The MRE11 complex: starting from the ends

Abstract

The maintenance of genome stability depends on the DNA damage response (DDR), which is a functional network comprising signal transduction, cell cycle regulation and DNA repair. The metabolism of DNA double-strand breaks governed by the DDR is important for preventing genomic alterations and sporadic cancers, and hereditary defects in this response cause debilitating human pathologies, including developmental defects and cancer. The MRE11 complex, composed of the meiotic recombination 11 (MRE11), RAD50 and Nijmegen breakage syndrome 1 (NBS1; also known as nibrin) proteins is central to the DDR, and recent insights into its structure and function have been gained from in vitro structural analysis and studies of animal models in which the DDR response is deficient.

Figure 1. The MRE11 complex regulates the mammalian DNA damage response

Double-stranded DNA (dsDNA) breaks are recognized by the MRE11 complex, which catalyses the activation of ataxia-telangiectasia mutated (ATM) in conjunction with other proteins such as the tat-interactive protein 60 kDa (TIP60; also known as KAT5) acetyltransferase and p53-binding protein 1 (53BP1)^,. ATM activation promotes cell-cycle checkpoint induction, influences DNA repair, and can activate apoptosis and senescence in certain cellular contexts. Depending on the cell-cycle phase and end-binding complexes or end modifications, breaks can be directed into two major repair pathways: homology-directed repair (HDR) or non-homologous end-joining (NHEJ; also known as classical (C)-NHEJ). a | HDR requires the 5′–3′ resection of dsDNA to generate single-stranded DNA (ssDNA)–dsDNA junctions. This is initiated by the MRE11 complex and CtBP-interacting protein (CtIP) and further bulk resection is carried out by exonuclease 1 (EXO1), BLM and DNA2 (refs 10,,–163). 3′ ssDNA tails generated by resection are bound by replication protein A (RPA), which activates ATR via ATR-interacting protein (ATRIP) binding to influence the checkpoint response. RPA on these 3′ tails is exchanged for RAD51 to promote strand invasion, HDR repair and resolution of repair intermediates. b | Ends bound by the Ku70–Ku80 heterodimer can be repaired by NHEJ in conjunction with the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), Artemis nuclease and DNA ligase 4, with the help of additional factors involved in end-modifications, gap filling and ligation. This NHEJ pathway is independent of the MRE11 complex. c | The MRE11 complex, in conjunction with CtIP, also regulates the poorly defined alternative NHEJ (A-NHEJ) pathway, which is characterized by large deletions and the frequent use of short microhomologies^–,–. This pathway is resection-dependent and requires several enzymatic activities for resection, flap trimming, synthesis and ligation. CDK, cell division protein kinase; DSB, double-strand break.

Figure 2. The MRE11 complex consists of a globular domain and extended coiled-coils

a | The MRE11 complex consists of a large globular domain, in which meiotic recombination 11 (MRE11), and Nijmegen breakage syndrome 1 (NBS1; also known as nibrin) associate with RAD50 and DNA, and extended coiled-coil domains of RAD50 in which the amino-terminal and carboxy-terminal regions of the coils associate in an antiparallel manner. At the apex of the RAD50 coils, the N-terminal and C-terminal regions fold back on themselves to form the `RAD50 hook' domain (image is not to scale). The RAD50 hook domain mediates formation of MRE11 complex assemblies. b | A dimeric MRE11 complex without DNA is shown by scanning force microscopy and in a schematic (left panel; the white bar represents scale along the horizontal plane, whereas the colour gradient on the right represents scale on the vertical plane). The RAD50 hook domain coordinates binding to a zinc atom. Upon DNA binding, the coiled-coil domains adopt a rigid parallel structure that bridges two DNA strands with a distances of ~1,000 Å (right panel). A, Walker A; B, Walker B; BRCT, BRCA1 C-terminal; FHA, Forkhead-associated. Images in panel b are reproduced, with permission, from ref. 37 © (2005) Macmillan Publishers Ltd. All rights reserved.

Figure 3. The MRE11 complex controls telomere homeostasis

At a functional telomere (green area, left), the MRE11 complex recognizes the newly synthesized telomeric ends and promotes their resection to create the 3′ overhang, which is a prerequisite for the formation of the t-loop — a DNA structure resembling the d-loop formed by strand invasion during homology directed repair (HDR). The t-loop is critical for normal telomere protection and maintenance. The MRE11 complex also recognizes dysfunctional telomeres (red area, right), leading to activation of ataxia-telangiectasia mutated (ATM) and `repair' (that is, fusion) of the telomere through non-homologous end-joining (NHEJ; also known as classical (C)-NHEJ); this ultimately precludes chromosome segregation and causes cell death. The MRE11 complex may also influence the degradation of the 3′ overhang before, or during, the fusion process. MRE11 complex hypomorphism impairs ATM activation, which sharply reduces the frequency of NHEJ-mediated telomere fusion; this also leads to impaired telomeric end processing on both leading and lagging strands, such that residual fusions are restricted to telomeres that have been replicated by the leading strands and are blunt.

Figure 4. The MRE11 complex in human disease and mouse models

a | Domain structure of the MRE11 complex. The Nijmegen breakage syndrome 1 (NBS1; also known as nibrin), meiotic recombination 11 (MRE11) and RAD50 components of the human MRE11 complex are illustrated. Domains are indicated by name with the corresponding amino acid numbers shown. Human disease mutations are indicated in green. Mouse alleles are indicated in red and `humanized' mouse alleles in blue. This figure is drawn to scale. b | The MRE11 complex has multiple roles in activating apoptosis after double-strand break (DSB) exposure. The complex activates ataxia-telangiectasia mutated (ATM) and facilitates the phosphorylation of select ATM substrates, including CHK2 and BH3-interacting domain death agonist (BID), to promote p53-dependent apoptosis through the carboxyl terminus of NBS1. CHK2 signals in parallel, and is possibly activated by the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). Mouse alleles affecting various steps in the signalling pathway are indicated. Alleles in red impair apoptosis in both the haematopoietic and nervous system and alleles in green affect the haematopoietic but not the nervous system. c | Genetic interactions between mouse MRE11 complex alleles. MRE11 complex alleles used for genetic analyses are shown in green, components of the non-homologous end-joining (NHEJ; also known as classical (C)-NHEJ) machinery are shown in blue and other DNA damage or cell-cycle regulators are shown in red. Connecting lines indicate that genetic crosses have been analysed. Blue lines indicate that no synthetic interactions were identified, green lines indicate that synthetic interactions were identified, and red lines indicate synthetic lethality. Dashed lines indicate incomplete penetrance of synthetic lethality. Interacting alleles are classified by their major functions of the DNA damage response, although they may affect other aspects of the response. ATLD, ataxia-telangiectasia-like disease; BRCT, BRCA1 C-terminal; FHA, Forkhead-associated; h, humanized; m, mouse; NBSLD, NBS-like disorder; PIKK, PI3K-related protein kinase.