Role of the Mre11 Complex in Preserving Genome Integrity

Abstract

DNA double-strand breaks (DSBs) are hazardous lesions that threaten genome integrity and cell survival. The DNA damage response (DDR) safeguards the genome by sensing DSBs, halting cell cycle progression and promoting repair through either non-homologous end joining (NHEJ) or homologous recombination (HR). The Mre11-Rad50-Xrs2/Nbs1 (MRX/N) complex is central to the DDR through its structural, enzymatic, and signaling roles. The complex tethers DNA ends, activates the Tel1/ATM kinase, resolves protein-bound or hairpin-capped DNA ends, and maintains telomere homeostasis. In addition to its role at DSBs, MRX/N associates with unperturbed replication forks, as well as stalled replication forks, to ensure complete DNA synthesis and to prevent chromosome rearrangements. Here, we summarize the significant progress made in characterizing the MRX/N complex and its various activities in chromosome metabolism.

Keywords: DNA damage checkpoint; DNA repair; DSB; MRX/N; Mre11; Rad50; Sae2/Ctp1/CtIP; Tel1/ATM; Xrs2/Nbs1; homologous recombination.

Figure 1

Damage recognition, end resection, and checkpoint activation. The Mre11-Rad50-Xrs2 (MRX) complex detects double-strand breaks (DSBs) and binds to the break ends (only one end is shown). Xrs2 recruits Tel1 and checkpoint signaling is activated. Resection follows a two-step, bidirectional mechanism. MRX, together with its cofactor Sae2, initiates resection by endonucleolytic cleavage of the 5′-terminated strand, generating an entry site for long-range resection machineries, Exo1 and Sgs1-Dna2, to proceed in the 5′ to 3′ direction. Meanwhile, the MRX complex proceeds back towards the double-stranded DNA (dsDNA) end using its 3′ to 5′ exonuclease activity. Single-stranded DNA (ssDNA) generated by resection is coated by replication protein A (RPA), which recruits Ddc2 and the Mec1 checkpoint kinase.

Figure 2

Overview of the DSB repair mechanisms. DSBs are repair by one of two major pathways: non-homologous end joining (NHEJ) or homologous recombination (HR). Classical NHEJ (C-NHEJ) directly re-ligates the two ends together while HR utilizes homologous template and is active in the S and G2 phases of the cell cycle when a sister chromatid is available. RPA initially binds to the 3′ ssDNA overhangs produced by end resection and is then replaced by Rad51 in a reaction requiring the Rad52 or BRCA2 mediator protein. The Rad51-ssDNA complex promotes the homology search and strand invasion, pairing the invading 3′ end with one strand of the donor duplex to template DNA synthesis. Resected intermediates can also be channeled to the MH-mediated end joining (MMEJ) pathway.

Figure 3

Domains and architecture of the MRX complex. (A) Mre11 consists a conserved phosphodiesterase nuclease domain and a capping domain at the N-terminus. The hydrophobic interaction domain for Rad50 resides towards the C-terminal region. Rad50 consists a bipartite ABC-ATPase domain at the N and C termini separated by two long coiled-coil domains and a zinc hook CxxC motif. Xrs2 harbors forkhead-associated (FHA) and BRCA1 C terminus (BRCT) domains at the N-terminus, and Mre11 and Tel1 interacting domains at the C-terminus. (B) Mre11, Rad50, and Xrs2 form a 2:2:2 heterohexameric complex, which undergoes a dramatic conformation change upon ATP binding. ATP binding by Rad50 induces the ‘closed’ form limiting access of the Mre11 nuclease active site to DNA. ATP hydrolysis opens the complex to allow Mre11 to initiate end processing.

Figure 4

Potential end tethering configurations of the MRX complex. Assemblies of MRX at both DSB ends could bridge ends through intermolecular hook-mediated dimerization. Alternatively, intra-molecular dimerization of Rad50 could mediate bridging of DNA ends and oligomerization of the coiled-coils could facilitate sister chromatid interactions. In both cases, proximity to the sister chromatid is maintained through cohesin enrichment in the vicinity of DSBs.