tinkering with life

TheScientist | In the late 1990s, a handful of physicists and engineers began to take a greater interest in biology. The Human Genome Project was spitting out more and more gene sequences—blueprints for the protein building blocks of the cell—generating a flood of new information about the molecular machinery of life. Trouble was, there were not enough biologists doing the job of figuring out how all these genes and proteins worked together to create a living, breathing organism.

It was around this time that Boston University bioengineer James Collins saw his chance to inject a little engineering know-how into the study of biology. There were two ways to go about it, he figured—either disassemble cells or build them. “A burgeoning young engineer [is] either the kind of kid who takes stuff apart to try to figure out how it works, or [he’s] the kid who puts stuff together,” Collins says. Though both approaches seemed promising, there simply wasn’t enough known about the structures or functions of the genes and their protein products to infer how all the parts worked together by taking a cell apart, piece by piece.

“Reverse engineering seems to be too challenging,” Collins recalls musing to his then grad student Tim Gardner. “But can we do forward engineering? Can we take parts from cells and put them together in circuits, just as an electrical engineer might?”

The answer was yes. After two years of tweaking various characteristics of transcriptional repressors in E. coli, the team succeeded in constructing biology’s first synthetic toggle switch—two repressor genes controlled by two promoters that caused their respective repressors to be expressed by default. The repressors were designed to inactivate each other, however, such that the two genes would never be fully expressed at the same time. The addition of a stimulus, such as a chemical pulse to suppress one gene long enough for the other to come on, allowed the system to flip from one stable state (gene A on, gene B off) to its other stable state (A off, B on).

The results were published in 2000, alongside a paper from physicist Stanislas Leibler’s lab at Princeton University, which had undertaken a similar, but independent, project. Much like Collins with Gardner, Leibler teamed up with his graduate student Michael Elowitz to build an oscillator, which, like Collins’s toggle switches, used transcriptional repressors in E. coli. The Princeton team engineered three genes to inhibit each other in a cyclical manner, rock-paper-scissors style, with each gene repressing the next when a threshold concentration of its gene product had been reached. The result was the periodic expression of all three genes—monitored by the periodic glow of green fluorescent protein (GFP), whose expression was linked to another copy of a promoter controlling one of the three repressors.

The two publications are now widely cited as the seminal papers of synthetic biology, though neither paper received much publicity at the time. “[We were] kind of a ragtag group of engineers and physicists who were essentially amateurs in molecular biology,” Collins says. But in the last decade, many trained molecular and cell biologists have turned to syn bio, designing synthetic circuits built from biological components and branching out from the transcriptional regulation tools of Leibler, now at Rockefeller University, and Collins to add translation and post-translation components.