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Molecular Engineering of Microbial Systems

Molecular Engineering of Microbial Systems seeks systems-level understanding of bacterial adaptive responses to environmental changes and interspecies interactions.

Molecular Engineering of Microbial Systems focuses on identifying the molecular function and biological role of proteins to enable manipulation of community (microbe-microbe and microbe-plant) interactions. The key players, such as enzymes, sensors, transporters and regulatory proteins, are identified by omics data modeling and machine learning and are characterized through determination of protein-protein, protein-ligand, and protein-membrane interactions. The knowledge about functions that enable communication, dictate specificity, and influence efficiencies of cell processes opens the way to the design and engineering of biological system response. To achieve this goal, we develop genome engineering methods for undomesticated strains in order to manipulate systems response using synthetic biology approaches.

The experimental systems used for these studies span a continuum from single bacterial species such as Pseudomonas and Rhodobacter to simplified mesocosms comprising Aspen, fungi, and bacteria that are used to study the bacterial functions mediating interactions with plants and fungi. The core expertise is in (i) biophysical and biochemical characterization of protein function including membrane proteins and protein-protein and protein-ligand interactions; (ii) engineering of protein nanosensors for imaging molecular interactions and metabolome sensing/mapping; (iii) building of computational models of ecosystem-scale phenomena such as dynamic plant-fungus-bacteria communities for biomass production, biofuels feedstocks, and ecosystem sustainability. Overall, the increased knowledge about function, regulation and system response combined with synthetic biology will open the way to manipulation of organism and community functions for human benefit.