Based on the DIP database information that purports YDR078C as a "hypothetical membrane protein," it would be interesting to assess this role. As discussed in Chapter 6 (480-483), pronase, a protein digestion enzyme, can be useful in determining whether a particular protein is present on the cell membrane or not. Because pronase digests proteins, the experiment is a "simple" comparison of the presence of YDR078C with or without the pronase treatment. If YDR078C is not present once the pronase treatment has been given (and is present in its absence), then we can reasonably conclude that YDR078C is most likely a membrane protein and confirm the preliminarily confirm the predictions from the DIP database.
The membrane and degradation interaction maps as well as the insignificant SCOP results (nucleotidyl transferase) indicate that YDR078C is somehow involved in RNA processing. Of course, there are many functions invovled in RNA processing, and the specific role of YDR078C can only be guessed. Beginning at the proteomics lab at Yale, we can determine the current status of proteomic information regarding YDR078C. The protein chip data is not yet available. If protein chip data becomes available, it would be possible to cluster the gene with others that have similar phenotypes. We could begin to see what other functional groups and phenotypes YDR078C expressed with, which would begin to indicate its function. The CYGD (Comprehensive Yeast Genome Database) indicates that YDR078C has physical interaction with several proteins, but because of the limited knowledge of all proteins involved, it is not yet possible to determine function. If intent on determining the function of YDR078C, it could be used as either the bait or prey in a Y2H experiment. All the range of protein-protein interactions could be determined from this experiment. The washington database indicates that this has not yet been done. YDR078C has been used as the prey twice, but complete interactions have not been determined, or, at least, made availble.
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