Synthetic biologists have added high-precision analog-to-digital signal processing to the genetic circuitry of living cells. The research, described in the journal Science, dramatically expands the chemical, physical and environmental cues engineers can use to prompt programmed responses from engineered organisms.

Using a biochemical process called cooperative assembly, researchers engineered genetic circuits that were able to both decode frequency-dependent signals and conduct dynamic signal filtering.

"You can think about cooperativity as the same type of signal-processing feature that gives you an analog-to-digital converter, a device that takes something that's basically linear and turns it into something switchlike," said co-lead author of the study.

Synthetically engineering cooperative assembly allowed the researchers to perform the type of combinatorial signal processing that cells naturally and elegantly do to accomplish intricate tasks, like those in embryonic development and differentiation.

In nature, cells often have to make black-and-white decisions based on information that's gray. For example, imagine a cell has a gene that allows it survive in a highly acidic environment, but it takes a good deal of energy to activate that gene and get the protection. Through billions of years of natural selection, cells that activate the gene too early or too late get outcompeted by those that make the decision at the optimum time to both ensure survival and expend the least amount of energy.

Researchers engineered cooperative self-assembly by inventing a modular system of synthetic protein components that can assemble into complexes of varying size. In this system, engineered cells are programmed to produce assembly components in response to whatever input the engineers wish to use to activate the circuit. For example, in their experiments, researchers programmed yeast to respond to two different drugs that were administered in varying concentrations via a microfluidic device.

In this way, the concentration of component molecules produced inside the yeast rose and fell in response to the analog input -- the concentration of drugs in the test chamber.

"Basically, these components bind to one another with extremely weak interactions," the author said. "But all of those weak interactions add up, in a bigger complex, to something that's really tight. So, when there's very few of them floating around, they won't form the complex. And when they reach a critical concentration, they see each other, and they can basically come together and form the complex."

The sharpness of a response -- one that happens quickly at precisely the intended time -- is key for digital precision. The researchers designed activation complexes that contained as few as two transcription-factor components and as many as six, and their experiments showed that the larger the complex, the sharper the critical response.

"Engineering this type of response into transcription factors was central for allowing us to program cells to perform a diverse array of complex functions, such as Boolean logic, time-dependent filtering and even frequency decoding," said the corresponding author on the study.

To demonstrate this aspect of the work, the team designed and demonstrated signal-processing circuits reminiscent of microelectronics, including low-pass filters that responded only to low-frequency drug inputs and band-stop filters that were activated only at high frequencies.

"Our work shows how the nonlinearity of transcription factor complexes can be used to engineer signal processing in synthetic gene circuits, expanding their functionality and real-world utility," said the co-author.

Going forward, the lab plans to use the analog-to-digital converter and other synthetic gene circuits to explore and manipulate the regulatory programs that guide immune and stem cell functions with an eye on developing transformational cell-based therapeutics from engineered human cells.

http://news.rice.edu/2019/04/18/bioengineers-program-cells-as-digital-signal-processors/

https://science.sciencemag.org/content/early/2019/04/17/science.aau8287