Synthetic biologists add tunable, analog-to-digital converter to their toolkit
Synthetic biologists have added high-precision analog-to-digital signal processing to the genetic circuitry of living cells. The research, described online today 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, Caleb Bashor of Rice University, Ahmad “Mo” Khalil of Boston University (BU) and colleagues from MIT, Harvard, the Broad Institute and Brandeis University 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 Bashor, co-lead author of the study and an assistant professor of bioengineering in Rice’s Brown School of Engineering.
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.
“This work is a tour de force of synthetic biology that addresses a major question in how cells process information at the DNA level,” said Tom Ellis, Reader in Synthetic Genome Engineering in the department of bioengineering at Imperial College London, who was not involved in the study. “It’s well known that nature has perfected very powerful information processing with only a small number of parts, but deconvoluting precisely how this works is virtually impossible in human cells due to their complexity. By recreating the way human cells process information at the DNA level, but in a simple yeast cell model with synthetic parts, they have been able to recreate complex signaling from first principles. This is an excellent example of how thinking like an engineer can unlock a new way to answer major biology questions.”
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.
“That type of precision is a desirable property to have in synthetic circuits, too,” said Bashor, who joined Rice in 2018 and began the project several years earlier during a postdoctoral stint at BU. “Nature often does it through a process called cooperative self-assembly, where several proteins called transcription factors self-assemble into a larger complex. Only when they come together is the switch thrown.”
Bashor, Khalil and colleagues 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, Bashor, Khalil and colleagues 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,” Bashor 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. Bashor and Khalil 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 Khalil, the corresponding author on the study.
Bashor said the bulk of the four-year project was spent refining a predictive model that can guide other engineers in using the system to design analog-to-digital converters that can respond as intended even to multiple incoming signals.
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 synthetic biologist and study co-author James Collins, who holds joint appointments at MIT, Harvard and the Broad Institute.
Going forward, Bashor’s Rice 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.
The Latest on: Engineered organisms
via Google News
The Latest on: Engineered organisms
- The language of metabolites can be decoded with new genome technologyon October 14, 2019 at 8:11 am
and homeostasis of an organism. A team of microbiologists and genomicists led by the Department of Energy Joint Genome Institute (JGI) has invented a genetic engineering tool that advances the study ...
- Unlocking the biochemical treasure chest within microbeson October 14, 2019 at 8:03 am
Co-first author Jing Ke, a scientific engineering associate at JGI, added ... "Aside from a few very well-studied microbes, the so-called model organisms like E. coli, we don't know whether a strain ...
- Manipulating the Patterns of Mechanical Forces That Shape Multicellular Tissueson October 13, 2019 at 8:59 am
Department of Mechanical Engineering, Columbia University, New York ... with a focus on recent experimental studies of epithelial tissue sheets in the embryo of the model organism Drosophila ...
- How the Global Food Supply Transition Is Like the Energy Transitionon October 10, 2019 at 2:37 pm
However, they are bumping up against conventional agricultural practices involving the use of pesticides and genetically modified organisms, or GMOs, within the global food supply. In that respect, ...
- The precautionary tale of golden riceon October 10, 2019 at 12:54 pm
The term genetically modified organisms (GMOs) inspires images of crazy crops: a single plant that bears tomatoes above ground and potatoes beneath, or a tree that bears a fruit with stripes of yellow ...
- Tea and banana plants have been genetically modified by bacteriaon October 8, 2019 at 9:29 am
ABOUT one in 20 flowering plants are naturally transgenic, carrying bacterial DNA within their genomes. The added genes can make them produce unusual chemicals, and the species they have been found in ...
- 'We don't want to be guinea pigs': how one African community is fighting genetically modified mosquitoeson October 8, 2019 at 3:23 am
In the summer of 2018, more than 1,000 people marched in the capital Ouagadougou against the use of genetically-modified organisms in the country, including the GM mosquitoes. The United Nations ...
- Stanley Qi gives CRISPR a makeover to redefine genetic engineeringon October 2, 2019 at 6:09 am
CRISPR/Cas9 has become one of the most powerful tools in molecular biology since its introduction in 2012. It is composed of an RNA (the CRISPR part) that guides a DNA-cutting enzyme called Cas9 to ...
- Scientists Engineered Bacteria to Produce Huge Amounts of Psilocybinon September 30, 2019 at 9:52 pm
Now, researchers have engineered bacteria that creates psilocybin in higher quantities that can be ... “We expect there is a lot of room for further enhancement of the organism and production process, ...
- 'Trippy' Bacteria Engineered to Brew 'Magic Mushroom' Hallucinogenon September 30, 2019 at 12:14 pm
Scientists modified E. coli to produce the psychoactive chemical that makes 'shrooms so trippy ... coli produced more psilocybin than any other organism retrofitted with "magic mushroom" DNA to date.
via Bing News