Reversible long-term memory devices in bacteria inspired by mammalian chromatin modification circuits

Enabling bacterial cells to remember long time environmental cues is essential for numerous processes including, sensing pollutants in water or soil, for recording biomarkers of stress in the human gut, and for triggering cell death to avoid escape in the environment. At the same time, if scientists can build this capability, they will also understand its principles, and thereby potentially shed light on how human cells can remember their identity for the life-time of an organism, a critical property that is broken in some biological processes.

The unique innovation of this project is the engineering of a circuit motif in bacteria that mimics processes associated with long-term memory of chromatin states in mammalian cells. This design is expected to enable long-term memory of gene states in bacteria. This project will enrich the curriculum of the Biomolecular Feedback Systems Course, which is taught every year at MIT.

This research will train graduate students in Mechanical, Biological, and Electrical Engineering at MIT, as well as provide undergraduate research experience to both MIT and non-MIT undergraduate students who come to the MIT campus yearly through the MIT Summer Research Program and Undergraduate Opportunity Research Program. MIT undergraduate students will further obtain a training opportunity under this project through the New Engineering Transformation Education Program.

Reversible memory devices in bacteria, which can be switched between two stable states with a transient input stimulus, have been engineered before. However, after the input stimulus is removed, memory of the stable state usually vanishes after only a few days. This limits the applicability of bacterial memory devices.

More broadly, there is a lack of understanding of the molecular mechanisms that control the temporal duration of memory. Here, the investigators seek to establish this understanding, engineer long-term memory devices in bacteria, and demonstrate these devices’ application to a biocontainment test-bed. To this end, the investigators propose to implement with bacterial processes the circuit motifs that are implicated in the long-term maintenance of chromatin states in mammalian cells.

The investigators will use DNA inversion through invertase enzymes as the core process of the design since, just like chromatin modification, DNA inversion is an enzymatic reaction. The key innovation, which mirrors mammalian chromatin modification circuits, is to introduce autocatalysis of DNA inversions by having the inverted DNA express an invertase enzyme that catalyzes the inversion itself.

The investigators propose to first demonstrate that autocatalysis of DNA inversion is required to achieve stability of the inverted DNA state. They then propose to show that two antagonistic autocatalytic DNA inversions, sharing the same substrate, create a bistable memory switch, and that the duration of memory of each of the two states hinges on the strength of autocatalysis.

They finally propose to demonstrate that they can extend memory to last several weeks, that they can quickly reverse it by small molecules, and that the design can be applied for biocontainment.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.