1. Yeast: Fermentation Pathway

2. E. Coli: Lycopene Synthesis Pathway

3. Our pathways in the greater context:

4. Fermentation in its metabolic context…

5. Lycopene synthesis in its metabolic context…

6. Jay Keasling’s pathway tinkering:
Keasling, JD et al. “Production of the antimalarial drug precursor artemisinic acid in engineered yeast.” Nature Apr 13;440(7086):940-3.

7. Our Researchers… Hal Alper Gregory Stephanopoulos
Both PhDs in Chemical Engineering and work in the Department of Chemical Engineering at MIT together.
Specifically, their lab is the Bioinformatics and Metabolic Engineering Lab at MIT.

8. Major question in both papers:
How do we know where to look when we want to optimize a specific pathway? Which pipes do we turn on and off?

9. Both papers turn to the selective forces of nature to get to the answer:
Start by presenting nature with a huge number of mutants generated by nature, then see which of these mutants is doing what the want the best.

10. Yeast paper
Global Transcription Machinery Engineering (gTME)

11. The Eukaryotic Promoter:
From Snustad and Simmons, 2000, Principles of Genetics

12. SPT15 – the TATA binding protein.
TAF25 – a particular TATA-binding factor.

13. Lycopene paper Mutants generated by random transposon insertions:
Perhaps the transposon enters in the middle of a gene, preventing expression.
SEE RIGHT SIDE IF FIGURE 1b IN THIS PAPER.

14. In the lycopene paper, the best knockout genes for lycopene synthesis identified by this combinatorial method were then compared with genes computer modeling predicted as good knockout sites.

15. The Yeast Paper

16. Figure 4
Model Selected
Transposon Selected

17. RATIONALE: If I alter the transcription machinery, I will change the expression levels of different genes on a large scale, rather than just working with a single gene predicted by a model.