Homologous recombination and its regulation

Abstract

Homologous recombination (HR) is critical both for repairing DNA lesions in mitosis and for chromosomal pairing and exchange during meiosis. However, some forms of HR can also lead to undesirable DNA rearrangements. Multiple regulatory mechanisms have evolved to ensure that HR takes place at the right time, place and manner. Several of these impinge on the control of Rad51 nucleofilaments that play a central role in HR. Some factors promote the formation of these structures while others lead to their disassembly or the use of alternative repair pathways. In this article, we review these mechanisms in both mitotic and meiotic environments and in different eukaryotic taxa, with an emphasis on yeast and mammal systems. Since mutations in several proteins that regulate Rad51 nucleofilaments are associated with cancer and cancer-prone syndromes, we discuss how understanding their functions can lead to the development of better tools for cancer diagnosis and therapy.

Figure 1.

Models for the repair of DNA double-strand breaks. DNA DSBs are resected to generate 3′-protruding ends followed by formation of Rad51 filaments that invade into homologous template to form D-loop structures. (A) After priming DNA synthesis, three pathways can be invoked. In the DSBR pathway, the second end is captured and a dHJ intermediate is formed. (B) Resolution of dHJs can occur in either plane to generate crossover or non-crossover products. Alternatively, dHJs can be dissolved by the action of Sgs1–Top1–Rmi1 complex to generate only non-crossovers. In the SDSA pathway (C), the extended nascent strand is displaced, followed by pairing with the other 3′-single-stranded tail, and DNA synthesis completes repair. Nucleolytic trimming might be also required. In the third pathway of BIR (D), which can act when the second end is absent, the D-loop intermediate turns into a replication fork capable of both lagging and leading strand synthesis. Two other Rad51-independent recombinational repair pathways are also depicted. In SSA (E), extensive resection can reveal complementary sequences at two repeats, allowing annealing. The 3′-tails are removed nucleolytically and the nicks are ligated. SSA leads to the deletion of one of the repeats and the intervening DNA. Finally, the ends of DSB can be directly ligated resulting in NHEJ. (F) Newly synthesized DNA is represented by dashed lines.

Figure 2.

Rad51 filament formation and regulation. RPA can be replaced by Rad51 from ssDNA with the help of recombination mediators, including Rad52 and Rad55/57. These proteins can promote both the formation and stability of Rad51 presynaptic filaments and they themselves also bind DNA during this process (not drawn here for simplicity). Rad51 presynaptic filaments perform homology search with help from Rad54 and Rhd54. Mph1 can promote the SDSA pathway by unwinding D-loop intermediates. Srs2 is capable of dismantling Rad51 filaments in an ATP-dependent manner, leading to the displacement of Rad51 by RPA. This prevents untimely or unwanted recombination. However, Rad52 and Rad55/57 can antagonize Srs2 activity. The Shu complex promotes Rad51 function during replication-associated repair but may also function by antagonizing Srs2. RPA–ssDNA complex can also lead to Rad51-independent repair wherein Rad52 and Rad59 replace RPA from DNA and anneal complementary strands. The balancing act of proteins with antagonistic roles as depicted here determines the fate of Rad51 nucleofilaments and the recombination outcome. Most proteins regulating Rad51 are modified by phosphorylation (P) and/or SUMOylation (S). The modifications are depicted on one form of the protein for simplicity; future work is needed to determine when the modification takes place. These modifications can dynamically change in response to DNA damaging agents and regulate the functions of the target proteins.