Saccharomyces cerevisiae as a Model System to Study the Role of Human DDB2 in Chromatin Repair

Abstract

Genetic and biochemical studies in Saccharomyces cerevisiae have made major contributions in elucidating the mechanism of several DNA repair pathways, including the nucleotide excision repair (NER) pathway that remove bulky DNA damage from the genome. Although NER is conserved from yeast to humans, there are differences in NER between yeast and humans. For example, no homolog of the human NER factor DNA damagebinding protein 2 (DDB2) has been identified in the budding yeast S. cerevisiae. Here, we present evidence suggesting that S. cerevisiae can be used to dissect the roles of DDB2 in initiating NER in chromatin. Ultraviolet light (UV) is a well studied genotoxic stress that induces bulky DNA damage. These UV lesions are repaired by the NER pathway (Hanawalt, 2002; Sancar & Reardon, 2004). The particular lesions induced by UV irradiation have been characterized, namely, cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4PPs). Both lesions result in the distortion of the DNA double helix, but 6-4PPs result in a greater distortion. Additionally, there are other minor differences between the two types of lesions. CPDs have been consistently shown to have higher incidence than 6-4PPs (Douki & Cadet, 2001). CPDs are induced both in nucleosome core and linker DNA, whereas 6-4PPs are formed with 6fold greater frequency in linker DNA. In addition, 6-4PPs are repaired much faster than CPDs, as reviewed by Smerdon (Smerdon, 1991). In humans, a defect in NER results in xeroderma pigmentosum (XP) and several other rare diseases (Kraemer et al., 2007). XP patients are extremely sensitive to UV light and have about 2000-fold higher incidence of sunlight induced skin cancers than the general population. NER lesion recognition is via protein interaction with the structural DNA changes that are induced. Other bulky DNA lesions repaired by NER include those induced by cigarette smoke, cisplatin treatment and a newly identified form of bulky oxidative DNA damage (Zamble et al., 1996; Setlow, 2001; Wang, 2008). NER has been extensively studied and the basic mechanism is understood. It consists of three main steps: 1) lesion detection, 2) dual incision to remove an oligonucleotide containing the lesion and 3) repair synthesis to fill the gap. There are two sub-pathways of NER, termed transcription coupled repair (TC-NER) and global genome repair (GG-NER) (Hanawalt, 2002). TC-NER is responsible for repair of damage on the actively transcribed