Final Activity Report Summary - AGE/CANCER (Structural Biology of Aging and Cancer)
The group of Nicolas Thomä at FMI recently published work in Cell where they report the structure of the 'damaged DNA binding' complex (UV-DDB) that recognizes damage induced by UV light (sunlight). This large and complicated structure gives profound insights into how DNA damage can be repaired. The genetic information within each cell is safeguarded against potential mutagens in the environment by various repair mechanisms. For example, skin exposed to sunlight is under constant attack from UV irradiation, which gives rise to covalent cross-links between neighbouring bases in the DNA, resulting in mutagenic photodimers. In bright sun conditions, each cell can accumulate up to 40,000 UV-damaged bases per cell and hour. Repair of this DNA damage in healthy cells proceeds via nucleotide excision repair (NER), involving a specific damage recognition step, followed by excision of the lesion and error-free re-synthesis. Photolesions, however, have biophysical parameters closely resembling undamaged DNA, impeding discovery through damage surveillance proteins. Xeroderma pigmentosum (XP) patients show heightened UV-sensitivity and diminished repair, often so pronounced that they become sunburned within minutes, even on cloudy days. XP patients also have a drastically increased incidence of all known skin cancers. The work now reported by the group of Nicolas Thomä at the FMI in Basel has focused on the mechanism by which the cell detects UV-damaged DNA and triggers a repair response. The research concentrated on the function of the xeroderma pigmentosum E (XPE) protein, which in conjunction with a further protein complex of 'damaged DNA binding' proteins 1 and 2 (DDB1-DDB2), forms the UV-DDB.
UV-DDB constantly scans the genome for the presence of DNA damage and then binds tightly to photo-damaged bases. DNA-bound UV-DDB in turn acts as a flag for the remainder of the nucleotide excision repair machinery, signalling the presence of damage. The authors present the three dimensional structure of the UV-DDB complex bound to damaged DNA. These results reveal a mechanism by which three amino acids originating from the surface of DDB2 are used to distinguish between photodimer-containing and undamaged DNA. The tightly localized probing of the photolesions, combined with proofreading in the photodimer pocket, enables DDB2 to detect lesions refractory to detection by other damage surveillance proteins. In the undamaged DNA helix, each base is stabilised by two neighbouring bases. Once a photodimer is present, the DNA becomes distorted and the two neighbouring bases surrounding the photodimer are no longer able to stabilize the photoproduct. With the help of three distinct amino acids, a DDB2 hairpin inserts itself into the DNA duplex.
This hairpin is not strong enough to insert into undamaged DNA. However, in the presence of a photodimer, where the stabilising effect of the neighbouring bases is absent, the protein inserts by flipping the damage out of the helix. Once inserted, DDB2 proof-reads the damage and then remains stably bound until other repair factors arrive. In xeroderma pigmentosum patients, DNA binding and the stability of the DDB2 protein are compromised and damage detection is diminished. Thus, the scanning activity of the UV-DDB complex for DNA damage serves as a major protection mechanism against skin cancer.
UV-DDB constantly scans the genome for the presence of DNA damage and then binds tightly to photo-damaged bases. DNA-bound UV-DDB in turn acts as a flag for the remainder of the nucleotide excision repair machinery, signalling the presence of damage. The authors present the three dimensional structure of the UV-DDB complex bound to damaged DNA. These results reveal a mechanism by which three amino acids originating from the surface of DDB2 are used to distinguish between photodimer-containing and undamaged DNA. The tightly localized probing of the photolesions, combined with proofreading in the photodimer pocket, enables DDB2 to detect lesions refractory to detection by other damage surveillance proteins. In the undamaged DNA helix, each base is stabilised by two neighbouring bases. Once a photodimer is present, the DNA becomes distorted and the two neighbouring bases surrounding the photodimer are no longer able to stabilize the photoproduct. With the help of three distinct amino acids, a DDB2 hairpin inserts itself into the DNA duplex.
This hairpin is not strong enough to insert into undamaged DNA. However, in the presence of a photodimer, where the stabilising effect of the neighbouring bases is absent, the protein inserts by flipping the damage out of the helix. Once inserted, DDB2 proof-reads the damage and then remains stably bound until other repair factors arrive. In xeroderma pigmentosum patients, DNA binding and the stability of the DDB2 protein are compromised and damage detection is diminished. Thus, the scanning activity of the UV-DDB complex for DNA damage serves as a major protection mechanism against skin cancer.