As I covered in this post, one of the main aims of synthetic biology is to produce modular building blocks for biology, to design and build up systems using registered and characterised parts. One thing this allows is the use of logic gates; by turning genes into abstract 'blocks' with certain properties engineers can use them to design biological circuits.
Here's an example from my work at the moment. One of the pigments I'm looking at is violacein - a purple pigment found in marine bacteria. Four genes are used to make this pigment, the first two take a molecule of tryptophan and modify it, the third joins the two modified molecules together, and the fourth further modifies this structure. This can be shown diagrammatically:VioA, vioB, vioC and vioD are the names of the genes. This diagram also shows that there is an intermediate colour within the pathway. If vioC is knocked out (so the gene can no longer function) the cells produce cyan pigment rather than violet.
This gives two separate 'states' for the cell to be in. The engineers start getting excited about this, because vioC needn't be completely destroyed in order for cyan to be produced, it can be put under the control of a certain input system, e.g an arsenic sensor. This means that the cells will normally be cyan, but in the presence of arsenic vioC is expressed and they turn violet. Instant biosensor. Easy to use, and easy to interpret.
As well as being explained biologically this can also be represented diagrammatically:
I like this diagram, because it shows just how useful a set of four genes making two colours can be. The vioA and vioD genes act as an AND gate. Putting them both under different input systems means that you can engineer bacteria that only turn cyan when two conditions are met; e.g correct temperature and correct levels of (say) iron. The vioC is then a further AND gate. Or...if the vioC is controlled by a repressor instead of an activator, a NOT gate. The possibilities are endless...
The really great thing about this is that it provides a level of abstraction for designers and engineers to work with biological systems. They don't need to know about the gene sequence, or the biological basis of gene activators and repressors. All they have to do is work with the blocks.
(Thanks to a fellow Lab Rat for the images!)
Stoopid environmental action
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