HMS researchers have synthesized a DNA-based memory loop in yeast cells, work that marks a significant step forward in the emerging field of synthetic biology.
After developing a predictive mathematical model and using it to design and construct genes from bits of DNA, researchers in the lab of Pamela Silver, HMS professor of systems biology, fashioned a genetic circuit in which a stimulus launches a recurring function that continues in the cell after the stimulus ends and in daughter cells after the cell divides.
“Synthetic biology is an incredibly exciting field, with more possibilities than many of us can imagine,” said Silver, senior author on the paper, in the Sept. 15 Genes and Development. “While this proof-of-concept experiment is simply one step forward, we’ve established a foundational technology that just might set the standard of what we should expect in subsequent work.” (For video interviews with Silver, see Understanding Synthetic Biology and Applying Synthetic Biology.)
A team in Silver’s lab led by Caroline Ajo-Franklin, now at Lawrence Berkeley National Laboratory, and postdoctoral fellow David Drubin demonstrated that not only could they construct circuits out of genetic material, but they could also develop mathematical models whose predictive abilities match those of any electrical engineering system.
“That’s the litmus test,” said Drubin, “namely, building a biological device that does precisely what you predicted it would do.”
The components of this memory loop were simple: two genes that coded for transcription factors. The researchers placed the genes into yeast cells and exposed the cells to galactose. The first gene, designed to be switched on by the sugar, expressed a transcription factor that activated the second gene.
It was at this point that the feedback loop began. The second gene also produced a transcription factor, but this protein bound to the gene from which it had originated, reactivating it. So the second gene again created the same transcription factor, which looped back and activated the gene again.
The researchers then eliminated the galactose, causing the first synthetic gene to shut off. Even with this gene gone, the feedback loop continued.
“Essentially what happened is that the cell ‘remembered’ that it had been exposed to galactose and continued to pass this memory on to its descendents,” said Ajo-Franklin.
Most important, the researchers’ mathematical model succeeded in guiding their construction of the DNA-based device. The model was derived from in vivo quantitative descriptions they obtained on the behavior of the individual transcription factors, which could be used in constructing the feedback loop. These precise descriptions, when incorporated into the model for the loop, told them which transcription factors would work and under what conditions.
For synthetic biology, this kind of specificity is crucial. “If we ever want to create biological black boxes, that is, gene-based circuits like this one that you can plug into a cell and have perform a specified task, we need levels of mathematical precision as exact as the kind that goes into creating computer chips,” Silver explained.
The researchers are now working to scale up the memory device into a larger, more complex circuit, one that can, for example, respond to DNA damage in cells.
“One day we’d like to have a comprehensive library of these so-called black boxes,” said Drubin. “In the same way you take a component off the shelf and plug it into a circuit and get a predicted reaction, that’s what we’d one day like to do in cells.”
