Fermentation Tutorial

This brief exercise will familiarize you with finding details regarding E. coli fermentation.

  1. Begin the tour at:  EcoCyc gene/protein page for pyruvate formate-lyase / 2-ketobutyrate formate-lyase
  2. Toward the bottom of the protein page, click on pflBto display regulators controlling pflB transcription from 8 start sites. (Regulation of pflB is complex!)
  3. In the operon diagram at the bottom of the gene page, click on the promoter to display:
  4. Toward the bottom of the transcription-unit page, click on "Fnr" to display
    • Transcription-factor page for Fnr.
  5. Back in the gene page for pflB click on
    • Genome browser focused on pflB to view genomic context.
  6. Back in the gene page for pflB, click on the "Align in Multi-Genome Browser" button in the set of buttons mid-way down the page. Select a set of organisms in the next page and click Submit near the bottom of the page. The resulting page will align the pflB gene across all the selected organisms, when present. Example:
    • Comparative genome browser with the pflB in the center.  Mouse over the pflB gene to bring up the protein name and the pathway where it operates, i.e., mixed acid fermentation.
  7. Go to Search in the blue header and click on pathways. Enter ”mixed acid fermentation” in the search box. Click on “mixed acid fermentation” to display
    • Pathway page for mixed acid fermentation. By mousing over the diagram you can show the individual reactions of the pathway.
  8. Within that pathway display click on the arrow leading from pyruvate to formate and acetyl-coA to display
  9. Click on the chemical structure of coenzyme A in the reaction page to display
  10. From the Tools menu at the top of the page, click on Cellular Overview to display the Cellular Overview (metabolic map diagram) for E. coli. This diagram can be magnified using the ladder on the left. In Cellular Overview right click on your mouse and call up “Highlight Pathway(s)”. Enter “fermentation” to highlight reactions of the mixed fermentation pathway
  11. From the Tools menu at the top of the page, click on Regulatory Overview  to display a regulatory network diagram for E. coli. This diagram can also be magnified. Right click on your mouse and call up “Highlight Genes by Name or Frame ID. Enter “Fnr”.
  12. Mouse over Fnr until you see a square, then right click on your mouse and choose “Highlight Gene fnr and its Direct Regulatees” to call up genes that are regulated by Fnr. The highlighting can be removed by right clicking the mouse away from Fnr and choosing “Clear All Highlighting”.  Explore which genes regulate transcription of Fnr in a similar manner.
  13. Let's now look at information for another organism, Bacteroides vulgatus. You can switch the current organism that BioCyc queries by clicking on the blue "change organism database" link in the upper-right corner of every page. In the “Quick Search” box enter “mixed acid fermentation” to see whether the genome of this bacterium contains the pathway. You are now directed to the mixed acid fermentation pathway in BioCyc and can explore this pathway and its regulation if data are available.