Base Excision Repair Pathway: How Cells Fix DNA Damage

Cells constantly face DNA damage from environmental factors and normal metabolic processes. If left unrepaired, these lesions can lead to mutations that contribute to aging and disease. To maintain genome stability, cells rely on various repair mechanisms, one of which is the base excision repair (BER) pathway.

This system targets small, non-helix-distorting base modifications caused by oxidation, alkylation, or deamination. BER ensures damaged bases are removed and replaced without compromising DNA structure.

Key Glycosylases

The BER pathway depends on DNA glycosylases to identify and remove damaged bases. Each glycosylase recognizes specific lesions from oxidative stress, alkylation, or hydrolytic reactions. By cleaving the N-glycosidic bond between the altered base and the sugar-phosphate backbone, glycosylases initiate repair, leaving behind an abasic (AP) site for further processing.

8-oxoguanine DNA glycosylase (OGG1) plays a crucial role in counteracting oxidative damage. Reactive oxygen species (ROS) frequently modify guanine, forming 8-oxoguanine (8-oxoG), which mispairs with adenine during replication, increasing the risk of G:C to T:A transversions. OGG1 excises 8-oxoG, preventing mutagenic consequences. OGG1-deficient mice show increased susceptibility to tumorigenesis, highlighting its role in genome maintenance (Klungland & Bjelland, 2007, Oncogene).

Uracil DNA glycosylase (UNG) removes uracil residues resulting from cytosine deamination or misincorporation of dUMP during replication. Uncorrected uracil can lead to G:C to A:T transition mutations, common in cancerous cells. UNG functions in both nuclear and mitochondrial DNA, ensuring broad protection against uracil-induced mutagenesis. Deficiencies in UNG activity are linked to immunodeficiency syndromes (Kavli et al., 2002, EMBO J).

Alkyladenine DNA glycosylase (AAG), also called methylpurine DNA glycosylase (MPG), recognizes alkylated bases such as 3-methyladenine and 7-methylguanine, which result from environmental carcinogens like tobacco smoke. AAG’s broad substrate specificity allows it to counteract alkylating agents used in chemotherapy, making it essential for both cellular defense and therapeutic resistance (O’Brien & Ellenberger, 2004, J Biol Chem).

Steps Of The Repair Process

Once a glycosylase removes a damaged base, BER proceeds through a series of steps to restore DNA integrity. These include processing the abasic site, filling the gap with the correct nucleotide, and sealing the strand.

Damaged Base Recognition

DNA glycosylases scan the DNA helix for structural irregularities and flip the altered base into their active site for verification. If the lesion is confirmed, the glycosylase cleaves the N-glycosidic bond, releasing the damaged base and leaving an abasic (AP) site. The specificity of glycosylases ensures only aberrant bases are removed, minimizing unnecessary disruptions.

Structural studies show glycosylases use a base-flipping mechanism to access lesions buried within DNA (Fromme & Verdine, 2004, Adv Protein Chem). This is particularly important for detecting oxidative lesions like 8-oxoguanine, which can evade standard proofreading mechanisms. Some glycosylases, such as OGG1, exhibit rapid excision kinetics, while others, like AAG, display broader specificity but slower turnover rates, influencing overall repair dynamics.

AP Site Cleavage

After base removal, the abasic site must be processed for repair. AP endonuclease 1 (APE1) cleaves the phosphodiester backbone at the AP site, generating a single-strand break with a 3′-hydroxyl and a 5′-deoxyribose phosphate (dRP) terminus. APE1 is the primary AP endonuclease in human cells, ensuring efficient processing of abasic sites (Tell et al., 2009, Antioxid Redox Signal).

APE1 activity is tightly regulated to prevent excessive strand breaks, which could destabilize the genome. In addition to its endonuclease function, APE1 has redox activity that modulates transcription factors involved in stress responses. Mutations or deficiencies in APE1 increase sensitivity to DNA-damaging agents and raise the risk of neurodegenerative disorders.

Gap Filling

After AP site cleavage, DNA polymerase β (Pol β) inserts the correct nucleotide. This enzyme also removes the 5′-dRP group left by APE1 before adding the appropriate base. Pol β is the primary polymerase in short-patch BER, replacing a single nucleotide, while long-patch BER involves multiple nucleotides inserted by replicative polymerases such as Pol δ or Pol ε (Beard & Wilson, 2006, Chem Rev).

Pol β’s fidelity is crucial for genome stability, as errors during gap filling introduce mutations. Structural studies show Pol β undergoes conformational changes to ensure correct base pairing before catalysis. Deficiencies in Pol β activity are linked to increased mutagenesis and cancer susceptibility.

Ligation

The final step in BER is sealing the DNA strand break. In short-patch BER, DNA ligase III, in complex with XRCC1, forms a phosphodiester bond between the newly inserted nucleotide and the existing DNA strand. XRCC1 acts as a scaffold protein, coordinating Pol β and ligase III (Caldecott, 2003, DNA Repair). In long-patch BER, DNA ligase I performs ligation, working with proliferating cell nuclear antigen (PCNA) to process longer repair tracts.

Proper ligation restores DNA continuity and prevents strand breaks that could lead to chromosomal instability. Mutations in ligase III or XRCC1 are associated with increased sensitivity to DNA damage and neurological disorders.

Coordination With Other Repair Pathways

BER does not function in isolation; it operates within a broader network of DNA repair mechanisms. When lesions exceed BER’s capacity or involve complex damage, nucleotide excision repair (NER), mismatch repair (MMR), and homologous recombination (HR) provide complementary functions.

BER and NER overlap in repairing oxidative and alkylation-induced lesions. While BER primarily handles small modifications, bulky adducts or lesions that stall replication may require NER. Oxidative damage to guanine can form cyclopurine lesions, which distort DNA structure and are preferentially removed by NER (Kuraoka et al., 2000, J Biol Chem). Damage recognition proteins, such as XPC, help direct lesions toward the appropriate repair pathway.

Mismatch repair (MMR) also interacts with BER in handling replication-associated errors. MMR proteins like MutSα (MSH2-MSH6 complex) recognize oxidative damage and initiate BER-mediated repair (Colussi et al., 2002, Proc Natl Acad Sci USA). This coordination is crucial in dividing cells, where replication errors and oxidative stress frequently coincide.

If BER-induced single-strand breaks persist, homologous recombination (HR) or non-homologous end joining (NHEJ) may be recruited to resolve more extensive damage. Persistent abasic sites or strand breaks can lead to replication fork collapse, requiring HR-mediated repair. PARP1 acts as a sensor of single-strand breaks, facilitating repair factor recruitment and linking BER to broader DNA damage responses (Caldecott, 2008, Nat Rev Mol Cell Biol). The choice between HR and NHEJ depends on the cell cycle phase and availability of a homologous template.

Connection To Disease

Defects in BER contribute to genomic instability and disease, particularly cancer and neurodegenerative disorders. Since BER corrects oxidative, alkylation, and deamination-induced DNA lesions, its failure leads to mutation accumulation.

Mutations in DNA glycosylases, such as OGG1 and MUTYH, are linked to colorectal and lung cancers. These enzymes correct oxidative guanine lesions that drive mutagenesis. Individuals with biallelic MUTYH mutations develop MUTYH-associated polyposis (MAP), significantly increasing colorectal cancer risk.

Beyond cancer, BER deficiencies contribute to neurodegenerative diseases, where oxidative damage is especially harmful due to high neuronal metabolic activity. Impaired AP endonuclease 1 (APE1) function is associated with amyotrophic lateral sclerosis (ALS) and Parkinson’s disease. Neurons rely on BER to counteract oxidative stress from mitochondrial activity, and dysfunction accelerates neuronal loss. Reduced APE1 expression correlates with increased DNA strand breaks in Alzheimer’s patients, implicating BER failure in disease progression.