KARMA, a new tool for specific protein degradation

Recently, the discovery of CRISPR led to a huge revolution in gene editing. The CRISPR-Cas9 system finds and cuts a specific DNA sequence with high precision. Research on this natural bacterial system led to the development of a versatile molecular tool that now allows us to easily target a specific sequence of nucleotides in order to add, change or delete any DNA or RNA in a very specific way.

However, this type of tool is not available when it comes to proteins.

But how to get a new molecular scissor that can target, with high specificity, a chosen protein ?

The first aim of our KARMA project is to propose a new tool for specific protein degradation. We want to target a protein of interest and break it down with the help of molecular scissors. In order to accomplish our idea, we thought about a fusion protein containing two parts: one for targeting the protein: a VHH (nanobody), and another for degrading the target: a protease.

The VHH will act as a homing missile that drag the protease to its target, which makes protein degradation more specific in a complex environment.

In order to demonstrate the feasibility and functionality of the KARMA tool that we imagined, we performed a complete proof of concept that characterizes in detail the action of the protease, both when it is alone and when it is fusied with the VHH. We compared these two cases in order to prove that KARMA was more specific than a protease alone.

We worked with well-known parts such as the TEV protease, an anti-GFP VHH, and well characterized systems such as the ClpXP - ssrA system.

We then considered the possible applications of this kind of tool, particularly to revert the antibiotic resistance mechanisms of bacteria, especially the ones caused by the secretion of antibiotic degrading enzymes like beta-lactamases.

A versatile tool...

By just changing the kind of protease and the kind of antibody we can imagine a huge panel of application...

We obtained the
Gold Medal