Bioengineers add cooperative molecules to their toolbox for signal processing programming

Molecular arrays developed within living cells enable them to detect and process many signals from the environment in order to perform the desired cellular functions. Synthetic biologists have been able to reconstruct and mimic simpler forms of this cellular signal processing. But now, a new set of tools optimized by self-assembling molecules and predictive modeling will enable researchers to build the complex calculus and signal processing found in eukaryotic organisms, including human cells.

The work of Assistant Professor Ahmad & # 39; Mo & # 39; Khalil (BME), Assistant Professor Caleb Bashor of Rice University, BME graduate student Nikit Patel, and other colleagues from MIT, Harvard, Broad Institute, and the University of New York. Brandeis University were published in Science.

The type of combinatorial signal processing that they have been able to conceive by synthesis is what cells do naturally and gracefully to enable complex tasks, such as those of embryonic development and differentiation.

"This work is a tour de force of synthetic biology that addresses a major question: how do cells process information at the DNA level," says Dr. Tom Ellis, a reader in the Department of Bioengineering at Imperial College London, involved in the study.

"By taking a common principle that we know in nature, namely the ability of regulatory molecules to collaborate and form higher order assemblies, you can program cells to perform computational problems." and very difficult combinatorics, "says Khalil. "This represents a very different way of designing genetic circuits compared to the traditional technique and can pave the way for a new class of cellular functions that we can mimic and control."

First, the researchers constructed a library of simple synthetic molecular components that can interact with each other. Each of these components has its own chemical and kinetic composition, which can be used to understand its behavior. Using these known properties, they built a quantitative model that can predict how different combinations of these molecules combine to build higher order assemblies. They could then use this predictive model as a guide to designing genetic circuits that leverage the combinatorial assembly to perform the desired signal processing functions.

"Basically, these components bind to each other with extremely weak interactions," says Bashor. "But all these weak interactions add up, in a larger complex, to something really narrow, so when they are very few, they do not form the complex." And when they reach a concentration critical, they see each other, and they can basically come together and form the complex. "

The complex itself is composed of three components: a synthetic transcription factor that controls the activation of genes, the DNA sequence where this transcription factor binds, and a synthetic molecule of "clamp" to fix the three pieces together. This complex can allow them to adjust the intensity of the response of the cell to an input signal and to activate and deactivate the response at the desired times. But it is also much more than that.

"What we are exploiting and trying to build is one of the most powerful and universal characteristics of biology: cooperativity," said Khalil. "One way of thinking about cooperativity is to allow the whole to be bigger than the sum of its parts."

"You can consider cooperativity as the same type of signal processing feature that gives you an analog-to-digital converter," Bashor said. "An analog-to-digital converter takes something basically linear and turns it into something that looks like a switch."

Using their system, the engineering cells are fabricated to produce assembly components in response to a desired chemical or environmental input. In one experiment, they programmed yeast cells to respond to two different chemicals, and specifically to address varying concentrations of both chemicals in an analog or digital manner.

In analog circuits, the answer is continuous. if a low concentration of one or the other or both chemicals is present, the response is graduated. But in digital circuits, there is a discrete response "all or nothing", similar to a signal conversion in binary code, consisting only of 0 and 1, intermittently.

By taking advantage of their new ability to adjust the cooperativity between the assembly components, they showed that they could convert the dull cell response to neat – the more the complex cooperated, the sharper the response was . The sharpness of an answer (the intensity with which a system responds when a signal reaches a critical threshold) is essential for digital signal processing.

"The engineering of this type of transcription factor response was essential to allow us to program cells to perform various complex functions, such as Boolean logic, time filtering, and even frequency decoding." says Khalil.

This upgrade from analog to digital is the culmination of years of research. The analog-to-digital converter and their other synthetic gene circuits can be used to explore and manipulate the regulatory programs that guide the functions of the immune system and stem cells with the ultimate goal of developing transformational cell-based therapies from modified human cells.

"It is well known that nature has developed a very powerful information processing with only a small number of components, but deconvolving its operation is virtually impossible in human cells because of their complexity," Ellis adds. , which was not part of the research. "By recreating how human cells process information at the DNA level, they have however been able to recreate complex signaling from basic principles.This is an excellent example of how which an engineer can unlock a new way of answering the big questions of biology ".