The dissolution of double Holliday junctions

Abstract

Double Holliday junctions (dHJS) are important intermediates of homologous recombination. The separate junctions can each be cleaved by DNA structure-selective endonucleases known as Holliday junction resolvases. Alternatively, double Holliday junctions can be processed by a reaction known as "double Holliday junction dissolution." This reaction requires the cooperative action of a so-called "dissolvasome" comprising a Holliday junction branch migration enzyme (Sgs1/BLM RecQ helicase) and a type IA topoisomerase (Top3/TopoIIIα) in complex with its OB (oligonucleotide/oligosaccharide binding) fold containing accessory factor (Rmi1). This review details our current knowledge of the dissolution process and the players involved in catalyzing this mechanistically complex means of completing homologous recombination reactions.

Figure 1.

Double Holliday junction processing pathways. (A) During HJ resolution, each HJ of a dHJ is cleaved by a structure-selective endonuclease (resolvase). Depending on the combination of cleavage orientations, which can be asymmetric or symmetric, this process can generate both crossover and noncrossover products. In contrast, during dissolution (B), each strand engaged in the dHJ is reassociated with its original complementary strand, preventing exchange of genetic material between the two homologous sequences (and hence generating exclusively noncrossover products). DHJ dissolution (B) is initiated by migration of the HJs toward one another. The fusion/collapse of the two HJs results in a hemicatenated intermediate. Decatenation of this intermediate regenerates the original DNA species present before the initiation of HR.

Figure 2.

Domain organization of RecQ helicases, topoisomerases IA, and RMI proteins. (A) Most of the RecQ helicase members share a superfamily 2 helicase domain (SF2), a RecQ conserved domain (RQC), and a helicase and RNase D carboxy-terminal domain (HRDC). Besides this “RecQ core” domain, some RecQ helicases contain amino-terminal and carboxy-terminal extensions that vary in size, sequence, and functionality (e.g., SLD2 homology domain in RECQ4, and a signature motif in the carboxy-terminal domain of RECQ5). The hatched boxes denote partially degenerate RQC domains. BLM/Sgs1 helicases share a common domain organization, including an amino-terminal extension that includes domains for interaction with both TopoIII/RMI1 (TR) and replication protein A (RPA), in addition to a region that has been proposed to be required for DNA strand exchange (SE) activity. (B) All type IA topoisomerases contain a conserved catalytic domain (topoisomerase IA). Some topoisomerase IA enzymes also exhibit a carboxy-terminal extension, frequently composed of zinc finger motifs (black boxes), which is believed to mediate protein–DNA and protein–protein interactions. The contribution of the carboxy-terminal extension to dissolution is unknown. The regions interacting with other components of the dissolvasome are unknown. (C) In RMI1 proteins, only the DUF1676 and the OB-fold domain 1 (OB1) are conserved from yeast to human. The OB1 associates with both BLM/Sgs1 and topoisomerase III (BT/ST). In addition, human RMI1 exhibits a carboxy-terminal extension, composed of a middle region, which mediates RPA binding, and a second OB fold (OB2), which is able to associate with RMI2. RMI2 is also an OB-fold protein (OB3) that stably associates with the dissolvasome in human cells. In total, therefore, the human RMI1/2 complex contains three OB folds.

Figure 3.

DHJ substrates. Several substrates have been used to study HJ dissolution in vitro. The oligoDHJ substrate (left) is generated by the annealing and ligation of two oligonucleotides, leading to the formation of two HJ separated by 14 bp of quasi-homology. The processing of this substrate by the dissolvasome requires little or no branch migration allowing the investigation of the decatenation step. Following dissolution, the two strands forming the oligoDHJ substrate are physically separated and remain circular. The plasmidDHJ (right) comprises two circular dsDNA molecules associated though a region of homology (depicted in black and red). This substrate permits the analysis of the entire dissolution reaction, which in this case will lead to the complete separation of the two plasmids.