ynthetic biology, or the application of engineering acids in ways never seen in nature. Advances in molecular engineer- principles to the design of life, presents world-changing ing are driving the construction of ever-more complex circuits made prospects. Could components of a living cell function from biological materials. And the ability to freeze-dry cellular tran- as tiny switches or circuits? How would that allow bio- scription machinery outside the confines of cells has enabled scien- medical engineers to build biological “smart devices”— tists to easily manufacture proteins at will, at any time and place. Sfrom sensors deployed inside the body to portable medical kits able Most synthetic biology today centers on single-celled organ- to produce vaccines and antibiotics on demand? Could bacterial isms, such as the bacterium Escherichia coli. In the spring of 2019, for “factories” replace the fossil-fueled industries that produce plas- example, researchers at the University of Cambridge announced tics, foods, and fertilizers? Will the secrets of living creatures that that they had synthesized an entire E. coli genome—the bacterium’s enter suspended animation during periods of drought and extreme complete set of genetic material—and swapped it into living E. coli cold be harnessed to keep human victims of trauma alive? And is cells. Their version, which at four million base pairs (the building the genetic information preserved in long-frozen or fossilized ex- blocks of the DNA double helix) was then the largest synthetic ge- tinct species, like woolly mammoths, sufficiently recoverable to nome created to date, was nevertheless a pared-down variant that help save living species? eliminated redundancies, thereby simplifying the biological com- These ideas, once the stuff of science fic- Synthetic biology plexity evolved over millennia and making tion, are now the stuff ofscience. Some aren’t the organism easier for human engineers to yet functioning realities, but others have understand and manipulate. Although the launched business applications, whether in and the frontiers bacteria with synthetic genomes were not medicine (such as hospital gowns that sig- as robust as their natural counterparts, and nal exposure to infection) or in land reme- of technology reproduced slowly, they survived. diation (where bacterial “factories” pow- The scientists who do this work know ered by the sun capture nitrogen from the that they are operating in a new domain, atmosphere to help plants grow). Someday, with transformative possibilities. James engineered forms of life that store carbon by Jonathan Shaw Collins, a core faculty member at the Wyss may even be one of the solutions to Earth’s Institute who 20 years ago created one of the climate-change problem. first biological circuits, believes this synthet- “Most of biology, historically, has been ic, engineered biology “will be a defining, if analyzing how nature works,” says Don- not the defining, technology of the century.” ald Ingber, director of Harvard’s Wyss Institute for Biologically Snapshots of the evolving technologies follow. Inspired Engineering. Systems biology is the culmination of that ef- fort to deconstruct natural processes. Now, with synthetic biology, Switches, Sensors, and Medicines on Demand he points out, scientists “are at the point where we know enough In January 2000, Collins and a team at Princeton, working sep- that we can actually engineer artificial and natural biological sys- arately, simultaneously published in Nature the first designs for tems.” Researchers today can build things from biological parts, and switches made from biological parts. That innovation arguably even create hybrid systems by linking them to non-living machines. marked the beginning of modern synthetic biology. Collins had Propelling the science forward are scores of innovations in bio- engineered a switch, like the push button on a desk lamp: press logical science, with new discoveries coming every month. Among once, the light turns on; press again, it turns off. Collins’s simple the most important are advances in genetic editing, including im- mechanism was not built from metal and plastic, but from two genes provements in accuracy, and the ability to make hundreds of changes that flip-flopped between on and off states when stimulated by at once. Another is computer-aided design, widely used to model chemical signals or changes in temperature. It was a simple circuit. biological systems, and to build new proteins by combining amino The simplicity of what Collins had created belied its potential. Harvard Magazine 37 Reprinted from Harvard Magazine. For more information, contact Harvard Magazine, Inc. at 617-495-5746 The ability to engineer biological circuits in this way meant that signed to combine systematically with an opposite RNA strand cells could represent binary states such as the zeros and ones that associated with a bacterial pathogen. That opens the switch, which are the basis of computer systems. They could perform simple logic. then releases a fluorescent particle that reveals the presence of And because they could be programmed to die after a certain num- the pathogen. ber of cell divisions, they enabled the creation of the first kill-switch To effect this, researchers must engineer biological circuits and safety mechanisms to prevent organisms with synthetic parts from insert them into living bacteria: a process that sounds formidably escaping into the environment. complex. But scientists know that different kinds of bacteria, in Many of the earliest biological switches were crude and prone the course of evolutionary history, have routinely exchanged whole to accidental triggering. The inside of even a single-celled bacte- “cassettes” of many genes, such as those that control metabolism. rium such as E. coli, where engineered synthetic circuits are often This swapping of genetic material is called “horizontal gene trans- James Collins introduced and tested, is very busy. There are “many molecules, fer.” Within these cassettes that control particular biological func- large and small, interacting in a very small space,” explains Col- tions, researchers have devised ways to alter specific genes, and then lins, who teaches in the Harvard-MIT Program in Health Sciences reinject the whole functioning circuit into a cell. and Technology. All this activity can lead to what engineers call These genetic circuits control what proteins the cell produces. “crosstalk,” instances when a stray signal can accidentally flip a Since the 1960s, biologists have known that the protein-synthesiz- simple switch. Such unpredictable behavior would be anathema ing machinery of a bacterium can even be plucked from within the in biomedical applications. cell’s protective outer membrane, placed in a laboratory test tube But biological switches have become much more robust since or petri dish, and still function. 2000, allowing them to be used in laboratory animals as reliable In October 2014, the field took another leap forward when the detectors that signal the presence of pathogens. In applications Collins lab published a serendipitous discovery that advanced the in the gut, for example, RNA-based switches have been designed practicality of using RNA-based switches as detectors in the field— to release appropriate probiotic therapies. Such an RNA-based and even as therapy-producing agents. While working to develop switch takes advantage of the fact that the bases on a single strand encapsulated cell-free genetic networks for cellular reprogramming, of RNA want to pair with opposite bases, just as “A[denine] goes postdoctoral student Keith Pardee discovered that a cell’s tran- to T[hymine] and G[uanine] goes to C[ytosine]” in DNA base pair- scription and translation machinery (the parts that build proteins ing, Collins explains. This means that an RNA probe can be de- from DNA instructions) could be spotted onto a piece of paper, 38 January - February 2020 Portraits by Jim Harrison Reprinted from Harvard Magazine. For more information, contact Harvard Magazine, Inc. at 617-495-5746 The lab’s first deployment of the technology was to create a detector for Ebola, a rare but deadly disease that has killed thousands of people in West Africa. freeze-dried, and then restored to full function when rehydrated. scription and translation—the parts that enable that modified DNA The lab’s first deployment of the technology was to create a detec- with its associated genes to be “turned on and express the relevant tor for Ebola, a rare but deadly disease that has killed thousands of proteins.” In the case of diagnostics, the rehydration that activates people in West Africa. Subsequent testing revealed that their Ebola protein production might be a patient’s blood, urine, or sputum. In detector remained viable for a year or more—without the need for the case of therapeutics, adding water is enough to revive the ma- refrigeration. This was significant, because Ebola often strikes in chinery for making vaccines or antibiotics. This has enabled his lab to remote regions poorly served by healthcare facilities. develop field kits the size of a small cellphone that could be carried The lab has subsequently used the same techniques to make di- “by soldiers or hikers or astronauts, athletes, or healthcare workers agnostics for the Zika virus, for gut microbiome analysis, and for detecting antibiotic resistance. “We now have ef- forts underway looking at Lyme dis- ease, HIV, TB, HPV, and hepatitis C,” says Collins.