Your goal is to engineer a bacterium that can be turned loos

Your goal is to engineer a bacterium that can be turned loose in the ocean to clean up an oil spill (bioremediation). You have genetically engineered its genome so that crude oil is an attractant and it can navigate toward it (e.g. chemotaxis). You want to design an operon for the bioremediation* of crude oil. Imagine that you can freely engineer the genome. What kind of regulation would you use? Describe the design of your operon (regulatory elements, gene order, etc). Describe the regulatory details of how your operon responds to the presence and absence of crude oil.

*Note: imagine that sequential activity of enzymes A, B, and C can turn crude oil into a product that can enter the normal metabolic pathway of the bacteria.

Solution

Bioremediation of crude oil is done by making the enzymes A, B and C express sequentially in the bacteria.

The expression of these enzymes that help in transferring the crude oil into a metabolic product of the bacteria can make easy for clearing the oil spills.

Now, to engineer an operon that comprises of these three genes and see that they are expressed to clear away the oil spill, they have to be built in such a way that they get expressed when they are stimulated by any allosteric effectors like oil.

The activator protein or repressor protein is known to have two states. In one state of conformation, the activator protein will not bind to DNA and in another it will bind. This happens by the interaction of two different sites present on the protein. One of them is DNA binding domain and another is allosteric domain that helps in keeping the protein in DNA binding state or non-functional state. Allosteric site is usually attacked by certain molecules called allosteric effectors.

In this operon, the inducers of A,B and C enzymes are allosteric effectors. Crude oil can be made as the operon inducer that can act as allosteric effector. When crude oil is available, it binds to the allosteric site of the activator protein and changes its conformation thereby allowing the DNA binding domain to be active. Then the protein binds to the DNA and allows the RNA polymerase to bind to the promoter and successfully carryout the transcription process.

This is called as positive regulation or positive control of the transcription in the operon. Transcription of all the three genes will produce the 3 enzymes that can convert crude oil into a product that can be metabolized by the bacteria.

The operon design will have a promoter upstream to the three genes A, B and C. The activator protein has to be present in the cell to be influenced by the allosteric effectors.