Comparative Genomics

1. Go to TIGR’s CMR (Comprehensive Microbial Resource) and align E. coli strains K-12 and O157:H7 whole genomes. Are the genomes colinear their entire lengths?

2. Since we need some E. coli to keep our intestines protected from virulent strains, traditional antibiotics are not ideal therapies. Would it be possible to devise a new class of antibiotics to target only O157:H7 and not K-12? Explain how you might develop this type of drug.

3. Read the PNAS abstract and discover the genomic diversity present in pathogenic E. coli. Do you think all pathogenic E. coli should be lumped into a single category? What could you do determine the extent of different E. coli pathogens?

4. Go to coliBASE and perform a search for the gene papK and follow the link until you see a graphic display of papK in the genome (small read arrowhead). Change the default option next to “Colour genes by” to “GC content and click “Redisplay”. Mouse over papK to see which gene it is; do all genes in this area have the same GC contents as papK?

5) Change “Colour genes by” to “orthologues” and click “Redisplay”.  On the new page, you will see many species next to checked boxes; click on the button that says “Uncheck all”, click on the button next to “Toggle Escherichia” to select this genus, then click on the “Colour by orthologs” button at the very bottom.
Does papK have orthologs in other E. coli strains?
Which genes have the highest number of orthologs in this view?
Given the percentage and the number of strains, how many orthologs exist?

6) Now click on the button next to “View MUMmer alignment with:” and choose the strain K-12 MG1655 (the first strain to be sequenced).
How well conserved is this region of strain CFT073’s genome in K-12 MG1655’s genome?
What challenges do these data present when designing a new drug to kill pathogenic strains but not the beneficial strains?


© Copyright 2005. Malcolm Campbell. Department of Biology, Davidson College, Davidson, NC 28035
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