Base Excision Repair And Nucleotide Excision Repair

Base Excision Repair (BER) and Nucleotide Excision Repair (NER): The Cellular Guardians Against DNA Damage

DNA, the blueprint of life, is constantly under assault from endogenous and exogenous sources. From the reactive oxygen species generated during normal metabolism to the damaging effects of UV radiation and environmental toxins, our genetic material faces a barrage of threats daily. Fortunately, cells have evolved sophisticated DNA repair mechanisms to counteract this damage and maintain genomic integrity. Two crucial pathways are Base Excision Repair (BER) and Nucleotide Excision Repair (NER), both vital for preventing mutations, cancer, and other deleterious consequences. This article will delve into the intricate details of these two pathways, highlighting their similarities, differences, and the critical roles they play in cellular health.

Understanding DNA Damage: A Primer

Before diving into the repair mechanisms, it's crucial to understand the types of DNA damage they address. DNA damage encompasses a wide spectrum of alterations, including:

• Base damage: This involves chemical modifications to individual DNA bases, often caused by oxidation, alkylation, or deamination. Examples include 8-oxoguanine (8-oxoG), a common oxidative lesion, and uracil, which arises from cytosine deamination.

• Single-strand breaks (SSBs): These are breaks in the phosphodiester backbone of a single DNA strand. They can be caused by various factors, including ionizing radiation and enzymatic processes.

• Double-strand breaks (DSBs): These are more severe breaks involving both DNA strands. DSBs are highly cytotoxic and can lead to genomic instability if not repaired correctly. They are often caused by ionizing radiation or certain chemotherapeutic agents.

• Bulky DNA adducts: These are large chemical modifications attached to DNA bases, often resulting from exposure to environmental mutagens like polycyclic aromatic hydrocarbons (PAHs) or UV radiation. These adducts distort the DNA helix and hinder replication and transcription.

Base Excision Repair (BER): The Specialist for Small Lesions

BER is the primary pathway for repairing small, non-helix-distorting base lesions. It's a highly versatile pathway that targets a diverse range of base modifications. The process involves several key steps:

1. DNA Glycosylase Recognition and Cleavage:

The BER pathway initiates with a DNA glycosylase, a family of enzymes that recognize and remove damaged bases. Each glycosylase is specific for a particular type of base lesion. The glycosylase flips the damaged base out of the DNA helix, cleaves the N-glycosidic bond linking the base to the sugar, creating an apurinic/apyrimidinic (AP) site.

2. AP Endonuclease Activity:

The AP site, a sugar residue lacking a base, is then processed by an AP endonuclease. This enzyme cleaves the phosphodiester backbone adjacent to the AP site, creating a nick in the DNA strand. Different types of AP endonucleases exist, each with slightly differing cleavage specificities.

3. DNA Polymerase β Action:

DNA polymerase β, a specialized polymerase, plays a crucial role in BER. It removes the 5'-deoxyribose phosphate (dRP) residue left behind after AP endonuclease action. It then synthesizes a new DNA strand, filling in the gap created by the removed base.

4. DNA Ligase Sealing:

Finally, DNA ligase seals the nick in the DNA backbone, completing the repair process. This results in the restoration of the original DNA sequence. The short-patch BER pathway only involves one nucleotide replacement; the long-patch pathway involves several nucleotides.

Key Enzymes in BER:

• DNA Glycosylases: A family of enzymes, each specific to a particular base lesion.
• AP Endonucleases: Cleave the DNA backbone at AP sites.
• DNA Polymerase β: Fills the gap created by base removal.
• DNA Ligase: Seals the nick in the DNA strand.

Nucleotide Excision Repair (NER): The Heavy Lifter for Bulky Lesions

NER is a more complex pathway designed to remove bulky DNA lesions that distort the DNA helix, such as those caused by UV radiation or environmental mutagens. It's crucial for repairing DNA damage that would otherwise block replication or transcription. The NER pathway is divided into two sub-pathways: global genome NER (GG-NER) and transcription-coupled NER (TC-NER).

Global Genome NER (GG-NER):

GG-NER is responsible for repairing lesions throughout the genome. The process involves several steps:

1. Damage Recognition: A complex of proteins, including XPC and RAD23B, scans the DNA for distortions. The complex recognizes the helical distortion caused by the bulky adduct.

2. DNA unwinding: TFIIH, a multi-subunit complex with helicase activity, unwinds the DNA around the lesion, creating a single-stranded bubble.

3. Incision: Two endonucleases, XPF and XPG, make incisions flanking the lesion, creating a short single-stranded DNA fragment containing the damage.

4. Excision: The damaged DNA fragment is released.

5. Resynthesis and ligation: DNA polymerase and DNA ligase fill the gap and ligate the newly synthesized DNA.

Transcription-Coupled NER (TC-NER):

TC-NER prioritizes the repair of lesions that block transcription. RNA polymerase II stalls at the lesion, recruiting repair factors like CSA and CSB. These proteins recruit other NER proteins to the site, initiating the repair process much like GG-NER, but with a faster response time.

Key Enzymes in NER:

• XPC-RAD23B complex: Recognizes DNA damage.
• TFIIH: Unwinds DNA around the lesion.
• XPF and XPG: Endonucleases that incise the DNA.
• DNA polymerases: Fill the gap.
• DNA ligase: Seals the nick.
• CSA and CSB: Crucial for TC-NER.

Comparing BER and NER: Similarities and Differences

While both BER and NER are vital DNA repair pathways, they differ significantly in their mechanisms and the types of damage they target:

Clinical Significance of BER and NER Defects

Defects in BER and NER pathways are associated with various human diseases. Mutations in genes encoding BER proteins can lead to increased sensitivity to certain genotoxins and an elevated risk of cancer. Similarly, defects in NER genes cause genetic disorders such as xeroderma pigmentosum (XP), Cockayne syndrome (CS), and trichothiodystrophy (TTD). These disorders are characterized by increased sensitivity to UV radiation, neurological abnormalities, and premature aging.

Conclusion: The Essential Role of DNA Repair

BER and NER are essential DNA repair pathways, crucial for maintaining genomic stability and preventing disease. They employ distinct yet efficient mechanisms to combat a wide range of DNA damage, safeguarding the integrity of our genetic information. Understanding the intricacies of these pathways provides valuable insights into human health and disease, paving the way for the development of novel therapeutic strategies for cancer and other genetic disorders. Further research continues to unravel the complexities of these fascinating processes, promising further advances in our understanding of DNA repair and its crucial role in life.