Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Optogenetic Control of a Dual Yeast-Yeast Consortia for Chemical Production


Sergio A. Garcia Echauri* (, Saurabh Malani* (, and Jose L. Avalos


Princeton University


The goal of this project is to develop optogenetic tools and applications—the use of light-responsive proteins to modulate biological processes—for the control of microbial consortia for biofuel and chemical production. Researchers have developed novel optogenetic circuits to control growth rates in several strains of yeast and bacteria; this allows the team to not only stabilize microbial consortia with light, but also optimize their population ratios for chemical production. The team will develop light-controlled co-culture fermentations and use mathematical models and feedback controls to advance basic understanding of these biological systems and optimize them for growth rate and chemical production. These technologies constitute a new paradigm for the engineering and control of microbial consortia, which could help to realize their promise for biofuel and chemical production.


Microbial co-culture fermentations can improve the production of chemicals and biofuels over single-strain fermentations; optimizing and segregating production modules among the consortia members can lower the metabolic burden from overexpression of metabolic enzymes (Zhou et al. 2015). Dynamically tuning the consortia composition is integral in optimizing multistep production processes, in which growth and production phases are uncoupled and therefore different for each consortia member. Optogenetics has enhanced the ability to seamlessly control gene expression with the input of light. Light as a gene inducer has many advantages when compared to traditionally used chemical inducers: it’s inexpensive, can be applied and removed instantly, is highly tunable, is active in different media compositions, and has minimal cellular side-effects. The lab has developed optogenetic tools to control gene expression in yeast with blue light (Lalwani et al. 2021). Using this system, researchers engineered two Saccharomyces cerevisiae strains with opposite growth phenotypes, one requiring blue light to grow and stops growing in darkness, while the other requires the absence of blue light (darkness) to grow and does not grow under blue light. Using these strains, researchers demonstrate the control of synthetic yeast-yeast consortia to achieve desired set-points of cell densities in batch and continuous culture conditions.


Lalwani, M. A., et al. 2021. “The Neurospora crassa Inducible Q System Enables Simultaneous Optogenetic Amplification and Inversion in Saccharomyces cerevisiae for Bidirectional Control of Gene Expression,” ACS Synthetic Biology 10, 2060–75.

Zhou, K., et al. 2015. “Distributing a Metabolic Pathway Among a Microbial Consortium Enhances Production of Natural Products,” Nature Biotechnology 33, 377–83.

Funding Information

This research was supported by the DOE Office of Science, Biological and Environmental Research (BER) Program, Award Number DE-SC0022155.