End-resection at DNA double-strand breaks in the three domains of life

Abstract

During DNA repair by HR (homologous recombination), the ends of a DNA DSB (double-strand break) must be resected to generate single-stranded tails, which are required for strand invasion and exchange with homologous chromosomes. This 5'-3' end-resection of the DNA duplex is an essential process, conserved across all three domains of life: the bacteria, eukaryota and archaea. In the present review, we examine the numerous and redundant helicase and nuclease systems that function as the enzymatic analogues for this crucial process in the three major phylogenetic divisions.

Figure 1. End-resection of DSBs in the three domains of life

(A) The bacterial RecBCD pathway (E. coli). (i) DNA end recognition by the RecBCD helicase–nuclease complex. (ii) The two DNA strands are translocated separately by the helicases RecD (green, 5′–3′ polarity) and RecB (orange, 3′–5′ polarity). The nuclease domain is located at the C-terminus of RecB. Before encountering a Chi site, the 3′ strand is cleaved more frequently than the 5′ strand. A loop of single-stranded DNA accumulates ahead of RecB, as a result of the higher translocation rate of RecD. (iii) After Chi recognition by the RecC subunit (blue), the nuclease activity of the complex is stimulated on the 5′ strand and suppressed on the 3′ strand. RecB mediates RecA loading on to the resulting 3′ single-stranded DNA tail. (B) The eukaryotic Dna2–Sgs1 complex pathway (S. cerevisiae). (i) DNA end recognition and limited processing by the MRX complex (Mre11, green; Rad50, red; Xrs1, orange; Sae2, purple). (ii) MRX recruits the Sgs1 helicase (light green, in complex with Top3-Rmi1) to the DSB end. Extensive end-resection is performed by the Dna2 exonuclease (blue) in association with the Sgs1 helicase, or is alternatively processed by the Exo1 nuclease (not shown). RPA bound to the unwound single–strands stimulates Dna2 activity on the 5′ strand, and inhibits 3′ strand degradation (inset). (iii) RPA is subsequently replaced by the Rad51 recombinase on the 3′ tail. (C) The archaeal HerA–NurA helicase–nuclease pathway (S. solfataricus). (i) Operon encoding the herA, mre11, rad50 and nurA genes. (ii) Either one or two strands of the duplex can pass through the core of the complex, resulting in either the single-stranded resection (right), or wholesale destruction of both strands (left). NurA dimer (blue); HerA hexamer (green). Mre11 and Rad50 may be involved in the initial processing of the break and the recruitment of HerA–NurA.