Base Excision Repair (BER) in Eukaryotes

What is base excision repair?

Base excision repair (BER) is a fundamental, evolutionarily conserved DNA repair pathway responsible for correcting small, non-helix-distorting base lesions that arise from oxidation, alkylation, deamination and spontaneous base loss. These types of damage are among the most frequent in the genome and are primarily caused by endogenous metabolic byproducts which generate reactive oxygen species (ROS) and spontaneous hydrolytic reactions such as depurination or deamination of cytosine to uracil.

BER acts continuously throughout the cell cycle, detecting and removing damaged or inappropriate bases through a multi-step enzymatic process that restores DNA to its correct sequence. By preserving the chemical integrity of individual nucleotides, BER plays a critical role in maintaining genomic stability, preventing mutagenesis and protecting cells from the onset of aging, cancer and neurodegenerative diseases. In addition to the nuclear genome, BER is also the primary repair pathway in mitochondria, safeguarding mitochondrial DNA from oxidative stress–induced damage.

Short-patch versus long-patch base excision repair

Short-patch and long-patch base excision repair (BER) are two sub-pathways within the BER system. While some pathway components are shared, they differ in others and in the number of nucleotides replaced during repair. Short-patch BER repairs single nucleotide changes with a simple gap-filling process. It is generally faster and is often the default pathway. In contrast, long-patch BER repairs longer stretches of damaged nucleotides (up to approximately 10) with more complex changes and a more involved flap excision process. It may be favored when the lesion affects the sugar-phosphate backbone or when short-patch processing has failed.

Steps in the base excision repair process

The BER process is generally broken down into five steps: recognition and removal of the damaged base or bases, backbone cleavage, end processing, DNA synthesis and finally ligation.

Recognition and removal

In the first and most critical step of the base excision repair process, DNA is scanned by a set of glycosylases that recognize and bind to different types of damaged bases. These damage-specific glycosylases are classified into two major groups: monofunctional glycosylases, such as uracil-DNA glycosylase (UNG), that only have glycosylase activity and bifunctional glycosylases, such as 8-oxoguanine DNA glycosylase-1 (OGG1), that have both glycosylase and AP lyase activity.

Both classes reorient the damaged base out of the helix, a process known as base flipping, breaking the N-gycosidic bond between the base and the backbone, removing the base and generating an abasic site with a missing base but intact sugar-phosphate backbone. Also known as an AP site (apurinic/apyrimidinic site), this intermediate structure will become mutagenic itself if not resolved in the following steps.

Backbone cleavage

In the next step, an endonuclease breaks the phosphodiester bond on the 5’ side of the AP site. In the case of monofunctional glycosylases, APE1 is required, creating a single-stranded break in the backbone that exposes a 5′-deoxyribose phosphate (5′-dRP). In contrast, bifunctional glycosylases use their AP lyase activity to directly nick the backbone, creating a break with modified ends.

End processing

Once the 5′-dRP is exposed, it must be removed. This is accomplished by DNA polymerase β. The modified ends generated by bifunctional glycosylases may require further cleanup by additional enzymes.

DNA synthesis

At this point in the BER process, the damaged base is replaced by DNA synthesis. In the case of short-patch BER, DNA polymerase β fills the gap by inserting a single nucleotide. In contrast, in long-patch BER, DNA polymerase δ or ε replaces a larger series of nucleotide through a process known as strand displacement synthesis. The displaced original strand forms a flap that is subsequently removed by FEN1.

Ligation

In the final step of BER, DNA ligase seals the remaining nick in the DNA backbone, fully restoring the strand. Shore-patch BER primarily utilizes DNA ligase IIIa while long-patch BER primarily utilizes DNA ligase I.

Key proteins involved in the base excision repair pathway

Multiple proteins and complexes are involved in the BER process. Key components include DNA glycosylases, APE1, DNA polymerase, FEN1 and DNA ligase.

DNA glycosylases

Individual DNA glycosylases each recognize a different DNA defect. One example is 8-oxoguanine DNA glycosylase-1 (OGG1) which selectively recognizes and removes 8-oxoguanine, a modified guanine resulting from oxidation caused by reactive oxygen species (ROS). A second example is uracil-DNA glycosylase (UNG) which selectively recognizes and removes uracil when it is mistakenly incorporated in DNA or created by deamination of cytosine.

APE1

Apurinic/Apyrimidinic endonuclease 1 (APE1) is an endonuclease that recognizes and acts on the AP site created by monofunctional glycosylases. It generates a single-stranded break in the DNA backbone, converting it to a structure that allows for DNA resynthesis.

DNA polymerase

DNA polymerases synthesize DNA at AP sites, filling the gap created by damage-detecting glycosylases and APE1. Pol β (DNA polymerase β) fills the single nucleotide gap as part of the short-patch BER pathway. It uses its dRP lyase capability to remove the 5′-dRP group exposed by APE1 cleavage, then, using the undamaged strand as a template, inserts the correct nucleotide. In contrast, Pol δ (DNA polymerase δ) and Pol ε (DNA polymerase ε) are utilized by the large-patch BER pathway. Working in coordination with the sliding clamp PCNA and FEN1, they replace a larger series of nucleotide through strand-displacement synthesis.

FEN1

Flap endonuclease 1 (FEN1) is a key component of the long-patch BER pathway, acting primarily to remove the displaced DNA structure called a flap that forms during strand-displacement synthesis by Pol δ or Pol ε.

DNA ligase

In the final step of the BER pathway, DNA ligases close the remaining gap in the DNA backbone. DNA ligase IIIa acts in short-patch BER, requiring stabilization at the repair site by scaffold protein XRCC1. In contrast, DNA ligase I acts in long-patch BER relying on the sliding clamp PCNA. DNA ligase I does not require XRCC1 and can substitute for DNA ligase IIIa when XRCC1 is absent.

Functional interplay and redundancy

Although BER specializes in small, non-helix-distorting lesions, there is functional overlap with nucleotide excision repair (NER) when bulky adducts are small enough to be recognized by glycosylases, and with mismatch repair (MMR) when lesions occur near replication forks.

Health consequences of dysfunction of the base excision repair system

Defects in BER cause accumulation of damaged bases which leads to propagation of mutations and cellular dysfunction.

Role in genomic instability, mutagenesis and cancer

Absent or defective base excision repair has a direct effect on increasing mutation load. First, when base lesions go unrepaired, they are more likely to mispair during DNA replication, leading to point mutations or small insertions or deletions. Second, when incomplete repair creates unresolved AP sites and strand breaks, the risk of generating double-strand breaks increases significantly.

As genomic instability and mutagenesis increase, cancer predisposition also increases. Mutations in MUTYH and OOG1 glycosylases as well as Pol β are frequently associated with increased risk of cancer including colorectal, lung and breast cancers.

Role in neurodegeneration

With their reliance on high levels of oxygen for energy generation, neurons are particularly vulnerable to oxidative DNA damage. As the major DNA repair pathway of neurons, defects in base excision repair have been identified as important contributing factors in neurodegenerative disorders including Alzheimer’s disease, Parkinson's disease and others.

References

1. Beard WA, Horton JK, Prasad R, Wilson SH. Eukaryotic base excision repair: New approaches shine light on mechanism. Annu Rev Biochem. 2019;88:137–162.
2. Grundy GJ, Parsons JL. Base excision repair and its implications to cancer therapy. Essays Biochem. 2020;64(5):831–843.
3. Leandro GS, Sykora P, Bohr VA. The impact of base excision DNA repair in age-related neurodegenerative diseases. Mutat Res. 2015;776:31–39.