Base Excision Repair Pathway

Figure1. Base Excision Repair Pathway

Base excision repair pathway overview

Base excision repair (BER) corrects small base lesions that do not significantly distort the DNA helix structure. It is initiated by a DNA glycosylase that recognizes and removes the damaged base, leaving an abasic site which is further processed by short-patch repair or long-patch repair. Short-patch repair or long-patch repair largely uses different proteins to complete BER. BER may take place in nuclei or mitochondria, largely using different isoforms of proteins or genetically distant proteins. For example, the endonucleases apurinic/apyrimidinic site endonuclease 1 (APE1) is highly enriched in nuclei relative to mitochondria while APE2 is enriched in mitochondria.

Scheme of Base Excision Repair Pathway

Figure 2. Scheme of Base Excision Repair Pathway

Base excision repair pathway

  1. Proteins involved in base excision repair
    DNA glycosylases: DNA glycosylases flip the damaged base out of the double helix, and cleave the N-glycosidic bond of the damaged base, leaving an AP site. They are responsible for initial recognition of the lesion in BER process. The evolutionary conservation of glycosylases is largely limited to the enzymatic core domain and mammalian DNA glycosylases have amino- and/or carboxy-terminal extensions that are not found in prokaryotic counterpart. There are two kinds of glycosylases, the monofunctional and the bifunctional. Monofunctional glycosylases only have glycosylase activity, whereas bifunctional glycosylases also possess AP lyase activity. Therefore, bifunctional glycosylases can convert a base lesion into a single-strand break without the need for an additional AP endonuclease. The difference between the AP site of a glycosylase and the AP endonuclease is that the former yields a 3' α, β-unsaturated aldehyde adjacent to a 5' phosphate, named β-Elimination, which differs from the AP endonuclease cleavage product. In addition, some glycosylase-lyases can further convert the 3' aldehyde to a 3' phosphate(δ-elimination). A wide variety of glycosylases recognize different damaged bases. Examples of DNA glycosylases include Ogg1(recognizes 8-oxoguanine), Mag1(which recognizes 3-methyladenine), and UNG (removes uracil from DNA).
    AP endonucleases: Apurinic/apyrimidinic (AP) endonucleases play inportant roles in the repair of damaged or mismatched nucleotides in DNA to create a nick in the phosphodiester backbone of the AP site created after DNA glycosylase removes the damaged base. There are two kinds of AP endonucleases in humans, APE1 and APE2. APE1 is considered to be the major AP endonuclease in human cells. It exhibits robust AP-endonuclease activity, which accounts for >95% of the total cellular activity. Mg2+ is requested in its active site in order to carry out its role in base excision repair. APN1 is the homolog of this enzyme in the yeast.
    End processing enzymes: Polynucleotide kinase-phosphatase (PNKP) promotes formation of hydroxyl on its 3' end and a phosphate on its 5' end during BER. Its phosphatase domain removes phosphates from 3' ends and the kinase domain phosphorylates 5' hydroxyl ends. Together, these activities are ready for single-strand breaks with damaged termini for further ligation. DNA polymerases: Enzymes synthesize DNA molecules from deoxyribonucleotides, the building blocks of DNA. These enzymes are essential for DNA replication and usually work in pairs to create two identical DNA strands from a single original DNA molecule. During this process, DNA polymerase "reads" the existing DNA strands to create two new strands that match the existing ones.
    Flap endonuclease: A class of nucleolytic enzymes that act as both 5'-3' exonucleases and structure-specific endonucleases on specialised DNA structures. The later role functions during the biological processes of DNA replication, DNA repair, and DNA recombination. The endonuclease activity of FENs was initially identified as acting on a DNA duplex which has a single-stranded 5' overhang on one of the strands (termed a "5' flap", hence the name flap endonuclease). FENs catalyse hydrolytic cleavage of the phosphodiester bond at the junction of single- and double-stranded DNA.
    DNA ligase: It is used for both DNA repair and DNA replication. DNA ligase catalyzes the formation of a phosphodiester bond to facilitate the joining of DNA strands together. It usually plays a role in repairing single-strand breaks in duplex DNA in living organisms, but some forms (such as DNA ligase IV) may specifically repair double-strand break.
  2. long-patch and short-patch repair
    After initiation of BER by a DNA glycosylase, further processing may take place by “short patch” BER or by long-patch BER. “Short patch” BER, is also called “single-nucleotide BER”, in which a single nucleotide gap is generated and subsequently filled and ligated, whereas in long-patch BER, a gap of 2–10 nucleotides is generated and filled. Short-patch BER requires several repair-specific proteins that do not participate in replication and is equally efficient in proliferating and nonproliferating cells. Long-patch repair mainly occurs in proliferating cells and replication proteins are used to a large extent for treatment after glycosylase action and strand cleavage by APE1. The major core proteins required in the different steps in short-patch repair are an initiating DNA glycosylase, AP-endonuclease APE1, DNA polymerase b (Pol β), and DNA ligase I or III (LIG1/3). These include DNA polymerase δ/ε, PCNA, FEN1, and LIG1.
    Base Excision Repair Pathway and disease
    Defects in a BER lead to cancer. Deletion mutations in BER genes have been shown to result in a higher mutation rate in a variety of organisms. Mutations in the DNA glycosylase MYH are known to increase susceptibility to colon cancer. In fact, somatic mutations in Pol β have been found in 30% of human cancers, and some of these mutations lead to transformation when expressed in mouse cells. In many cases, if the damage is not repaired, the cell may resort to induction of apoptosis or necrosis. Thus, many DNA-damaging agents are used in cancer therapy to induce apoptosis of tumor cells. Multiple factors (such as telomere shortening, hormone levels and multiple targets of ROS), can contribute to aging and life span, making it difficult to establish a direct role of the BER enzymes in counteracting aging. In addition, studies have shown that defects in several BER enzymes shorten chronological life span in yeast. BER potentially has a number of promising targets for improving cancer therapy. Thus, it is quite clear that a better understanding of the molecular defects of the individual cancers is required for developing an effective therapy.


  1. Hans E. Krokan and Magnar Bjørås. Base Excision Repair. Cold Spring Harb Perspect Biol. 2013, 5(4): a012583.
  2. Weissman L, et al. Defective DNA base excision repair in brain from individuals with Alzheimer's disease and amnestic mild cognitive impairment, Nucleic Acids Res. 2007, 35(16):5545-55.
  3. Maynard S, et al. Base excision repair of oxidative DNA damage and association with cancer and aging. Carcinogenesis. 2009 Jan;30(1):2-10.
  4. Alfonso Bellacosaa, and Alexander C. Drohatb. Role of base excision repair in maintaining the genetic and epigenetic integrity of CpG sites.DNA Repair (Amst). 2015, 32: 33–42.

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