We previously described the use of quantitative proteomics to studymacromolecular complexes. Applying the method to analyze a yeast RNA polymeraseII preinitiation complex, we identified a new 8-kDa protein, encoded by theuncharacterized open reading frame YDR079c-a, as a potential new component of thepreinitiation complex. Here we show that YDR079c-a is a bona fide component ofpolymerase II preinitiation complexes and investigate its role in transcription. YDR079c-a is recruited to promoters both in vivo and in vitro and is required forefficient transcription in vitro and for normal induction of GAL genes. Inaddition, YDR079c-a is a core component of general transcription and DNA repairfactor IIH and is required for efficient recruitment of TFIIH to a promoter.Yeast lacking YDR079c-a grow slowly, and, like strains carrying mutations in coreTFIIH subunits, are sensitive to ultraviolet radiation. YDR079c-a is conservedthroughout evolution, and mutations in the human ortholog account for a DNArepair-deficient form of the tricothiodystrophy disorder called TTD-A(2). Theidentification of a new, evolutionarily conserved, core TFIIH subunit isessential for our understanding of TFIIH function in transcription, DNA repairand human disease.

Nucleotide excision repair is a major pathway for repairing UV light-induced DNA damage in most organisms. Using insertional mutagenesis, we isolated aUV-sensitive mutant of Chlamydomonas reinhardtii that is blocked in the excision of cyclobutane pyrimidine dimers. The mutant is also sensitive to the alkylating agent, methyl methanesulphonate. We have cloned REX1, a novel gene that rescuesthe mutant. The gene is unusual in a eukaryotic organism in that it is predicted to encode two different proteins, a small protein (8.9 kDa) and a larger protein (31.8 kDa). Neither protein is homologous to known DNA repair proteins. Partialcomplementation is achieved with subclones of the gene encoding only the 8.9-kDa protein. The 8.9-kDa protein has homologues in many organisms includingSaccharomyces cerevisiae, Arabidopsis, and humans. The 31.8-kDa protein appearsto be less conserved. These findings may be of general importance for DNA repair in other organisms.