Transcript PPT file for assistance

Yeast: Fermentation Pathway
http://fig.cox.miami.edu/~cmallery/255/255atp/mcb8.5.fermentation.jpg
E. Coli: Lycopene Synthesis Pathway
http://www.microbialcellfactories.com/content/5/1/20/figure/F3
Our pathways in the greater context:
http://www.colby.edu/chemistry/BC368/meta
bolism.jpg
Fermentation in its metabolic
context…
http://genomebiology.com/content/figures/gb-2001-2-11reports4026-1.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.
Our Researchers…
Gregory Stephanopoulos
Hal Alper
http://web.mit.edu/cheme/people/faculty/steph.html
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.
• 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)
The Eukaryotic Promoter:
From Snustad and Simmons, 2000, Principles of Genetics
SPT15 – the TATA binding protein.
TAF25 – a particular TATA-binding factor.
Lycopene paper
Mutants generated by random transposon insertions:
Perhaps the transposon
enters in the middle of a
gene, preventing expression.
http://www.discoverygenomics.net/images/sbts_cut-paste.gif
SEE RIGHT SIDE IF FIGURE 1b IN THIS PAPER.
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.