The integrity of the genetic code is under constant threat, necessitating robust systems to maintain genomic stability. Cells possess DNA repair pathways that actively monitor and correct damage to the DNA molecule. If these repair systems fail, the potential for permanent alterations in the genetic code increases significantly. The protein Rad4, known in humans as XPC, initiates one of the cell’s most versatile repair processes. This protein acts as a molecular scout, continuously surveying the genome for signs of structural imperfection. Its function ensures that damage is recognized quickly and accurately, preventing the accumulation of errors that compromise cell function and survival.
The Context: Why DNA Repair Matters
The DNA within every cell is subjected to thousands of damaging events daily, originating from the environment and the cell’s own metabolism. External sources include physical agents like ultraviolet (UV) radiation and chemical agents such as pollutants. These agents directly alter the chemical structure of DNA bases, leading to lesions that distort the double helix.
Internal sources involve reactive oxygen species (ROS) produced as byproducts of normal metabolic processes. These highly reactive molecules can cause base modifications or breaks in the DNA strands. If left uncorrected, DNA damage creates physical roadblocks that halt fundamental cellular processes like replication and transcription.
Failure to repair damaged DNA leads to permanent changes, or mutations, during DNA replication. These accumulating mutations compromise the cell’s ability to function and drive cellular senescence, programmed cell death, and the uncontrolled proliferation associated with cancer.
Rad4/XPC: Molecular Identity and Conservation
Rad4 is the name given to this DNA repair protein in the model organism Saccharomyces cerevisiae, or budding yeast. This protein is highly conserved, meaning its structure and function have remained largely unchanged across diverse species. The functional counterpart to Rad4 in humans is the Xeroderma Pigmentosum Complementation Group C protein, abbreviated as XPC.
The study of the simpler yeast protein, Rad4, has provided significant insight into the mechanism of the human XPC protein. Human XPC forms a heterotrimeric complex with two accessory proteins: RAD23B and Centrin 2 (CETN2). The association with these partners stabilizes the XPC protein and enhances its ability to bind to damaged DNA.
The core function of Rad4/XPC is conserved because the protein domains responsible for binding DNA and recognizing damage are structurally similar between yeast and humans. The crystal structure of the yeast Rad4 protein bound to damaged DNA has been used as a template to model the human XPC protein.
Initiation of Nucleotide Excision Repair
The primary role of Rad4/XPC is to initiate the Global Genome Repair (GGR) sub-pathway of Nucleotide Excision Repair (NER). GGR is responsible for scanning the entire genome for damage. Rad4/XPC functions as a sensor that detects structural anomalies in the DNA helix rather than recognizing specific chemical lesions. It is proficient at finding bulky lesions that significantly distort the double-helix structure, such as photoproducts caused by UV light.
The protein complex constantly patrols the DNA to find sites of structural strain. Upon encountering a potential lesion, the Rad4/XPC complex non-specifically deforms or “twists” the DNA to test the helix’s stability. If the DNA is destabilized by an underlying lesion, the protein uses this flexibility to “open” the DNA structure.
This opening occurs when a specific structural element, a beta-hairpin motif, inserts itself into the DNA duplex. This insertion forces the two damaged base pairs out of the helix, a process called base flipping, which creates an open conformation. The XPC protein does not directly contact the damaged nucleotides but binds tightly to the exposed, undamaged nucleotides on the complementary strand.
This indirect binding mechanism allows Rad4/XPC to have a broad substrate specificity, recognizing a wide variety of structurally diverse lesions. Once the damage is confirmed and the DNA is opened, the XPC complex acts as a platform to recruit the next set of repair proteins. It specifically recruits the large, multi-subunit Transcription Factor IIH (TFIIH) complex to the lesion site, which uses its helicase subunits, like XPD, to unwind the DNA further and verify the damage.
Consequences of Rad4/XPC Dysfunction
When the human XPC gene is mutated and its protein product is non-functional, it leads to the rare genetic disorder Xeroderma Pigmentosum, complementation group C (XP-C). This failure means the Global Genome Repair pathway cannot be initiated to fix bulky DNA damage.
The most prominent symptom of XP-C is extreme sensitivity to sunlight, causing severe sunburn after minimal UV exposure. Because XPC cannot remove UV-induced lesions like pyrimidine dimers, these unrepaired lesions rapidly lead to mutations in skin cells. This deficiency results in a dramatically increased lifetime risk of developing skin cancers, including basal cell carcinoma, squamous cell carcinoma, and melanoma.
The incidence of non-melanoma skin cancer in XP patients is over 10,000-fold higher than in the general population, with cancers often appearing in childhood. While other forms of XP involve severe progressive neurological degeneration, patients with a defect only in XPC typically present with skin and eye symptoms but lack these severe neurological problems. XPC failure has also been linked to an increased susceptibility to non-dermatologic cancers, such as hematologic malignancies and sarcomas.