Nucleotide excision repair of DNA in yeast

Nucleotide excision repair (NER) is a complex biochemical process required for the removal of multiple forms of base damage from the genome. In S. cerevisiae at least 20 proteins are involved. In this yeast the initial steps of damage-recognition and the specific incision of the DNA strand bearing sites of base damage may be effected by a preformed multi-protein complex (nucleotide excision repairosome) comprising at least 14 known proteins. Among these are a stable sub-complex comprising the 7 core subunits of the RNA polymerase II (RNAP II) basal transcription factor IIH (TFI1H), including the Rad3 and Ssl2 DNA helicases. Following specific binding of the NER machinery to sites of base damage these two helicases (which have opposite directionality) may melt a region of the DNA duplex that includes the damage, generating a "repair bubble" -27-30 nucleotides in size. A similar "transcription bubble" may be generated during RNAP II transcription initiation, hence the dual role of TFIIH in NER and transcription. The remaining proteins thus far identified in the rcpairosome include the junction specific endonuclease Rad2, which catalyzes nicking of DNA at duplex-5' single stranded junctions (i.e., 3' to sites of damage) and the junction-specific nuclcase Radl/RadK), which catalyzes nicking of DNA at duplex-3' single stranded junctions (i.e., 5' to sites of damage). The Radl4, Rad23 and Rad4 proteins may play a role in damage-specific recognition. The Rad7 and Rad 16 proteins interact with one another and are required for NER in regions of DNA that arc transcriptionally silent. Rad26 protein (and possibly Rad28 protein) apparently play a role in NER of transcriptionally-aclivc DNA.