Regulation of DNA pairing in homologous recombination

Abstract

Homologous recombination (HR) is a major mechanism for eliminating DNA double-strand breaks from chromosomes. In this process, the break termini are resected nucleolytically to form 3' ssDNA (single-strand DNA) overhangs. A recombinase (i.e., a protein that catalyzes homologous DNA pairing and strand exchange) assembles onto the ssDNA and promotes pairing with a homologous duplex. DNA synthesis then initiates from the 3' end of the invading strand, and the extended DNA joint is resolved via one of several pathways to restore the integrity of the injured chromosome. It is crucial that HR be carefully orchestrated because spurious events can create cytotoxic intermediates or cause genomic rearrangements and loss of gene heterozygosity, which can lead to cell death or contribute to the development of cancer. In this review, we will discuss how DNA motor proteins regulate HR via a dynamic balance of the recombination-promoting and -attenuating activities that they possess.

Figure 1.

DNA double-strand break repair (DSBR) by homologous recombination. (A) Nucleolytic resection of the DNA ends produces 3′ ssDNA overhangs, one of which is engaged by the Rad51 recombinase to form a presynaptic filament capable of locating and invading a homologous sequence. The free end in the resulting D-loop then primes DNA synthesis. (B) The extended D-loop can be resolved by one of several pathways. Synthesis-dependent strand annealing (SDSA), being the most prevalent noncrossover mechanism in mitotic cells, entails D-loop dissociation by a helicase. If the second DNA end is captured, then a double Holliday junction (dHJ) will form. Resolution of the dHJ by a HJ resolvase, as in DSBR, yields either noncrossover or crossover recombinants. Alternatively, the dHJ can be dissolved via convergent migration of the two DNA junctions and DNA decatenation to yield noncrossover products.

Figure 2.

Functions of Sgs1 and BLM in homologous recombination. (A) Sgs1-Top3-Rmi1 (STR), Dna2, and RPA in S. cerevisiae or BLM-DNA2-RPA and BLM-EXO1-RPA in humans perform long-range resection and produce 3′ ssDNA overhangs. Note that the initial, short-range resection is mediated by a protein complex that harbors the conserved Mre11 nuclease (not shown). (B) The STR or BLM-TOPO IIIa-RMI1-RMI2 (BTR) complex dissolves the double Holliday junction (dHJ) to produce noncrossover products.

Figure 3.

Roles of Srs2/RECQ5, Mph1/Fml1/FANCM, and Rad54 in homologous recombination. (A) Srs2 and RECQ5 displace Rad51 from ssDNA, leading to suppression of inappropriate recombination events. (B) Mph1/Fml1/FANCM can (i) release the invading strand from the D-loop to promote SDSA, and (ii) mediate regression of a blocked replication fork to bypass a DNA lesion. (C) Rad54 stimulates Rad51-mediated D-loop formation and facilitates DNA synthesis via the release of Rad51 from the DNA joint.