ContainELMs – Material-centric genetic programming of biocontainment in engineered living materials

• Applicants: Dr. Meike König; Dr. Shrikrishnan Sankaran
• Subject Area: Biomaterials ; Biological and Biomimetic Chemistry
• Term: since 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 541297755

Engineered living materials (ELMs) are emerging as enabling solutions for the real-world applicability of synthetic biology. By encasing genetically modified organisms inside materials, they can be fabricated in application-suitable and user-friendly formats, stored stably and deployed large-scale. With several studies demonstrating these capabilities and professing the rapid transfer of this technology to solve real-world problems, the focus on biocontainment of genetically modified organisms in ELMs is starting to grow. This is particularly true when bacteria are used as the living component, due to their fast growth rates, small size and ability to thrive in various environments. Few studies have thus far addressed their biocontainment in ELMs using multilayered material designs in which the bacteria are in an inner layer, surrounded by a stable outer layer that physically prevents their escape. However, these designs do not account for damage of the material during its lifetime or fabrication errors when mass-produced, which would result in release of the encapsulated bacteria. Synthetic biology offers biocontainment solutions like auxotrophy and kill-switches that can be programmed into the bacteria although these strategies are susceptible to mutational escape due to evolutionary mechanisms in the cell. As the challenges hindering both these biocontainment strategies are orthogonal, a combination of them could overcome their individual drawbacks. ContainELMs systematically explores this possibility by not only combining both strategies, but by doing so in a synergistic manner such that the bacteria are adapted to the microenvironment engineered into the material for its survival. The bacteria will be encoded with survival-switches that ensure bacterial survival only under permissive conditions like the presence of a specific small-molecule, peptide or pH value. The encapsulating material will be designed to internally offer this permissive condition, in contrast with its surroundings. Thus, survival of the bacteria will be sustained within the material but not on the outside, reducing both the pressure for escape mutants to develop and the reliance on the integrity of the physical barrier. This strategy will be developed with a synthetic biology model bacterium, E. coli, and a non-model lactobacillus strain, both of interest for health and environmental applications. The ELM will be fabricated as fibers and meshes using electrohydrodynamic jetting to create the bacterial layer with survival-supporting conditions and chemical vapor deposition to create a physical barrier coating. Biocontainment testing and characterization will be done for at least one month by simulating field conditions where the ELM would be used for river water bioremediation. The tools, techniques and knowledge generated in ContainELMs are expected to enable wide adaptation of this material-centric active biocontainment strategy among hybrid ELMs.

• DFG Programme: Priority Programmes
• Subproject of: SPP 2451: Engineered Living Materials with Adaptive Functions
• Co-Investigator: Professor Dr. Joerg Lahann