Rapid Design and Engineering of Smart and Secure Microbiological Systems

Pilot Science Focus Area Project: Argonne National Laboratory

Principal Investigator: Dionysios Antonopoulos¹
Co-Investigators: Gyorgy Babnigg¹, Michael Fonstein¹, Christopher Henry¹, Michael Jewett², Mark Mimee³, Arvind Ramanathan¹, Yasuo Yoshikuni⁴
Participating Institutions: ¹Argonne National Laboratory, ²Northwestern University, ³University of Chicago, ⁴Lawrence Berkeley National Laboratory

Summary

Secure Biodesign. Researchers are using CRISPR-enabled strategies to control specific populations of microorganisms and are leveraging machine-learning algorithms to better understand the precision of these mechanisms. Here, the activity of CRISPR guide RNA (gRNA) over time is overlaid on a depiction of the Escherichia coli MG1655 genome. Increased CRISPR gRNA activity is shown in green and decreased activity in red. The inset shows where CRISPR activity is particularly high in the middle of an intergenic region (arrow pointing to long green peak). [Courtesy ANL]

Designing and applying successfully engineered secure biosystems requires understanding how engineered microbes will interact with other organisms, either as direct competitors or as members of microbial consortia. Engineering microorganisms for nonlaboratory, environmental applications using a first principles approach to biological design is inherently challenging because engineered microbes tend to quickly revert to their wild-type behaviors and typically display reduced fitness (i.e., an unfavorable metabolic burden), making them less competitive than invasive contaminating species. A key question is how microbial sensing, signaling, and metabolism contribute to the stabilization and destabilization of interactions between engineered microbes and other organisms. This project investigates the organization, control, stabilization, and destabilization of natural and engineered microbes using a synthetic biology approach. This approach enables development of (1) single-strain systems capable of detecting and responding to target organisms in the environment, (2) a pipeline for refining and engineering biological constructs in new nonmodel host organisms, and (3) improved systems for the rapid design, engineering, and assaying of new and secure biological modules. The coupled approach of designing and building safeguard systems for intrinsic biocontainment that are predictable and portable across bacterial species focuses on beneficial members of the plant microbiome. A long-term goal of this research is to enable engineering of microbial communities, using first principles of biological design, that mimic the smart performance of microorganisms observed in natural systems. This would enable a new vision of biosecurity and biocontainment that harnesses the underlying mechanisms of resource management occurring within and between organisms.