Arsenic Biosensor

From 2006.igem.org

Revision as of 17:17, 29 June 2006

This is our first formalised project idea. The details are as follows:

Aim

Develop a bacterial biosensor that responds to a range of arsenic concentrations and produces a change in pH that can be calibrated in relation with the arsenic concentration.

Background

This project is motivated by the needs of parts of the developing world. For details, see http://2006.igem.org/Arsenic_Biosensor_Background Background

Possible mechanism 1 - the bare minimum

INPUT [Arsenate/Arsenite] -> Detector -> Reporter -> OUTPUT [H+]

The arsR gene codes for a repressor which binds to the arsenic promoter in the absence of arsenate or arsenite. These two genes can be linked to the lacZ gene, in order to place lactose metabolism under the control of an arsenic activated promoter.

The ability to metabolise lactose should result in the acidification of the medium, and an output of H+ ions, giving a pH response to the input of arsenate/arsenite molecules.

It should be possible to obtain a curve for pH vs. arsenic concentration, where a range of pH values representing an unsafe level, a safe level, or an intermediate level of arsenic is present can be elucidated after calibrating the biosensor with known concentrations of arsenic.

Parts needed: Arsenic binding repressor protein Arsenic repressor protein responsive promoter lacZ protein coding gene

Possible mechanism 2 - more ambitious

After discussion, it was decided that it would be unfeasible to try and engineer a sensitive enough analogue output just using the pH - instead, a set of a couple of defined 'stepped' outputs would be preferable.

In order to increase the range that is indicated by the biosensor, the following mechanism might be worth considering.

Sample: Water sample + Lactose + Bacterial culture

The mechanism involves 3 'devices' inside the bacteria.

Device 1: The lac operon regulatory region is connected to an enzyme which, if activated, catalyses a reaction that produces an excess of OH-, thus making the surrounding solution alkali.

Device 2: A promoter that's regulated by a repressor very sensitive to arsenic. Thus anything above 5 ppb of arsenic would bind to the repressor and enable gene expression. This promoter is connected to a gene that expresses a molecule that represses the lac operon in device 1, thus keeping the pH at neutral. The usual lac repressor molecule wouldn't work since there's lactose in the solution to bind to it, so either we would have to make a lac operon regulatory region that also happens to respond to another repressor, or we would have to come up with a different solution for the problem (like somehow utilising an anti-switch or something?)

Device 3: A promoter regulated by a repressor that's somewhat less sensitive to arsenic, so only switches on at, say, 20 ppb. Connected to lacZ, as detailed above in Possible mechanism 1.

So, if all goes according to plan, we would get the following results:

If no arsenic is present:

Problems

The arsenic promoter shows some background activity even when arsenic is not present. It may be possible to reduce this noise by adding an extra control method to repress the lacZ gene parallel to the action of the arsR product, with for example an antiswitch.

It will not be possible to get a linear relationship between pH and the arsenic concentration because the relationship between gene expression and the cofactor concentration is not linear.

The arsenic concentration has to be the limiting factor in the reaction to result in the steady state obtained being the correct pH in relation to arsenic concentration. If the cell number is the limiting factor the pH may not drop low enough to indicate the arsenic level present in the time taken before measuring.

Experiments required

A lot of this project will be calibrating the sensor, finding the time to reach a steady state, finding out which amount of cells is ideal for reaching the steady state which gives distinct results for each pH range, and finding out which pH range represents which concentration of arsenic. It would be ideal to have the threshold for the legal limit of arsenic at the point of the curve which gives the most accurate result.