Mechanisms of damage tolerance and repair during DNA replication

Abstract

Accurate duplication of chromosomal DNA is essential for the transmission of genetic information. The DNA replication fork encounters template lesions, physical barriers, transcriptional machinery, and topological barriers that challenge the faithful completion of the replication process. The flexibility of replisomes coupled with tolerance and repair mechanisms counteract these replication fork obstacles. The cell possesses several universal mechanisms that may be activated in response to various replication fork impediments, but it has also evolved ways to counter specific obstacles. In this review, we will discuss these general and specific strategies to counteract different forms of replication associated damage to maintain genomic stability.

Figure 1.

General strategies to bypass and repair DNA damage during replication. (A) A DNA lesion (black triangle) on the leading strand stops replication fork movement. (B) The DNA damage leads to the functional uncoupling of DNA polymerases and the replicative helicase, since the helicase can bypass the lesion without association with the polymerase. Several pathways are employed to bypass or repair the damage through (C) lesion skipping, where repriming occurs downstream the lesion; (D) template switching, where the newly synthesized DNA strand is used as the template; (E) fork reversal, where the nascent strands reanneal, giving the chance for DNA repair pathways to remove the damage without collapsing the replication fork; (F) or translesion synthesis, where specialized TLS polymerases temporarily replace the replicative polymerases to bypass the lesion.

Figure 2.

Genomic ribonucleotide repair and bypass during replication. (A) DNA polymerases incorporate ribonucleotides (blue ‘R’) during replication which can be bypassed, removed by ribonucleotide excision repair (RER), or processed by topoisomerase I (TOP1). (B) Left unrepaired, a replication fork would encounter a ribonucleotide in the template strand. The replicative DNA polymerases are inefficient in bypassing template ribonucleotides, leading to replication stress. In this case, translesion synthesis (TLS) or template switching (TS) are activated to bypass the ribonucleotides to complete replication. (C) During RER, RNase H2 incises 5′ to the embedded ribonucleotide, DNA polymerase δ generates a flap which is nucleolytically processed by FEN1, followed by ligation, leading to error-free repair. (D) In the absence of RER, TOP1 mediates the removal of genomic ribonucleotides. TOP1 incises 3′ to the embedded ribonucleotide. Then, nucleophilic attack by the 2′-OH group on the ribose generates a 2′,3′-cyclic phosphate and releases TOP1. The 2′,3′-cyclic phosphate can be reversed by TOP1 or removed by a second TOP1 cleavage, or by various nucleases. Alternatively, the trapped TOP1 can be removed in a manner which may lead to a small deletion, or via TDP1 in an error-free manner.

Figure 3.

DNA–protein crosslink (DPC) repair and bypass during replication. (A) A DPC blocks replication fork progression. The repair of the DPC begins with proteolysis of the DPC by various proteases. (B) The repair of topoisomerase induced DPCs is a special case, because TOP-DPCs are flanked by a single strand break (SSB) or double strand break (DSB), in case of topoisomerase I and II, respectively. The collision of the replication fork with trapped topoisomerases will eventually lead to a DSB by ‘replication run-off’. For simplicity, only the collision of replication fork with topoisomerase I-induced DPC is depicted here. After proteolysis, the peptide-DNA crosslink can be removed by TDP1 or nucleases. The resulting DSB is repaired by homologous recombination (HR) to induce fork restart and progression. Although not depicted here, the replication fork can avoid the collision with trapped topoisomerases and the generation of DSB by inducing fork reversal ahead of the DPC. (C) For all forms of DPCs, the remaining peptide–DNA crosslink can be bypassed by translesion synthesis (TLS), and subsequently removed by nucleotide excision repair.

Figure 4.

Interstrand crosslink (ICL) repair during replication. (A) The mechanism of ICLs repair depends on the type of ICL. While the Fanconi anemia (FA) pathway is the general mechanism to repair most forms of ICLs during replication, other repair mechanisms have evolved to repair specific types of ICLs. All ICL repair mechanisms require the conversion of replication forks. The E3 ligase, TRAIP, functions to regulate different repair pathways by controlling CMG ubiquitination. (B) Extensive ubiquitination of CMG by TRAIP lead to the CMG unloading, which is an essential step to activate the FA pathway. FA pathway regulates the incision of ICLs by nucleases, then activates translesion synthesis (TLS) to bypass the adduct, which is subsequently removed by nucleotide excision repair. The double strand break (DSB) at one strand is repaired by homologous recombination (HR), using the other strand as the template. (C) In the case of abasic (AP)-ICL and psoralen-ICL, TRAIP adds short ubiquitin chains on CMG that channels the damage to NEIL3, which incises the ICL without inducing a DSB. TLS bypasses the adduct and the AP site. (D) In case of acetaldehyde-ICL (AA-ICL), another mechanism has been recently identified that acts to bypass this lesion. The role of TRAIP or specific enzymes that incise this type of ICL is unknown. This repair pathway does not induce DSB or an AP site intermediate. All ICL repair converges through TLS bypass of the adduct to complete the repair in an error-prone manner.