Rescue of arrested replication forks by homologous recombination

Abstract

DNA synthesis is an accurate and very processive phenomenon; nevertheless, replication fork progression on chromosomes can be impeded by DNA lesions, DNA secondary structures, or DNA-bound proteins. Elements interfering with the progression of replication forks have been reported to induce rearrangements and͞or render homologous recombination essential for viability, in all organisms from bacteria to human. Arrested replication forks may be the target of nucleases, thereby providing a substrate for doublestrand break repair enzyme. For example in bacteria, direct fork breakage was proposed to occur at replication forks blocked by a bona fide replication terminator sequence, a specific site that arrests bacterial chromosome replication. Alternatively, an arrested replication fork may be transformed into a recombination substrate by reversal of the forked structures. In reversed forks, the last duplicated portions of the template strands reanneal, allowing the newly synthesized strands to pair. In bacteria, this reaction was proposed to occur in replication mutants, in which fork arrest is caused by a defect in a replication protein, and in UV irradiated cells. Recent studies suggest that it may also occur in eukaryote organisms. We will review here observations that link replication hindrance with DNA rearrangements and the possible underlying molecular processes. Large genome rearrangements, such as duplications, deletions, translocations and insertions, are mainly catalyzed by three classes of molecular processes that differ by length of homology of the joined sequences. Recombination events formed by joining of homologous sequences are mediated by specific enzymes. The key enzyme, RecA in prokaryotes and RecAhomologues in eukaryotes, catalyzes the strand exchange reaction and is highly conserved from bacteria to human (1, 2). A second type of recombination, called illegitimate, is characterized by the joining sequences whose length is below the minimal length required for recognition of homology by RecA (Minimal Efficient Processing Segment, or MEPS). In prokaryotes, illegitimate recombination can result from simple ligation of unrelated sequences (reviewed in ref.3). In eukaryotes, this process is promoted by a battery of specialized enzymes and is called nonhomologous end-joining (NHEJ; reviewed in refs. 4 and 5). In addition, recombination between tandemly repeated sequences forms a distinct class of events that may be catalyzed by several specific pathways (reviewed in ref. 6). All classes of DNA rearrangements are important in human health, as they may cause cancers (reviewed in ref. 7) or hereditary disorders (reviewed in refs. 8 and 9) and are important in evolution (ref. 10; reviewed in ref. 11). All classes of rearrangements can result from the formation and repair of DNA double-strand breaks (DSBs) and have been shown to occur at an increased frequency in DNA regions difficult to replicate or when DNA replication is affected by a mutation. The correlation between replication hindrance and rearrangem...

Base Excision Repair Intermediates Induce p53-independent Cytotoxic and Genotoxic Responses

“…However, once BER is initiated, damage-specific glycosy- lases give rise to accumulation of ␤-pol substrates (5Ј-dRP). 5Ј-dRP causes a complete block to replication fork progression and possibly induces fork regression and resolution by BLM and WRN (40,46). ␤-pol deficiency therefore results in an increase in damage-induced recombination and toxicity in a p53-independent and mismatch DNA repair-independent mechanism.…”

“…Recombination-DNA damage-induced arrest of the replication fork may be overcome by homologous recombination mechanisms of lesion avoidance (46,47). Since ␤-pol substrates or BER intermediates (5Ј-dRP) block replication (Fig.…”

Long CTG·CAG Repeats from Myotonic Dystrophy Are Preferred Sites for Intermolecular Recombination

“…Hence, we propose a model wherein the stalling of the replication fork at the secondary structures leads to nicks and/or double-strand breaks in the repeating tract. Discontinuities in the duplex right-handed B-DNA structure inhibit replication fork progression or cause its collapse (78,79), and stalled replication forks induce DNA repair and recombination (78,80,81). The recombination proteins may then be recruited to the TRS loci due to the affinity of these proteins to unusual secondary structures or to the strand discontinuities.…”

Genetic interactions between RAD51 and its paralogues for centrosome fragmentation and ploidy control, independently of the sensitivity to genotoxic stresses

“…One hypothesis is that few or spontaneous damages would be enough to generate centrosome fragmentation (a very low threshold), whereas sensitivity would require a higher amount of damages per cells (a high threshold). HR is also an efficient way to resume replication that has been stalled (Cox et al, 2000;Michel et al, 2001). Moreover, XRCC3 and RAD51 have been shown to be required for replication on DNA matrix bearing damage (Henry-Mowatt et al, 2003).…”