Chassis Effects Flashcards
Define a chassis
A structural framework of a system which is able to support other parts and devices
Define a biological chassis:
a cell (bacterial, algal, fungal, mammalian) capable of living, replicating and expressing the synthetic biology parts/devices we introduce
What is already present in the chassis?
Gives you the functions that make sure the cell can already survive, reproduce respire etc.
Define metabolic burden
The amount of resources (raw materials and energy) taken from the host for maintaining and expressing foreign DNA and producing novel compounds
Explain specific burden
Resources for the new function you have inserted are redirected from respiration (reduction of resources for directly linked metabolic pathways)
Explain generic burden
the reduction in growth rate affects the rate of DNA and cell wall turnover indirectly (reduction of energy available for cell division)
What is Artemisinin?
An anti-malarial drug
What is the disadvantage of synthetic artemisinin production?
It is expensive
What is the name of the plant that naturally produces artemesinin?
Sweet wormwood
What is the problem with harvesting artemisinin from sweet wormwood?
The price will fluctuate with the weather and any major weather events due to the variation in crop growth
What did Youyou Tu win a Nobel Prize for in 2015?
For showing that the active ingredient in the sweet wormwood extract was arteseminin
Who was the first person to demonstrate that artemisinin could be made in ecoli?
Jay Keasling
Which two compounds are the core precursers for producing artemisinin?
IPP and DMAPP
What gene is ecoli missing to produce artemisinin?
ADS
What is FPP used for in both sweet wormwood and ecoli?
Sweet wormwood - artemisinin
Ecoli - making cell wall components
Which pathway produces FPP in ecoli?
The DXP pathway
Which pathway produces FPP in yeast?
The mevalonate pathway
What was the effect of putting all the genes that create FPP in yeast into ecoli?
The specific burden was too great and production slowed.
What is the function of FPP in yeast?
Makes the cell wall
Why does producing artemisinin in yeast have a lesser metabolic burden than in ecoli?
Because you are introducing less new proteins into the organism
What other device was introduced into yeast to decrease the amount of organic synthesis required and how?
CYP by converting amorphadiene to a compound closer to artemisinin (artemisinic acid)
What process was carried out to increase the specific yield of artemisinic acid production in yeast?
Decreased the expression of the enzymes that produced ergosterol by using a weaker promotor, so not as much as was usually used to sustain cell wall synthesis was produced.
What process was carried out to remove the bottleneck in FPP production in yeast?
Increased the copy number of the enzyme to catalyse the bottleneck reaction was inserted so that twice as much existed and more mevalonate was produced and therefore more FPP.
What is the compound that is the start block for artemisinin production?
Acetyl-CoA
How was the production of Acetyl-CoA increased?
By using the technique of changing promoters and copy numbers
What is a synthetic scaffold?
A protein (not an enzyme so it doesn’t have a function as such) that has pockets for the other proteins in the pathway to bind to, which increases their proximity. Increasing the proximity of the enzymes increases the reaction rate because the local concentration of the product will be quite high so the next step of the reaction will proceed faster.
What does Jay Keasling have to say about modern synthetic biology methods?
That the artemisinin project would not have taken him 10 years had the tools such as abstraction, modularisation and standardisation had existed when he started.
When can the synthetic biology way of making artemisinin be used?
Only when the natural stock of sweet wormwood is depleted and there is not enough artemisinin available
