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. 2017 Jul 6;67(1):19-29.e3.
doi: 10.1016/j.molcel.2017.05.019. Epub 2017 Jun 8.

Rad52 Inverse Strand Exchange Drives RNA-Templated DNA Double-Strand Break Repair

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Free PMC article

Rad52 Inverse Strand Exchange Drives RNA-Templated DNA Double-Strand Break Repair

Olga M Mazina et al. Mol Cell. .
Free PMC article

Abstract

RNA can serve as a template for DNA double-strand break repair in yeast cells, and Rad52, a member of the homologous recombination pathway, emerged as an important player in this process. However, the exact mechanism of how Rad52 contributes to RNA-dependent DSB repair remained unknown. Here, we report an unanticipated activity of yeast and human Rad52: inverse strand exchange, in which Rad52 forms a complex with dsDNA and promotes strand exchange with homologous ssRNA or ssDNA. We show that in eukaryotes, inverse strand exchange between homologous dsDNA and RNA is a distinctive activity of Rad52; neither Rad51 recombinase nor the yeast Rad52 paralog Rad59 has this activity. In accord with our in vitro results, our experiments in budding yeast provide evidence that Rad52 inverse strand exchange plays an important role in RNA-templated DSB repair in vivo.

Keywords: DNA end resection; DNA strand exchange; DNA-RNA pairing; RNA-dependent DNA repair; Rad51; Rad52 N-terminal domain; Rad59; Sae2; double-strand DNA repair; homologous recombination.

Figures

Figure 1
Figure 1. Rad52 Promotes Inverse DNA Strand Exchange with High Efficiency
(A) Top: the scheme of inverse strand exchange. Asterisk represents 32P-label. Oligonucleotide sequences are shown in Table S1. hRad52 (900 nM) was incubated with the 3′-tailed DNA (no. 1/no. 117; 68.6 nM) followed by addition of ssDNA (no. 2; 68.6 nM). Bottom: analysis of the reaction products by electrophoresis in a polyacrylamide gel. (B) Top: the scheme of the forward DNA strand exchange. hRad52 (900 nM) was incubated with ssDNA (no. 2; 68.6 nM) for 15 min at 37°C, and then the reaction was initiated by adding the 3′-tailed DNA (no. 1/no. 117; 68.6 nM). Bottom: analysis of the reaction products by electrophoresis in a polyacrylamide gel. (C) Data from (A) and (B) were plotted as a graph. In “no protein” control, hRad52 was substituted by storage buffer. (D) hRad52 promotes inverse DNA strand exchange more efficiently than hRad51. The reaction conditions were as in (A), except that a 3-fold excess of ssDNA (205.8 nM) and 7-fold excess of ssDNA (480.2 nM) were used in reactions with Rad52 and Rad51, respectively. (E) yRad52 promotes inverse DNA strand exchange. The DNA substrates and conditions for forward and inverse reactions were the same as for hRad52 in (B) and (D), respectively. In “no protein” or “sp” reactions, Rad52 was substituted with storage buffer. The experiments were repeated at least three times; error bars indicate SD. See also Figure S1.
Figure 2
Figure 2. Rad52 Promotes Inverse Strand Exchange between 3′-Tailed dsDNA and Homologous ssRNA
(A) The reaction with hRad52 was conducted as in Figure 1D, except that ssDNA was replaced with ssRNA (no. 2R; 205.8 nM). The reaction products were analyzed by electrophoresis in a polyacrylamide gel. (B) Data from (A) are plotted as a graph. The DNA inverse exchange graph from Figure 1D is shown for comparison. (C) yRad52 promotes inverse strand exchange with ssDNA or ssRNA. The reaction conditions were as in (A), except that a 10-fold excess of ssRNA (no. 2R; 686 nM) was used. (D and E) hRad52 R55A has low inverse (D) DNA and (E) RNA strand exchange activity. All reactions were carried out in the presence of hRad52 R55A (900 nM), 3′-tailed DNA (no. 117/no. 1; 68.6 nM), and ssDNA (no. 2; 205.8 nM) or RNA (no. 2R; 205.8 nM) as described in Figure 1D and (A). The inverse DNA and RNA strand exchange graphs for WT hRad52 from (B) are shown for comparison. The experiments were repeated at least three times; error bars indicate SD. See also Figure S2.
Figure 3
Figure 3. Different Specificity in Inverse Strand Exchange Promoted by hRad521-209 NTD and yRad59
(A) The reactions were carried out in the presence of hRad521-209 (1 μM), 3′-tailed DNA (no. 117/no. 1; 68.6 nM), and ssRNA (no. 2R; 686 nM) or ssDNA (no. 2; 686 nM) for 1 hr at 37°C; the products were analyzed by electrophoresis in polyacrylamide gels. (B) Graphical representation of the data from (A). (C) Rad59 promotes inverse strand exchange with ssDNA, but not with RNA. To form nucleoprotein complexes, Rad59 (3.5 μM) was incubated with 32P-labeled 3′-tailed DNA (68.6 nM) for 15 min at 37°C. The reactions were initiated by addition of free ssDNA (no. 2, 63-mer; 686 nM) or ssRNA (no. 2R, 63-mer; 686 nM) and carried out for 1 hr; the products were analyzed by electrophoresis in a polyacrylamide gel. (D) The data from (C) are shown as a graph. (E) Rad59 promotes annealing between ssDNA and ssRNA. Top: experimental scheme. Asterisk represents 32P-label. Rad59 (125 nM) was incubated with a 48-mer 32P-labeled ssDNA (no. 65; 5 nM) for 10 min at 30°C. To initiate annealing reactions, complementary 48-mer ssDNA (no. 64; 5 nM) or ssRNA (no. 64R; 5 nM) were added. In controls, protein storage buffer was added instead of Rad59. The products of annealing reactions were analyzed by electrophoresis in polyacrylamide gels. In (A) and (C), asterisks mark traces of ssDNA in tailed dsDNA preparation. The experiments were repeated at least three times; error bars indicate SD. See also Figure S3.
Figure 4
Figure 4. RPA Stimulates Rad52-Promoted Inverse RNA Strand Exchange in a Species-Specific Manner
(A) Experimental scheme. Asterisk represents 32P-label. (B and C) Human RPA (B) inhibits inverse DNA strand exchange, but (C) stimulates inverse RNA strand exchange promoted by hRad52. (D) Yeast RPA does not stimulate inverse RNA strand exchange promoted by hRad52. (E) Yeast RPA stimulates inverse RNA strand exchange promoted by yRad52. (F) hRPA does not stimulate inverse RNA strand exchange promoted by hRad5210-209 NTD (1.4 μM). All reactions were initiated by adding either ssDNA (no. 2; 205.8 nM) or ssRNA (no. 2R; 205.8 nM) that were pre-incubated with RPA (500 nM) to the hRad52-tailed dsDNA (no. 117/no 1; 68.6 nM) complexes. In “no Rad52” or “no protein” controls, Rad52 and RPA were substituted with their storage buffer. The experiments were repeated at least three times; error bars indicate SD.
Figure 5
Figure 5. Rad52 Promotes Inverse RNA or DNA Strand Exchange with Blunt-Ended dsDNA
(A) Experimental scheme. Asterisk represents 32P-label. (B) The kinetics of inverse RNA strand exchange promoted by hRad52 (900 nM) between labeled 63 bp dsDNA substrates (68.6 nM) containing either no ssDNA tail (no. 1/no. 2) or 3′ ssDNA tails of different lengths: 10-nt tail (no. 1/no. 518), 20-nt tail (no. 1/no. 519), and 31-nt tail DNA (no. 1/no. 117). The reactions were initiated by adding ssRNA (no. 2R; 205.8 nM). (C) hRPA (432.2 nM) stimulates inverse strand exchange promoted by hRad52 between blunt-ended dsDNA (no. 1/no. 2; 68.6 nM) and ssRNA (no. 2R; 205.8 nM). (D) The kinetics of inverse DNA strand exchange promoted by hRad52 (900 nM) between dsDNA (68.6 nM) containing either no ssDNA tail (no. 1/no. 2), or 10-nt tail (no. 1/no. 518), 20-nt tail (no. 1/no. 519), and 31-nt tail DNA (no. 1/no. 117) and ssDNA (no.2; 205.8 nM). The experiments were repeated at least three times; error bars indicate SD.
Figure 6
Figure 6. Proposed Mechanism of RNA-Dependent DSB Repair via Rad52 Inverse RNA Strand Exchange
Rad52 forms a complex with DSB ends either blunt ended or minimally processed by exonucleases/helicases, and then promotes inverse RNA strand exchange with homologous RNA transcript. The RNA transcript provides a template for guiding end joining or for a short gap filling synthesis (bridging template mechanism). Short DNA synthesis on RNA templates can be carried out by DNA polymerases, which have limited reverse transcriptase activity, or by reverse transcriptases (Keskin et al., 2014). The single-stranded tails are removed by flap nucleases, the gaps are filled in, and any remaining nicks are sealed by DNA ligases, restoring the original DNA sequence in an error-free manner.

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