Design

Here we describe the complete and detailed implementation of our ideas into one project and working parts.

Plasmid design

Optogenetical AND-gate construct (high copy): The basic idea of the logical gate we are using was developed at UCSF in the lab of Prof. Voigt [1]. It is based on amber stop-codon suppression via the non-canonical supD tRNA. We designed the part as followed: Our plasmid insert starts with the sequences (K322123 and I15010) needed to produce the red light sensing chromophores. Each part includes a constitutive promotor and a terminator sequence. Downstream, we cloned the red light sensing promotor (R0082) in front of the subD tRNA (K228001). To stop the transcription directly behind the subD tRNA we put in a double terminator sequence (B0015) downstream. This is followed by a blue light sensing promotor (K238010). In order to allow ribosome-binding upstream of the next part we introduced a ribosome binding site (J44001J44001) directly downstream of the blue light sensing promotor. The AND-gate construct is completed by a T7 polymerase with the amber stop codon mutation (K228000). Since all standard biobrick vectors include a termination sequence after suffix there was no need to introduce a further
termination sequence.

Reporter construct (low copy): Our second plasmid carries the reporter construct, which can be exchanged, depending on what kind of reporter system you want to use. For simple proof of principle we used lacZ (I732017) as reporter gene downstream of the T7 promotor (I712074). Since the used lacZ part already includes a ribosome-binding site (rbs), it is not necessary to add another rbs. For the same reason as mentioned under "Optogenetical AND-gate construct" we do not add a terminator sequence downstream of lacZ.

Bacteria and block matrix

We could obtain some heat resistant bacteria (MG1655) [2], which endure temperatures up to 50°C. This is really essential to us since we have chosen a matrix named GELRITE to immobilize our bacteria. It can be penetrated by light with only little refraction and it contains a minimum of nutrient to enable growth and protein synthesis but it polymerizes at 46°C. To ensure an even distribution of the bacteria we need to add them into the liquid gel which in turn means that they need to endure more than 46°C for at least 2 or 3 minutes.

How the final construct should work

By addition of S-Gal to the GELRITE matrix a fully functional AND-gate should lead to dark spots/colonies when hit with blue and red light. For proof of principle, one could also think about GFP coupled to fluorescence detection.

Since the red light sensor is active in the ground state, one needs to shut down the signalling. This can be achieved by irradiation with light of 650 nm [3]. Afterwards, bacteria get hit by both far red light (705 nm [3]) and blue light (465 nm [4]) beams. The red light induces the autophosphorylation at the cytosolic site of cph8[5]. This leads to phosphorylation of OmpR [6] which subsequently binds to OmpC promotor and enables transcription of the supD t-RNA. This signal transduction pathway is supposedly also responsible for sensing of aspartate [7], a substance which is present in LB as well as other common media for E. coli. Hence a strain with EnvZ knockout is desireable. For this the strain CP919 (V1012) can be used. When YcgF senses blue light it dimerizes and binds to the repressor YcgE. The formation of the YcgE-YcgF complex leads to the unbinding of YcgE from the YcgZ promoter which activates the transcription of T7ptag (T7 Polymerase with the amber stop codon mutation) if enough supD tRNA is available!

This AND-gate should ensure that expression of T7ptag is only induced when we both wavelengths hit the bacteria. Since the reporter gene is under the control of a T7 promoter, lacZ expression is only enabled when the generated T7ptag binds to the T7 promoter.

Cloning Scheme: