Mechanisms of Post-Replication DNA Repair

Abstract

Accurate DNA replication is crucial for cell survival and the maintenance of genome stability. Cells have developed mechanisms to cope with the frequent genotoxic injuries that arise from both endogenous and environmental sources. Lesions encountered during DNA replication are often tolerated by post-replication repair mechanisms that prevent replication fork collapse and avert the formation of DNA double strand breaks. There are two predominant post-replication repair pathways, trans-lesion synthesis (TLS) and template switching (TS). TLS is a DNA damage-tolerant and low-fidelity mode of DNA synthesis that utilizes specialized 'Y-family' DNA polymerases to replicate damaged templates. TS, however, is an error-free 'DNA damage avoidance' mode of DNA synthesis that uses a newly synthesized sister chromatid as a template in lieu of the damaged parent strand. Both TLS and TS pathways are tightly controlled signaling cascades that integrate DNA synthesis with the overall DNA damage response and are thus crucial for genome stability. This review will cover the current knowledge of the primary mediators of post-replication repair and how they are regulated in the cell.

Keywords: DNA damage response; DNA damage tolerance; post replication repair; template switching; trans-lesion synthesis.

Figure 1

Many mechanisms efficiently repair DNA damage on the DNA double helix. Lesions in the double stranded DNA can be efficiently repaired by mechanisms corresponding to the specific type of DNA damage. Base-specific damage can be directly reversed by particular enzymes such as photolyases and O6-methylguanine DNA methyltransferase (MGMT) (reviewed in [4]). The majority of base-specific damage is repaired by base excision repair (BER) and nucleotide excision repair (NER). In BER and NER, the damaged base or surrounding DNA is excised from the double stranded DNA. The gap left behind is then filled by a DNA polymerase. Single stranded breaks (SSBs) are recognized by poly(ADP-ribose) polymerase 1 (PARP1), which activates downstream signaling that leads to gap-filling by DNA polymerases. Double stranded breaks (DSBs) are repaired by end joining (EJ) or by homologous recombination (HR). EJ directly ligates the exposed DSB with DNA ligase, while, during HR, break sites are replicated using undamaged homologous sequences of sister chromatid templates. In contrast, DNA lesions in single stranded DNA (ssDNA) cannot be repaired by BER, NER, HR, or EJ and must be remediated using alternative mechanisms (as suggested by the question mark in the figure). Post replication repair is a mechanism specialized in tolerating lesions in single stranded template.

Figure 2

DNA lesions in single stranded DNA (ssDNA) are detrimental to the replication fork. DNA lesions on an ssDNA template act as road blocks for replicative polymerases but not for the replicative DNA helicase. An uncoupling of replicative DNA polymerase and DNA helicase activities generates single stranded DNA tracts. Persistent ssDNA is fragile and prone to breakage, generating lethal DSB.

Figure 3

Post replication repair efficiently returns lesions in ssDNA to double helix. PRR utilizes trans-lesion synthesis (TLS) or template switching (TS) to bypass or avoid DNA lesions and prevent accumulation of ssDNA gaps. After being restored to its double-stranded state, damaged DNA may be repaired via the mechanisms described in Figure 1.

Figure 4

Structure of a monoubiquitinated PCNA ring (picture from reference [22]). (A) Back view of monoubiquitinated PCNA ring showing the two domains of a single PCNA subunit and the inter-domain connecting loop (IDCL). Ubiquitin is shown in red. Three individual PCNA molecules (shown in blue, green, and yellow) constitute the ring shape; (B) Side view of the monoubiquitinated PCNA where the back surface is to the left and the front surface is to the right of the figure. Notice that the ubiquitin is located on the back surface of the PCNA ring while IDCL is to the front side of the PCNA ring.