How Bacterial Growth-Phase Reshapes Synthetic Gene Circuit Function

In recent years, the advancement of biological engineering tools has enabled the embedding of novel functions into living organisms. Simultaneously, our comprehension of the interaction between synthetic genetic circuits and their host organisms has grown significantly over the past decade, leading to the creation of context-aware predictive models.

However, predicting the long-term function of these circuits in real-world conditions remains challenging. Specifically, synthetic genetic circuits, which are usually assessed during exponential growth, must function for extended periods in nutrient-limited environments where bacteria enter the stationary growth phase.

To address this issue, researchers have developed a mathematical model that accounts for the dynamics of a genetic circuit as cells transition into the stationary growth phase. They constructed synthetic genetic circuits equipped with fluorescent reporter outputs and monitored plasmid DNA copy number, mRNA levels, protein levels, and live cell counts over the course of a week in the stationary growth phase.

The findings revealed that transcription rates decrease sharply shortly after entering the stationary phase but stabilize at a basal value dependent on the promoter and ribosome binding site. Similarly, translation rates decline in stationary phase, but protein accumulation due to cell division cessation can result in protein levels surpassing those observed during the exponential phase.

The model successfully replicated these observations and demonstrated its capability to predict the output of new genetic circuits. This model can thus be utilized as a valuable tool to anticipate how genetic circuit designs might evolve over extended periods when cells enter the stationary growth phase.