Living factories of the future

This feat is a prime example of synthetic biology, in which scientists reprogramme cells to replicate products found in nature — or even make more-specialised materials that would never normally be produced by a natural organism. Synthetic biologists are ambitious.

“We’d all love to imagine a world where we could adapt biology to manufacture any product renewably, quickly and on demand,” says Michael Jewett, a synthetic biologist at Northwestern University in Evanston, Illinois.

Synthetic biologists are going beyond simply producing materials — they are creating complex systems by “wiring up” genetic parts into circuits. This approach has already resulted in various living switches and sophisticated sensors. For example, Martin Fussenegger’s group at the Swiss Federal Institute of Technology (ETH) in Zurich has built biomedical sensors that can detect disease-relevant metabolites in the blood and trigger the production of therapeutic compounds. In mice, these biosensors successfully staved off gout and obesity, and treated the skin disease psoriasis. This young field has already spawned some success stories, but making and putting together genetic parts currently involves substantial guesswork and unpredictability.

Genetic data
To build an artificial product, synthetic biologists begin by selecting DNA parts on a computer and manufacturing them with specialised instruments. The parts can then be inserted into the DNA of microorganisms and cells to reprogramme them.

Thanks to the plummeting cost of DNA sequencing, there is now a vast collection of genetic data through which synthetic biologists can sift to find useful genes. One leading database, the US National Center for Biotechnology Information’s GenBank, contains more than 190 million DNA sequences from 1,00,000 organisms. Some of the most widely used genetic parts encode enzymes — proteins that are essential for manufacturing.

Other favourites in the genetic designer’s palette are promoters — stretches of DNA that regulate the activity of nearby genes and cause them to be expressed. When proteins called transcription factors bind to a promoter, the process of transcribing a gene begins.

But promoters operate too slowly for some synthetic biology applications. “We’re trying to build things that operate fast — on millisecond time-scales,” says biologist Pamela Silver of Harvard Medical School in Boston, Massachusetts. Scientists are therefore examining alternative mechanisms that allow gene expression to be controlled directly by signals in the environment, such as toxins or antibiotics.

With myriad synthetic DNA pieces at their disposal, synthetic biologists can indulge their creativity. Christopher Voigt, a synthetic biologist at the Massachusetts Institute of Technology in Cambridge is enthusiastic about the possibilities: “The nice thing about biology is that there are lots of ways to do the same thing — and as an engineer, you can pick the way that is easiest to design.” But genetic parts must perform consistently if the goal of setting up industrial processes is to be realised. “One of the key problems for biology in general is the lack of reproducibility,” says Richard Kitney, chairman of the Institute of Systems and Synthetic Biology at Imperial College London. “In synthetic biology this is totally unacceptable — you have to have reproducibility if you’re going to do industrial translation.”

Cellular software
Thanks to greater automation, it is now simpler and cheaper than ever before to make synthetic DNA parts. But connecting those parts to form genetic circuits that can work together to provide sophisticated, computing like behaviours is still a challenge. “Any time you physically connect DNA you’re creating a new sequence at that interface — as DNA is so information-rich, you could create a new promoter or change the beginning of the RNA,” says Christopher.

Even carefully designed circuits can malfunction and cause unwanted expression of a gene or interference between the genetic elements in the biological circuit — outcomes that cannot be foreseen in computer models. “The community is very much operating in a world where we cannot predict what is going to happen in our systems when we build them,” says Reshma Shetty, co-founder of the synthetic biology company Ginkgo Bioworks in Boston, Massachusetts.

This uncertainty means that many of the steps in engineering a synthetic system need to be tested and optimised. Software tools and robotics are speeding up each part of this process, from building the artificial DNA to inserting it into a microbe. “You can use high-throughput prototyping to just build every variant, and hopefully one of them will hit,” says Jay Keasling, a biochemical engineer at the University of California, Berkeley, and a pioneer in the field. The push for automation has led a number of synthetic biology research centres and firms to install “biofoundry” facilities in which robotic assembly lines create, test and optimise microbes at a much larger scale than could be done by hand.

Biofoundries are enabling synthetic biologists to embark on ambitious projects.  Some biologists remain sceptical about the rush to scale up and automate, and favour a more theory-driven strategy. But Richard, who co-directs SynbiCITE, considers automation to be an inevitable step in the evolution of synthetic biology. “You can rapidly run a whole series of experiments in parallel to see which configuration works best,” he says.

Medical cells
When it comes to medical applications, synthetic biologists are engineering mammalian cells rather than microbes. Such designer cells could produce drugs in response to disease or take over certain physiological tasks in people with metabolic disorders such as diabetes. But engineering mammalian cells introduces a new set of challenges.

The easiest cells to cultivate are tumour-like, immortalised cell lines, which are inherently “defective” and therefore not representative of healthy tissues. Conversely, tissue-derived primary cells are hard to cultivate and manipulate, and differences between cell types confound efforts to build toolkits that can be applied across the body. “Something that works in a kidney cell will not necessarily work in the lung or liver,” says Martin. To get around this, the ETH team is engineering ‘prosthetic gene circuits’,  which are introduced into host cells that can be implanted at the site of disease. Tinkering with genomes can also present problems. Even ‘smart’ genome-editing tools — such as CRISPR–Cas9, a system for introducing targeted modifications at specific DNA sites — can have unpredictable outcomes.

Others want to do away with the cell altogether. Michael is studying cell-free systems in which bacterial extracts are purified to obtain only the ‘useful’ parts of the cellular machinery. Michael’s team has shown that this approach can efficiently churn out medically useful proteins such as erythropoietin, a hormone that stimulates red blood cell production. “It’s not yet a replacement for existing technologies, but the yields are sufficient to serve as a complement,” he says.

The field is still in its infancy — indeed, the earliest demonstrations of engineered genetic circuits appeared only in early 2000 — and it can be dauntingly complex. Even so, a growing number of scientists grounded in conventional molecular biology are keen to give genetic design a try.