1.^[3]

Phenotypes

In contrast to the profound immunodeficiency phenotype of XLF deletion in humans, deletion of XLF alone has a mild phenotype in mice.^[4] However, combining a deletion of XLF with deletion of the ATM kinase causes a synthetic defect in NHEJ, suggesting partial redundancy in the function of these two proteins in mice.^[5]

Structure

XLF is structurally similar to XRCC4, existing as a constitutive dimer with an N-terminal globular head domain, an alpha-helical stalk, and an unstructured C-terminal region (CTR).^[6]

Interactions

XLF has been shown to interact with XRCC4,^[7] and with Ku protein,^[8] and it can also interact weakly with DNA.^{[9] [10]} Co-crystal structures of XLF and XRCC4 suggest that the two proteins can form hetero-oligomers via head-to-head interaction of alternating XLF and XRCC4 subunits.^{[11] [12] [13]} These XRCC4-XLF filaments have been proposed to bridge DNA prior to end ligation during NHEJ. Formation of XRCC4-XLF oligomers can be disrupted by interaction of the C-terminal domain of XRCC4 with the BRCT domain of DNA ligase IV.^[11]

Hematopoietic stem cell aging

Deficiency of NHEJ1 in mice leads to premature aging of hematopoietic stem cells as indicated by several lines of evidence including evidence that long-term repopulation is defective and worsens over time.^[14] Using a human induced pluripotent stem cell model of NHEJ1 deficiency, it was shown that NHEJ1 has an important role in promoting survival of the primitive hematopoietic progenitors.^[15] These NHEJ1 deficient cells possess a weak NHEJ1-mediated repair capacity that is apparently incapable of coping with DNA damages induced by physiological stress, normal metabolism, and ionizing radiation.^[15]

Further reading

• Pastwa E, Malinowski M . Non-homologous DNA end joining in anticancer therapy . . 7 . 3 . 243–50 . May 2007 . 17504121 . 10.2174/156800907780618284 .
• Dai Y, Kysela B, Hanakahi LA, Manolis K, Riballo E, Stumm M, Harville TO, West SC, Oettinger MA, Jeggo PA . Nonhomologous end joining and V(D)J recombination require an additional factor . Proceedings of the National Academy of Sciences of the United States of America . 100 . 5 . 2462–7 . Mar 2003 . 12604777 . 151363 . 10.1073/pnas.0437964100 . 2003PNAS..100.2462D . free .
• Buck D, Malivert L, de Chasseval R, Barraud A, Fondanèche MC, Sanal O, Plebani A, Stéphan JL, Hufnagel M, le Deist F, Fischer A, Durandy A, de Villartay JP, Revy P . Cernunnos, a novel nonhomologous end-joining factor, is mutated in human immunodeficiency with microcephaly . Cell . 124 . 2 . 287–99 . Jan 2006 . 16439204 . 10.1016/j.cell.2005.12.030 . 13075378 . free .
• Ahnesorg P, Smith P, Jackson SP . XLF interacts with the XRCC4-DNA ligase IV complex to promote DNA nonhomologous end-joining . Cell . 124 . 2 . 301–13 . Jan 2006 . 16439205 . 10.1016/j.cell.2005.12.031 . 12902760 . free .
• Callebaut I, Malivert L, Fischer A, Mornon JP, Revy P, de Villartay JP . Cernunnos interacts with the XRCC4 x DNA-ligase IV complex and is homologous to the yeast nonhomologous end-joining factor Nej1 . The Journal of Biological Chemistry . 281 . 20 . 13857–60 . May 2006 . 16571728 . 10.1074/jbc.C500473200 . free .
• Revy P, de Villartay JP . [Cernunnos, a novel DNA repair factor essential for the immune system] . Médecine/Sciences . 22 . 6–7 . 569–70 . 2006 . 16828027 . 10.1051/medsci/20062267569 . free .
• Cantagrel V, Lossi AM, Lisgo S, Missirian C, Borges A, Philip N, Fernandez C, Cardoso C, Figarella-Branger D, Moncla A, Lindsay S, Dobyns WB, Villard L . Truncation of NHEJ1 in a patient with polymicrogyria . Human Mutation . 28 . 4 . 356–64 . Apr 2007 . 17191205 . 10.1002/humu.20450 . 15221701 . free .
• Lu H, Pannicke U, Schwarz K, Lieber MR . Length-dependent binding of human XLF to DNA and stimulation of XRCC4.DNA ligase IV activity . The Journal of Biological Chemistry . 282 . 15 . 11155–62 . Apr 2007 . 17317666 . 10.1074/jbc.M609904200 . free .
• Tsai CJ, Kim SA, Chu G . Cernunnos/XLF promotes the ligation of mismatched and noncohesive DNA ends . Proceedings of the National Academy of Sciences of the United States of America . 104 . 19 . 7851–6 . May 2007 . 17470781 . 1859989 . 10.1073/pnas.0702620104 . 2007PNAS..104.7851T . free .
• Deshpande RA, Wilson TE . Modes of interaction among yeast Nej1, Lif1 and Dnl4 proteins and comparison to human XLF, XRCC4 and Lig4 . DNA Repair . 6 . 10 . 1507–16 . Oct 2007 . 17567543 . 2064958 . 10.1016/j.dnarep.2007.04.014 .
• Wu PY, Frit P, Malivert L, Revy P, Biard D, Salles B, Calsou P . Interplay between Cernunnos-XLF and nonhomologous end-joining proteins at DNA ends in the cell . The Journal of Biological Chemistry . 282 . 44 . 31937–43 . Nov 2007 . 17720816 . 10.1074/jbc.M704554200 . free .

Notes and References

1. Web site: Entrez Gene: NHEJ1 nonhomologous end-joining factor 1.
2. Buck D, Malivert L, de Chasseval R, Barraud A, Fondanèche MC, Sanal O, Plebani A, Stéphan JL, Hufnagel M, le Deist F, Fischer A, Durandy A, de Villartay JP, Revy P . Cernunnos, a novel nonhomologous end-joining factor, is mutated in human immunodeficiency with microcephaly . Cell . 124 . 2 . 287–99 . Jan 2006 . 16439204 . 10.1016/j.cell.2005.12.030 . 13075378 . free .
3. Callebaut I, Malivert L, Fischer A, Mornon JP, Revy P, de Villartay JP . Cernunnos interacts with the XRCC4 x DNA-ligase IV complex and is homologous to the yeast nonhomologous end-joining factor Nej1 . The Journal of Biological Chemistry . 281 . 20 . 13857–60 . May 2006 . 16571728 . 10.1074/jbc.C500473200 . free .
4. Li G, Alt FW, Cheng HL, Brush JW, Goff PH, Murphy MM, Franco S, Zhang Y, Zha S . Lymphocyte-specific compensation for XLF/cernunnos end-joining functions in V(D)J recombination . Molecular Cell . 31 . 5 . 631–40 . Sep 2008 . 18775323 . 2630261 . 10.1016/j.molcel.2008.07.017 .
5. Zha S, Guo C, Boboila C, Oksenych V, Cheng HL, Zhang Y, Wesemann DR, Yuen G, Patel H, Goff PH, Dubois RL, Alt FW . ATM damage response and XLF repair factor are functionally redundant in joining DNA breaks . Nature . 469 . 7329 . 250–4 . Jan 2011 . 21160472 . 3058373 . 10.1038/nature09604 . 2011Natur.469..250Z .
6. Andres SN, Modesti M, Tsai CJ, Chu G, Junop MS . Crystal structure of human XLF: a twist in nonhomologous DNA end-joining . Molecular Cell . 28 . 6 . 1093–101 . Dec 2007 . 18158905 . 10.1016/j.molcel.2007.10.024 . free .
7. Deshpande RA, Wilson TE . Modes of interaction among yeast Nej1, Lif1 and Dnl4 proteins and comparison to human XLF, XRCC4 and Lig4 . DNA Repair . 6 . 10 . 1507–16 . Oct 2007 . 17567543 . 2064958 . 10.1016/j.dnarep.2007.04.014 .
8. Yano K, Morotomi-Yano K, Wang SY, Uematsu N, Lee KJ, Asaithamby A, Weterings E, Chen DJ . Ku recruits XLF to DNA double-strand breaks . EMBO Reports . 9 . 1 . 91–6 . Jan 2008 . 18064046 . 2246615 . 10.1038/sj.embor.7401137 .
9. Tsai CJ, Chu G . Cooperative assembly of a protein-DNA filament for nonhomologous end joining . The Journal of Biological Chemistry . 288 . 25 . 18110–20 . Jun 2013 . 23620595 . 10.1074/jbc.M113.464115 . 3689955. free .
10. Lu H, Pannicke U, Schwarz K, Lieber MR . Length-dependent binding of human XLF to DNA and stimulation of XRCC4.DNA ligase IV activity . The Journal of Biological Chemistry . 282 . 15 . 11155–62 . Apr 2007 . 17317666 . 10.1074/jbc.M609904200 . free .
11. Andres SN, Vergnes A, Ristic D, Wyman C, Modesti M, Junop M . A human XRCC4-XLF complex bridges DNA . Nucleic Acids Research . 40 . 4 . 1868–78 . Feb 2012 . 22287571 . 3287209 . 10.1093/nar/gks022 .
12. Wu Q, Ochi T, Matak-Vinkovic D, Robinson CV, Chirgadze DY, Blundell TL . Non-homologous end-joining partners in a helical dance: structural studies of XLF-XRCC4 interactions . Biochemical Society Transactions . 39 . 5 . 1387–92, suppl 2 p following 1392 . Oct 2011 . 21936820 . 10.1042/BST0391387 . 8814152 .
13. Ropars V, Drevet P, Legrand P, Baconnais S, Amram J, Faure G, Márquez JA, Piétrement O, Guerois R, Callebaut I, Le Cam E, Revy P, de Villartay JP, Charbonnier JB . Structural characterization of filaments formed by human Xrcc4-Cernunnos/XLF complex involved in nonhomologous DNA end-joining . Proceedings of the National Academy of Sciences of the United States of America . 108 . 31 . 12663–8 . Aug 2011 . 21768349 . 3150875 . 10.1073/pnas.1100758108 . 2011PNAS..10812663R . free .
14. Avagyan S, Churchill M, Yamamoto K, Crowe JL, Li C, Lee BJ, Zheng T, Mukherjee S, Zha S . Hematopoietic stem cell dysfunction underlies the progressive lymphocytopenia in XLF/Cernunnos deficiency . Blood . 124 . 10 . 1622–5 . 2014 . 25075129 . 4155271 . 10.1182/blood-2014-05-574863 .
15. Tilgner K, Neganova I, Singhapol C, Saretzki G, Al-Aama JY, Evans J, Gorbunova V, Gennery A, Przyborski S, Stojkovic M, Armstrong L, Jeggo P, Lako M . Brief report: a human induced pluripotent stem cell model of cernunnos deficiency reveals an important role for XLF in the survival of the primitive hematopoietic progenitors . Stem Cells . 31 . 9 . 2015–23 . 2013 . 23818183 . 10.1002/stem.1456 . 3623309 . free .