NCBI

Lab 10

I have decided to introduce you to some of the genome-based resources that may be useful in the design and execution of your term projects rather than to describe databases themselves during this exercise.  Some aspects of this exercise will illustrate how useful database capabilities might be in analyzing genome information.

Saccharomyces cerevisiae is probably the organism best-studied in a genome-wide sense.  In this lab, I hope that we accomplish 3 objectives:

• Familiarize you with a variety of genome-wide projects:  genome, transcriptome, proteome, and others
• Stimulate simple consideration of how one might use genome-wide information in a practical application: antifungal drug design.
• Convince you that "simple" WWW access to data is not sufficient for many "simple" biological questions.

First, some genomics resources of great value.  Please visit each resource and "prowl around".

• Saccharomyces Genome Database
• Yeast Gene Expression Database
• Yeast Proteome Database
• Saccharomyces Genome Deletion Project
• Saccharomyces Gene Fusion and Disruption Project
• Saccharomyces Gene Fingerprinting Project
• MIPS Yeast Project

Resources from other fungi that may be valuable, but are not generally as complete or as well-organized:

• Candida albicans Genome Project
• Schizosaccharomyces pombe Genome Project

  There are many other fascinating and useful genome-wide databases.   One of special interest is the metabolic database.

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The questions, proceeding from simple to difficult.  I DO NOT want you to spend over 3 hours OUTSIDE of lab on these questions.  I will mark those that you must answer, but on the others, I want you to spend time thinking about HOW you would

1. What is the e-mail address of Alan Sachs, the first person to purify polyA-binding protein?
2. We have worked with Sge1p, a multidrug transport protein encoded by the SGE1 gene.
   1. What is/are the phenotypes of a yeast cell that lacks Sge1p?
   2. Is SGE1 mRNA abundance  regulated in response to glucose deprivation?
   3. Does SGE1 transcript abundance change in response to either TUP1 or YAP1 abundance?
   4. Can you determine whether Sge1p protein abundance changes under any of these conditions?
   5. Is a yeast strain that contains a complete deletion of SGE1 readily available?
   6. Is a yeast strain that contains a labelled Sge1p-fusion polypeptide readily available?
   7. Is a yeast strain that overexpresses Sge1p readily available?
3. Does any fungus have an ortholog of Sge1p that is more closely related to it than are the Sge1p paralogs in S. cerevisiae?  If not, what does that suggest about the evolutionary date of the gene duplication/gene deletions event that made this occur?
4. How many genes are increased in expression at least 5 fold in Saccharomyces during a shift from high to very low glucose?
5. Of those genes, how many are essential to growth?  Are they essential for growth in glucose or for growth in glycerol?
6. Of these genes, how many have orthologs in BOTH C. albicans and S. pombe?   Both of these organisms undergo a diauxic shift like S. cerevisiae.

Okay, now the really hard question. 

Because you got an A in bioinformatics, you have been hired by Eli Lilly to use the current databases (although you can invent new database queries) to identify an ideal, broad-spectrum antifungal agent.  This drug should be capable of inhibiting fungal growth under all conditions known to you.  The target's function should be essential.   It should be conserved in all fungi.  The target should not be essential to humans, or the human target must be very different from that of the fungus.

Describe, in approximately 1 page, the way in which you will try to identify the candidate drug targets.

Please print or e-mail these responses by next Friday, 11/20/98.

Chuck Staben, copyright reserved || 11/11/98