Acellular systems rapidly develop the potential of synthetic biology, opening the way for a new wave of applications in living organisms.
When engineering an organism, most laboratories synthesize genes, insert them into cells, and see if the desired effect occurs. There are many limitations to this approach. The process can be time consuming and often the genes do not work as expected. As a result, many in the field now view cell-free systems - an in vitro tool for studying biology - as an easily accessible approach for prototype genes before they are inserted into a living cell. Cell-free systems have some crucial advantages over living organisms and can be made from whole cell extracts or individually purified components, such as PURE.
Cell-free systems can be used to produce toxins in high yields, unlike living cells, and components can generally be added or removed without consequence, while the deletion in vivo of an protein could kill the cell.
Protein Production 2.0: Unblock unnatural chemicals
But then many still do not see the potential of cell-free systems: It's an incredibly powerful approach to dissecting complex biological problems. Synthetic biology laboratories now exploit acellular systems to produce proteins with unnatural chemical properties, to create prototypes of metabolic pathways and even to detect biomolecules of clinical importance in just a few minutes.
Cell-free systems have long been used to produce natural proteins because the preparation of an extract takes only a few days and toxic proteins can be produced while the chemical environment is tightly controlled. But some laboratories are looking beyond the production of natural proteins.
In living organisms, unnatural amino acids are usually incorporated into proteins with a method called Stop Codon Suppression. In this method, a rarely used stop codon, typically UAG, is reaffected to produce another protein. In this way, an orthogonal tRNA that recognizes UAG can be expressed, but instead of signaling the translation to stop, it incorporates an unnatural amino acid. More than 100 unnatural amino acids have been incorporated into proteins using this approach 3.
Compared to living cells, acellular systems have a higher tolerance to toxicity caused by unnatural components, no cellular membrane barrier limits the transport of unnatural amino acids, more flexible control of the reaction is possible by freely adjusting the composition of the system and there is a higher incorporation efficiency non-natural amino acids.
Beyond Protein Production: Acellular Systems for Prototyping Lanes
While synthetic biologists adopt acellular systems to produce proteins that are decorated with unnatural amino acids, others are eagerly applying new capabilities to simultaneously probe tens of interacting proteins.
Acellular systems are more than a prototyping tool of autonomous genetic parts.
These are tools to test entire metabolic pathways. By creating numerous cell extracts, each with only a portion of the expressed pathway, it is possible to transform cell-free systems into a modular system that can be used to assemble any desired pathway in vitro. This smart approach, combined with automation and machine learning, could dramatically accelerate the way scientists test combinations of metabolic pathways. Nevertheless, there are fundamental limitations to our ability to apply the results of cell-free systems to living organisms.
Sensors on demand
The abundance of data allowed by this approach even allows us to go beyond the metabolic pathways; this could also be useful for the creation of acellular systems for the clinical biosonde.
The cells constantly detect their environment, react to the signals and act with caution. It follows naturally that the brilliant reactivity and programmability of biology could then be used to detect molecules of clinical importance for humans.
Cell-free systems have been developed for biosensing applications, with the goal of accurately diagnosing disease in minutes rather than hours.
Biosensors have focused on the application of acellular systems to design genetically encoded biosensors that measure biomarkers in clinically relevant samples. Although many models of biosensors work in the laboratory, few have been tested on real clinical specimens.
The reason that cell-free systems are preferable to living systems [as biosensors] in some contexts is that tests are economical, fast, quantitative, scalable and automated, and reproducible. They also offer advantages for biocapture in that they can be lyophilized on surfaces such as paper, they are not genetically modified organisms and are therefore more acceptable for use in clinical and field environments.
In the coming years, cell-free systems will be increasingly used in the clinic, especially in situations where a rapid pre-test is desirable.
A more distant future without cells
Yuan Lu, for example, is considering the use of cell-free systems in areas other than biology. "For this to happen, cell-free systems can not simply focus on biological transcription and translation," he says. "To achieve revolutionary development, cell-free systems must be strongly integrated with materials science, neuroscience, electronic engineering, 3D printing, artificial intelligence and other next-generation technologies. . "
Ashty Karim believes that cell-free systems will be increasingly used for "direct-to-use" applications. "We will begin to look at cell-free sensors as diagnostics in agriculture, defense and medicine, and we will see on-demand biofabrication of therapies, vaccines and commodities," she said. he said, pointing out that these advances are made possible by improvements in cell-free preparations and mixtures, such as "cell-free systems that can glycosylate proteins and cell-free systems containing orthogonal transcription factors".
The most ambitious application of cell-free systems, exemplified by the Build-a-Cell Consortium, aims to build a minimal synthetic cell from scratch. According to Paul Freemont, a member of the consortium, this effort will be facilitated by cell-free systems. He explains, "If we build a series of modules that mimic various aspects of living systems [in cell-free systems] like motility, detection and regulation, then the real challenge will be how to interface these different modules to produce a more complex synthetic cell. ".