Despite a great deal of work, many facets of the mechanism of activated transcription remain completely unclear, and yet this is a central problem that must be solved for a proper understanding of gene regulation. In order to increase our understanding of this fundamental process, we are setting up an efficient system for in vitro transcription using yeast as a model system, specifically the yeast CUP1 gene. We chose this gene because its biological function (the gene encodes a copper-metallothionein) and its mechanism of induction are relatively simple and well-understood at the molecular level: copper ions bind to the DNA-binding domain of a transcriptional activator (Ace1p) which then folds and is able to recognize upstream activating sequences (UASs) in the CUP1 promoter. Ace1p is small (225 residues) with two domains; the other domain is a typical acidic activation domain. It is our aim to reconstitute this system in vitro using purified homologous (yeast) components and using as template either a plasmid containing CUP1, or minichromosomes containing CUP1 isolated from induced and uninduced cells. Such a system should also allow us to evaluate the role of chromatin structure in the regulation of a eukaryotic gene. Toward these ends, we have engineered a yeast strain containing a tagged gene for the large subunit of RNA polymerase II (RPB1). This has allowed us to isolate the yeast RNA polymerase II holoenzyme rapidly and effectively. This is an essential step toward setting up an efficient transcription system. We have purified recombinant Ace1p and we are in the process of preparing other recombinant yeast transcription factors (yTBP, yTFIIB, yTFIIE, etc.). A method for the isolation of yeast minichromosomes in relatively large quantities is also in the final stage of development. In a collaborative venture with Drs. Clore and Gronenborn, we are preparing the DNA-binding domain of Ace1p to solve the structure of its complex with DNA by two-dimensional NMR. This should be a very interesting and unique structure because of the role of copper ions in folding the domain.
