DNA replication meets genetic exchange: chromosomal damage and its repair by homologous recombination

Abstract

Proceedings of the National Academy of Sciences Colloquium on the roles of homologous recombination in DNA replication are summarized. Current findings in experimental systems ranging from bacteriophages to mammalian cell lines substantiate the idea that homologous recombination is a system supporting DNA replication when either the template DNA is damaged or the replication machinery malfunctions. There are several lines of supporting evidence: (i) DNA replication aggravates preexisting DNA damage, which then blocks subsequent replication; (ii) replication forks abandoned by malfunctioning replisomes become prone to breakage; (iii) mutants with malfunctioning replisomes or with elevated levels of DNA damage depend on homologous recombination; and (iv) homologous recombination primes DNA replication in vivo and can restore replication fork structures in vitro. The mechanisms of recombinational repair in bacteriophage T4, Escherichia coli, and Saccharomyces cerevisiae are compared. In vitro properties of the eukaryotic recombinases suggest a bigger role for single-strand annealing in the eukaryotic recombinational repair.

Figure 1

DNA replication vs. homologous recombination. Chromosomes are shown as double lines. Parental strands are filled; daughter strands are open. (A) A chromosome. (B) Chromosome replication has been initiated. (C) Chromosome replication is nearing completion. (D) Chromosome replication is complete. (E) Strand degradation in preparation for homologous recombination has started. (F) Strand degradation is nearing completion, whereas annealing of the complementary strands is going on.

Figure 2

The pathways of replication fork stalling/disintegration with subsequent resetting/repair. DNA duplexes are shown as double lines; a protein tightly bound to DNA is shown as a bricked circle. For all Holliday junctions, one of the two possible resolution directions is indicated by the small arrows. (A) A replication fork. (B) The replication fork approaching a single-strand interruption in template DNA. (C) The replication fork has collapsed at the interruption. (D) Double-strand end invasion to restore the replication fork structure. (E) A stalled replication fork. (F) Regression of the stalled replication fork forms a double-strand end and a Holliday junction. (G) Double-strand end invasion to restore the replication fork structure. Resolution of the Holliday junction in F leads to replication fork breakage (C). Resolution of the Holliday junctions in D or G, or exonucleolytic degradation of the linear tail in F leads to restoration of the replication fork structure (A).

Figure 3

Two ways to repair a replication fork by single-strand annealing. DNA duplexes are shown as double lines; sister chromatid cohesion is indicated by thin dumbbells. (A) A replication fork approaching a single-strand interruption in template DNA. (B) The replication fork has collapsed. (C) Rad52-promoted reannealing of the detached end with the complementary single-strand gap on the full-length chromatid. (D) Repair of the single-strand interruption. (E) Filling-in the single-strand gap on the full-length chromatid. Sister chromatid alignment is shown. The thin arrows indicate a hypothetical signal from the Rad52-bound double-strand end to the intact sister chromatid. (F) Rad54-catalyzed unwinding of the intact chromatid in the vicinity of the double-strand end. (G) Rad52-catalyzed annealing of the double-strand end with the open sister duplex to generate a replication fork structure.