Base Excision Repair Vs Mismatch Repair

DNA, the blueprint of life, is constantly under attack from both internal and external sources. These attacks can lead to various types of DNA damage, which, if left unrepaired, can result in mutations, cell death, and diseases like cancer. To combat this, cells have evolved sophisticated DNA repair mechanisms. Among these, base excision repair (BER) and mismatch repair (MMR) are two crucial pathways that maintain genomic integrity. While both aim to correct DNA errors, they operate on different types of damage and employ distinct mechanisms. Understanding the nuances of each pathway is essential for comprehending how cells safeguard their genetic information.

Introduction to DNA Repair Mechanisms

The stability of the genome is paramount for the survival and proper functioning of all organisms. DNA is susceptible to a range of damages, including:

• Base modifications: Alkylation, oxidation, deamination
• Single-strand breaks: Caused by radiation or chemicals
• Double-strand breaks: More severe, can lead to chromosomal rearrangements
• Mismatched bases: Incorrect base pairings during replication

To address these threats, cells utilize a diverse array of DNA repair pathways. These pathways can be broadly categorized based on the type of damage they repair and the mechanisms they employ. Key DNA repair pathways include:

• Base Excision Repair (BER): Removes damaged or modified single bases.
• Nucleotide Excision Repair (NER): Repairs bulky DNA lesions, such as those caused by UV radiation.
• Mismatch Repair (MMR): Corrects mismatched base pairs and insertion/deletion loops introduced during DNA replication.
• Homologous Recombination (HR): Repairs double-strand breaks using a homologous template.
• Non-Homologous End Joining (NHEJ): Repairs double-strand breaks without a template, often leading to insertions or deletions.

This article focuses on two of these pathways: base excision repair (BER) and mismatch repair (MMR), providing a detailed comparison of their mechanisms, substrates, and biological significance.

Base Excision Repair (BER): Correcting Damaged Bases

BER is a major pathway for removing small, non-helix-distorting base lesions from the genome. These lesions typically arise from oxidation, alkylation, deamination, or spontaneous loss of a base (depurination or depyrimidination). BER is essential for maintaining genomic stability by preventing the accumulation of these damaged bases, which can lead to mutations if left unrepaired.

The BER Pathway: A Step-by-Step Breakdown

The BER pathway involves a series of enzymatic steps, each carefully orchestrated to ensure accurate and efficient repair. The main steps are:

1. Recognition and Removal of the Damaged Base: The first step in BER is the recognition and removal of the damaged base by a DNA glycosylase. Different DNA glycosylases exist, each specific for a particular type of damaged base. For example, UNG (uracil-DNA glycosylase) removes uracil from DNA, which can arise from the deamination of cytosine. MYH glycosylase removes adenine that is mispaired with guanine, a common error caused by oxidative damage. Once the damaged base is recognized, the DNA glycosylase cleaves the N-glycosidic bond, which links the base to the deoxyribose sugar, creating an apurinic/apyrimidinic (AP) site.

2. Incision at the AP Site: The AP site is then recognized by an AP endonuclease (APE1 in mammals), which cleaves the phosphodiester backbone 5' to the AP site. This creates a single-strand break in the DNA.

3. DNA Polymerase Processing: Following incision, a DNA polymerase processes the break to create a suitable substrate for ligation. There are two main sub-pathways of BER, short-patch BER and long-patch BER, which differ in how this step is carried out.

   • Short-Patch BER: In short-patch BER, a single nucleotide is inserted to replace the damaged one. DNA polymerase β (Pol β) is the primary polymerase involved in this sub-pathway. Pol β has both polymerase and dRP lyase activity. The dRP lyase activity removes the 5' deoxyribose phosphate (dRP) group left after the AP endonuclease cleavage. Pol β then inserts the correct nucleotide into the gap.

   • Long-Patch BER: In long-patch BER, several nucleotides are displaced and replaced. This sub-pathway is initiated when Pol β cannot efficiently remove the 5' dRP group. In this case, the flap endonuclease 1 (FEN1) removes the dRP group, and DNA polymerase δ or ε (Pol δ/ε) synthesizes a short stretch of new DNA, displacing the existing strand.

4. Ligation: The final step in BER is the sealing of the nick in the DNA backbone by a DNA ligase. In short-patch BER, DNA ligase IIIα (LigIIIα) forms a complex with XRCC1 to complete the repair. In long-patch BER, DNA ligase I (LigI) is typically involved.

Key Enzymes in BER

• DNA Glycosylases: Recognize and remove specific damaged bases. Examples include UNG, OGG1 (removes 8-oxoguanine), and MYH.
• AP Endonuclease (APE1): Cleaves the DNA backbone at AP sites.
• DNA Polymerase β (Pol β): Primarily involved in short-patch BER; has polymerase and dRP lyase activity.
• Flap Endonuclease 1 (FEN1): Removes the 5' dRP group in long-patch BER.
• DNA Polymerase δ/ε (Pol δ/ε): Involved in DNA synthesis during long-patch BER.
• DNA Ligases (LigI, LigIIIα): Seal the nick in the DNA backbone.
• XRCC1: Scaffold protein that interacts with LigIIIα and other BER proteins.

Regulation of BER

The BER pathway is tightly regulated to ensure efficient and accurate repair. Regulation can occur at multiple levels, including:

• Expression of BER Enzymes: The expression levels of BER enzymes can be regulated by various factors, including stress signals and cell cycle stage.
• Post-translational Modifications: BER proteins can be modified by phosphorylation, ubiquitination, and acetylation, which can affect their activity and interactions.
• Protein-Protein Interactions: The formation of protein complexes is crucial for the efficient execution of BER.

Biological Significance of BER

BER plays a crucial role in maintaining genomic stability and preventing disease. Defects in BER have been linked to increased susceptibility to cancer, neurodegenerative diseases, and aging. For example:

• Mutations in MUTYH (encoding MYH glycosylase) are associated with an increased risk of MUTYH-associated polyposis (MAP), a hereditary colorectal cancer syndrome.
• Defects in APE1 have been implicated in neurodegenerative diseases such as Alzheimer's disease.
• Reduced BER activity has been observed in aged cells, contributing to the accumulation of DNA damage and cellular senescence.

Mismatch Repair (MMR): Ensuring Replication Fidelity

MMR is a highly conserved DNA repair pathway that corrects base-base mismatches and insertion/deletion loops (IDLs) that arise during DNA replication and, to a lesser extent, during recombination. The primary role of MMR is to maintain the fidelity of DNA replication by correcting errors that escape the proofreading activity of DNA polymerases.

The MMR Pathway: A Detailed Process

The MMR pathway is more complex than BER, involving the coordinated action of several proteins. The key steps in MMR are:

1. Mismatch Recognition: The first step in MMR is the recognition of the mismatch by a mismatch recognition complex. In E. coli, the MutS protein recognizes a wide range of mismatches and small IDLs. In eukaryotes, the MutS homologues MSH2 and MSH6 form a heterodimer (MSH2-MSH6, also known as MutSα) that recognizes base-base mismatches and small IDLs. Another heterodimer, MSH2-MSH3 (MutSβ), primarily recognizes larger IDLs.

2. Recruitment of Additional Proteins: Once the mismatch is recognized, the MutS complex recruits other MMR proteins to the site of the mismatch. In E. coli, MutS recruits MutL, which then recruits MutH. In eukaryotes, the MutS complex recruits MLH1-PMS2 (MutLα), MLH1-MLH3 (MutLβ), or MLH1-PSH2 (MutLγ) heterodimers, depending on the specific mismatch and cellular context.

3. Strand Discrimination: A crucial step in MMR is the ability to discriminate between the newly synthesized strand (which contains the error) and the template strand (which is correct). In E. coli, this is achieved through DNA methylation. The template strand is methylated at GATC sequences, while the newly synthesized strand is transiently unmethylated. MutH specifically nicks the unmethylated strand at a GATC site. In eukaryotes, the mechanism of strand discrimination is less well understood but is thought to involve factors associated with the replication machinery, such as proliferating cell nuclear antigen (PCNA), as well as single-strand breaks.

4. Excision of the Mismatch-Containing Strand: After strand discrimination, the mismatch-containing strand is excised. In E. coli, this is accomplished by an exonuclease that degrades the strand from the MutH nick to the mismatch site. In eukaryotes, the excision process is more complex and can involve several exonucleases, including EXO1. The length of the excised strand can vary, ranging from a few nucleotides to several hundred.

5. DNA Synthesis and Ligation: The gap created by the excision is then filled in by a DNA polymerase, using the template strand as a guide. In E. coli, DNA polymerase III is responsible for this step. In eukaryotes, DNA polymerase δ (Pol δ) is the primary polymerase involved. Finally, the nick in the DNA backbone is sealed by a DNA ligase.

Key Enzymes in MMR

• MutS Homologues (MSH2-MSH6, MSH2-MSH3): Recognize mismatches and IDLs.
• MutL Homologues (MLH1-PMS2, MLH1-MLH3, MLH1-PSH2): Coordinate downstream events.
• MutH (in E. coli): Nicks the unmethylated strand at GATC sites.
• Exonucleases (EXO1): Degrade the mismatch-containing strand.
• DNA Polymerase δ (Pol δ): Fills in the gap after excision.
• DNA Ligase: Seals the nick in the DNA backbone.
• PCNA: Involved in strand discrimination in eukaryotes.

Regulation of MMR

The MMR pathway is also tightly regulated to ensure its proper function. Regulation can occur through:

• Expression of MMR Genes: The expression of MMR genes can be affected by various factors, including DNA damage and cell cycle stage.
• Post-translational Modifications: MMR proteins can be modified by phosphorylation, ubiquitination, and SUMOylation, which can affect their activity and interactions.
• Protein-Protein Interactions: The formation of stable MMR complexes is essential for efficient repair.

Biological Significance of MMR

MMR is crucial for maintaining genomic stability and preventing cancer. Defects in MMR are associated with:

• Hereditary Non-Polyposis Colorectal Cancer (HNPCC) or Lynch Syndrome: This is the most common hereditary colorectal cancer syndrome, caused by germline mutations in MMR genes such as MLH1, MSH2, MSH6, and PMS2. Individuals with Lynch syndrome have a high risk of developing colorectal cancer, as well as other cancers, such as endometrial, ovarian, and gastric cancers.
• Microsatellite Instability (MSI): MMR-deficient cells exhibit MSI, which is characterized by changes in the length of microsatellite sequences (short, repetitive DNA sequences). MSI is a hallmark of MMR deficiency and is used as a diagnostic marker for Lynch syndrome and other cancers.
• Increased Mutation Rate: MMR deficiency leads to a dramatic increase in the mutation rate, which can drive tumor development and progression.

Base Excision Repair vs. Mismatch Repair: A Detailed Comparison

While both BER and MMR are essential DNA repair pathways, they differ significantly in their substrates, mechanisms, and biological roles. Here's a detailed comparison:

Overlap and Cross-Talk Between BER and MMR

While BER and MMR are distinct pathways, there is some evidence of overlap and cross-talk between them. For example:

• Processing of Oxidative Damage: Oxidative DNA damage, such as 8-oxoguanine, can be processed by both BER and MMR. OGG1, a DNA glycosylase involved in BER, removes 8-oxoguanine. However, if 8-oxoguanine is mispaired with adenine, the MMR pathway can also be involved in correcting this mismatch.
• Interaction of Repair Proteins: Some studies have suggested that certain BER and MMR proteins can interact with each other, potentially influencing the efficiency of both pathways.
• Coordination in Response to DNA Damage: Both BER and MMR are part of a larger network of DNA damage response pathways. Activation of one pathway can influence the activity of other pathways, leading to a coordinated response to DNA damage.

Future Directions in BER and MMR Research

Research on BER and MMR continues to advance, with ongoing efforts to:

• Identify novel BER and MMR proteins and their functions.
• Elucidate the mechanisms of regulation of BER and MMR.
• Develop new therapeutic strategies targeting BER and MMR for cancer treatment and prevention.
• Understand the role of BER and MMR in aging and age-related diseases.
• Investigate the interplay between BER and MMR with other DNA repair pathways.

Conclusion

Base excision repair (BER) and mismatch repair (MMR) are two critical DNA repair pathways that protect the genome from damage and maintain genomic stability. BER primarily removes damaged or modified single bases, while MMR corrects base-base mismatches and insertion/deletion loops. These pathways differ in their mechanisms, substrates, and biological roles, but both are essential for preventing mutations, cancer, and other diseases. Understanding the intricacies of BER and MMR is crucial for developing new strategies to prevent and treat diseases associated with DNA damage and genomic instability. Future research will undoubtedly continue to shed light on the complexities of these pathways and their importance in maintaining human health.