DNA damage is a constant threat to our genetic material. From everyday cellular processes to environmental factors, our DNA faces numerous challenges. This section explores the various types of DNA damage and the intricate repair mechanisms cells employ to maintain genomic integrity.
Understanding DNA damage and repair is crucial for grasping how cells preserve their genetic information. These processes play vital roles in preventing mutations, cancer, and aging, highlighting the importance of DNA maintenance in overall cellular health.
DNA Damage Types and Causes
Endogenous and Exogenous Sources of DNA Damage
- DNA damage occurs through endogenous sources (cellular processes) or exogenous sources (environmental factors) leading to various DNA lesions
- Endogenous sources include reactive oxygen species from cellular metabolism and spontaneous hydrolysis of DNA
- Exogenous sources encompass ultraviolet (UV) radiation, ionizing radiation, and chemical mutagens (cigarette smoke)
Chemical Modifications and Structural Alterations
- Base modifications alter the chemical structure of nucleotides potentially causing mutations
- Oxidation transforms guanine to 8-oxoguanine, which can mispair with adenine
- Alkylation adds methyl or ethyl groups to bases (O6-methylguanine)
- Deamination converts cytosine to uracil, changing base-pairing properties
- Single-strand breaks (SSBs) and double-strand breaks (DSBs) disrupt the DNA backbone
- SSBs often result from oxidative damage or aborted topoisomerase activity
- DSBs can be caused by ionizing radiation or certain chemotherapeutic agents (etoposide)
- Pyrimidine dimers form by UV radiation distorting the DNA helix
- Cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts are common UV-induced lesions
- These dimers interfere with replication and transcription by blocking polymerase progression
Complex DNA Lesions and Replication Errors
- DNA-protein crosslinks occur when proteins become covalently bound to DNA
- Induced by certain chemotherapeutic agents (cisplatin) or ionizing radiation
- Interfere with DNA metabolism and can lead to replication fork collapse
- Interstrand crosslinks (ICLs) form covalent bonds between opposite DNA strands
- Caused by bifunctional alkylating agents (nitrogen mustards) or psoralen plus UV light
- Prevent strand separation during replication and transcription, highly toxic to cells
- Incorrect nucleotide incorporation during DNA replication leads to base mismatches
- Can result from polymerase errors or presence of damaged or modified bases
- If left unrepaired, mismatches can lead to point mutations in subsequent replication cycles
DNA Repair Mechanisms
Excision Repair Pathways
- Base excision repair (BER) removes and replaces damaged bases
- DNA glycosylases recognize and excise specific types of damaged bases (uracil-DNA glycosylase removes uracil)
- Short-patch BER replaces a single nucleotide, while long-patch BER replaces 2-10 nucleotides
- Nucleotide excision repair (NER) removes bulky DNA lesions
- Global genomic NER (GG-NER) surveys the entire genome for helix-distorting lesions
- Transcription-coupled NER (TC-NER) specifically repairs lesions in actively transcribed genes
- NER involves damage recognition, dual incision, excision of a 24-32 nucleotide patch, gap-filling synthesis, and ligation
Double-Strand Break Repair
- Homologous recombination (HR) uses a homologous template for accurate DSB repair
- Primarily active in S and G2 phases when sister chromatids are available
- Involves end resection, strand invasion, DNA synthesis, and resolution of Holliday junctions
- Non-homologous end joining (NHEJ) directly ligates broken DNA ends without a template
- Active throughout the cell cycle, but can introduce small insertions or deletions
- Key proteins include Ku70/80, DNA-PKcs, and DNA ligase IV
Specialized Repair Mechanisms
- Direct reversal repair mechanisms reverse specific types of DNA damage
- Photolyase uses light energy to directly reverse pyrimidine dimers (not present in placental mammals)
- O6-methylguanine-DNA methyltransferase (MGMT) removes alkyl groups from O6-position of guanine
- Translesion synthesis (TLS) allows replication to proceed past DNA lesions
- Utilizes specialized polymerases (Pol η, Pol κ, Pol ι, and Rev1) with lower fidelity but higher tolerance for damaged templates
- Can introduce mutations but prevents replication fork collapse and allows completion of DNA replication
Mismatch Repair for DNA Integrity
Mismatch Recognition and Repair Process
- Mismatch repair (MMR) recognizes and corrects base-base mismatches and small insertion/deletion loops
- Eukaryotic MMR system involves MutS homologs (MSH) for mismatch recognition
- MSH2-MSH6 (MutSα) primarily recognizes base-base mismatches and small loops
- MSH2-MSH3 (MutSβ) recognizes larger insertion/deletion loops
- MutL homologs (MLH) coordinate repair activities
- MLH1-PMS2 (MutLα) is the primary MutL complex in eukaryotic MMR
- MMR distinguishes newly synthesized strand from template strand
- In bacteria, strand discrimination uses DNA adenine methylation (DAM) patterns
- In eukaryotes, strand discontinuities or PCNA orientation may guide strand discrimination
MMR Mechanism and Significance
- MMR process involves several steps:
- Mismatch recognition by MutS homologs
- Recruitment of MutL homologs and exonuclease (EXO1)
- Excision of error-containing region (up to 1-2 kb)
- Resynthesis of correct sequence by DNA polymerase δ
- Ligation to complete the repair
- MMR enhances DNA replication fidelity by reducing error rate 50-1000 fold
- Plays crucial role in preventing mutations and maintaining genomic stability
- Defects in MMR genes associated with microsatellite instability
- Leads to increased cancer susceptibility (hereditary nonpolyposis colorectal cancer, HNPCC)
Additional Roles of MMR
- MMR contributes to cell cycle regulation and checkpoint activation
- Can trigger cell cycle arrest in response to certain types of DNA damage
- Involved in apoptosis signaling in response to excessive DNA damage
- Participates in antibody diversification processes (somatic hypermutation and class switch recombination)
- Contributes to triplet repeat expansion, relevant in certain neurodegenerative diseases (Huntington's disease)
Consequences of Unrepaired DNA Damage
Genomic Instability and Cellular Dysfunction
- Accumulation of unrepaired DNA damage leads to mutations and genomic instability
- Point mutations can alter protein function or expression (activating oncogenes or inactivating tumor suppressors)
- Chromosomal aberrations (translocations, deletions, amplifications) can disrupt gene dosage and regulation
- Persistent DNA damage triggers cell cycle arrest through checkpoint activation
- ATM and ATR kinases initiate signaling cascades in response to DNA damage
- p53 activation leads to expression of p21, causing G1/S arrest
- Prolonged arrest can result in cellular senescence or apoptosis
Impaired Cellular Processes and Tissue Function
- Unrepaired DNA lesions block transcription, reducing or altering gene expression
- Can disrupt cellular processes and protein function across various pathways
- Accumulation of damaged proteins due to transcription errors can overwhelm protein quality control systems
- DNA damage in stem cells impairs tissue regeneration and contributes to aging
- Reduced stem cell pool and diminished differentiation capacity affect organ function
- Contributes to age-related decline in various tissues (hematopoietic system, skin, intestinal epithelium)
Genetic Disorders and Cancer Susceptibility
- Inherited defects in DNA repair pathways associated with various genetic disorders
- Xeroderma pigmentosum extreme UV sensitivity and skin cancer predisposition (NER defect)
- Cockayne syndrome developmental abnormalities and premature aging (TC-NER defect)
- Fanconi anemia bone marrow failure and cancer predisposition (ICL repair defect)
- Increased cancer susceptibility major consequence of impaired DNA repair
- Accumulated mutations can lead to hallmarks of cancer (sustained proliferation, resistance to cell death)
- Lynch syndrome (hereditary nonpolyposis colorectal cancer) results from MMR defects
Neurodegeneration and Developmental Abnormalities
- DNA damage accumulation in neurons linked to neurodegeneration and cognitive decline
- Neurons have limited capacity for replacement in adult brain, making them vulnerable to accumulated damage
- Oxidative DNA damage implicated in Alzheimer's and Parkinson's diseases
- Exposure to DNA-damaging agents coupled with inadequate repair can lead to developmental issues
- Fetal alcohol syndrome involves DNA damage from ethanol metabolism
- Maternal smoking during pregnancy increases risk of birth defects and childhood cancers