Yeast: Fermentation Pathway

http://fig.cox.miami.edu/~cmallery/255/255atp/mcb8.5.fermentation.jpg

http://www.microbialcellfactories.com/content/5/1/20/figure/F3

E. Coli: Lycopene Synthesis Pathway

Our pathways in the greater context:

http://www.colby.edu/chemistry/BC368/metabolism.jpg

Fermentation in its metabolic context…

http://genomebiology.com/content/figures/gb-2001-2-11-reports4026-1.jpg

Lycopene synthesis in its metabolic context…

http://www.microbialcellfactories.com/content/5/1/20/figure/F1?highres=y

Jay Keasling’s pathway tinkering:

Keasling, JD et al. “Production of the antimalarial drug precursor artemisinic acid in engineered yeast.” Nature. 2006 Apr 13;440(7086):940-3.

http://web.mit.edu/cheme/people/faculty/steph.html

Gregory Stephanopoulos Hal Alper

http://www.engr.utexas.edu/che/directories/faculty/alper.cfm

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.

Our Researchers…

• 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?

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.

Yeast paper

• Global Transcription Machinery Engineering (gTME)

From Snustad and Simmons, 2000, Principles of Genetics

The Eukaryotic Promoter:

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

Lycopene paperMutants generated by random transposon insertions:

http://www.discoverygenomics.net/images/sbts_cut-paste.gif

SEE RIGHT SIDE IF FIGURE 1b IN THIS PAPER.

Perhaps the transposon enters in the middle of a gene, preventing expression.

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.

The Yeast Paper

Figure 4

Model Selected

Transposon Selected

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.