One of the main research focus in the lab is the development and application of bacterial biosensors.
We design and engineer bacteria to react to the presence of chemical signals with the production of an easily quantifiable reporter protein.They can be used as simple alternative measuring methods for environmental pollutants or toxicity.
Current projects focus on integrating bioreporter strains in microfluidics platforms, on designing new sensory proteins in order to achieve different effector recognition capabilities, on developing faster-reacting sensors, and on their field-testing.
On the right a picture of the Envirobot: the 'eel-like' modular robot that can swim at the water surface and sample water quality parameters. The different modules enable to load and connect different physico-chemical or biological sensors. Communication to the shore enables the robot to locate itself in the water and move independently as a function of input parameters.
Sensory protein design
This PhD project, which is advanced by Diogo Tavares, focuses on bioreporter bacteria, which are genetically engineered to produce an easy measurable signal in response to a specific chemical compound. Bioreporters exploit sensory proteins, which upon binding of a target compound, can modify expression of a reporter protein. Current designs mostly use natural sensory proteins, but these cover only a limited range of detectable compounds.
The goal of Diogo’s project is to design sensory proteins with novel recognition specificities, based on the E. coli ribose binding protein (RbsB) as a starting point. He is using computational simulations (Rosetta) to predict variants, which instead of ribose may bind compounds with cyclic aliphatic and aromatic rings. These variants are then produced and screened in libraries to isolate those with changed ligand binding properties, which are further characterized biochemically. Simulations and screenings are still a big challenge on a flexible protein such as RbsB, because the methods are not perfect and (for now) the gain of new ligand binding is small. We hope to be able to improve these methods so that ligand-binding design can become easier.
In this project, which was advanced by Clémence Roggo, we tried to exploit bacterial chemotaxis for rapid chemical sensing. Three approaches were followed:
1) Quantitative microfluidic readout of chemotactic cell accumulation (Roggo et al., Environmental Microbiology, 2018)
2) Heterologous expression of methylaccepting chemotaxis proteins for aromatic compounds in E. coli (Roggo et al., Applied and Environmental Microbiology, 2018)
3) Chemotaxis activity probing of cells using fluorescent proteins (Roggo et al. BIORXIV/2018/367110)
In the FP7 project BRAAVOO we designed an automated bacterial biosensor reader that could hold strips with freeze-dried bacterial sensor cells. The instrument would revive the cells by injecting the sample and read out the bioluminescence of the cells during a two hour measurement. After that, the instrument would advance to the next strip and take a new measurement. With one sample analysis per day, we estimated that the instrument could work autonomously for about 1 month. The BIOLUM instrument was fabricated by the HES-SO in Sion.