Team:ESBS-Strasbourg/Project

Our device construction is divided into 4 components :

1. Degradation system
2. Light detection system
3. Protein Tagging
4. Light controllable protease

Notebook

A light-controllable specific protein degradation system as new standard for synthetic biology

The aim of our project is to engineer a new fundamental component that could be universally used to build more complex or more controllable biological circuits inside chassis organisms. This new component consists of the E.coli protease ClpXP to which the phytochrome B of arabidopsis thaliana is fused. Any given protein can be degraded as long as it is tagged with our especially designed Biobrick containing a PIF sequence. This Biobrick can be added to the C-terminal end by standard assembly methods. The activity of this system is tightly controlled and reversible by light inducement.

The system can be constitutively expressed in the chassis but remains inactive for the tagged protein. However it is expected to stay active for the background of naturally SsrA tagged proteins and so it will not interfere with the metabolism of E.coli. Instantly after the light inducement the system is turned on, due to the lack of transcriptional or translational delay and is expected to remain active until another light signal turns it off.

In our modeling part we will used this system for a genetic oscillator which could be used for multi step synthesis.

Theoretical Background:

Our system contains several parts: the bacterial ClpXP protease from E. Coli as the specific recognition sequences (DAS-tag) for ClpX for the degradation part and the photoreceptor protein phytochrome B (PhyB) and the phytochrome interacting factor (PIF3/6) from A. thaliana for the light-dependent part of the system.

- Degradation : The ClpXP proteases consist of three main parts: the ClpX unit and two units of ClpP. The ClpX forms a hexametric ring and binds to a double heptamer of ClpP. The ClpX is responsible for recognizing proteins bearing a specific degradation tag, unfolding and leading them into the catalytic core of the enzyme, the two ClpP subunits which break down peptide bonds.

- Light sensitivity: PhyB is characterised by a red/far-red photochromicity. Through red-light absorption (650–670 nm )PhyB undergoes a rapid conformational change from its ground state Pr to its active state Pfr. The structural change allows the binding of different interacting factors (PIF).The process is completely reversible through absorption in the near infra-red spectrum (705-740nm).
PhyB is fused the N terminus of a trimeric form of ClpX-N in which the subunits were connected with a flexible linker to stabilize the enzyme (thanks to the findings of Baker & Sauer in 2005) .

Target proteins are fused to the PIF and tagged with the specific degradation sequence which, through light activation, brings the degradation sequence in proximity to ClpX and guides them to the catalytic core of the protease. Therefore a specific degradation of proteins containing the degradation sequence can be induced by a light signal.


Note : In the native organism, the SsrA tag is added to incomplete proteins whose translation has been aborted. Thus, misfunctionnal proteins do not accumulate inside the cell.

To engineer controlled degradation, Baker and Sauer (2006) designed a series of modified ssrA tags that have weakened interactions with ClpXP. The DAS tag has a higher Kd value than wild type SsrA tag, thus degradation of DAS-tagged proteins is not significant within the range of physiological concentrations. However, through the action of an adaptor protein (SspB) which hepls tethering the tagged protein to the protease, DAS-tagged proteins are significantly degraded.

Our idea is to replace this adaptator system with a light sensitive tethering system.