A biophysical model linking chromatin compaction and light dosing to the stability of optogenetic yeast strains

Abstract

Metabolically engineered populations of the yeast strain Saccharomyces cerevisiae are increasingly used for biomanufacturing of drugs, chemicals, and materials. However, cells containing synthetic gene circuits tend to lose their function over time due to the emergence of mutant cells that bypass genetic control and overgrow the population; this phenomenon is known as evolutionary instability. In evolutionary game theory, such individuals, which receive a benefit at the expense of other cooperating individuals in the population, are known as cheaters. Gonzalez et al. show that expressing two proteins involved in compacting cellular chromatin, the intracellular complex that holds DNA, more than doubles the stability time of a metabolically engineered yeast strain. There are several mechanistic hypotheses for whether and how the expression of chromatin-compacting proteins extends strain stability, and what effects it has on cells beyond this, but they are costly to test experimentally and have not been thoroughly explored through simulations. In this thesis, I model strain stability in a population of optogenetically engineered yeast which grow in the presence of blue light and incorporate the effects of chromatin compaction on strain stability. Using experimental data from optogenetically engineered yeast with and without the genes for the chromatin-compacting proteins SpSwi6 and SpClr4, I test mechanistic hypotheses about how chromatin compaction extends strain stability, including mutation rate reduction and growth rate reductions caused by metabolic burden, to evaluate the benefits and drawbacks of chromatin compaction as a stability-improving intervention. I also examine the benefits of periodic light exposure, which induces cell growth, on strain stability. Finally, using the mechanistic interpretations offered by the model and its predictions of cell population behavior in untested conditions, I suggest experimental conditions that could improve strain stability.