Building Better Bacteria

Synthetic biology brings together engineers and biologists to reprogram cells from the ground up. These re-engineered organisms have the potential to revolutionize how we produce fuel, clean up hazardous waste, interact with the environment and treat human disease. CREDIT: Janet Iwasa and the MIT Synthetic Biology Center. View full size image

This Behind the Scenes article was provided to LiveScience in partnership with the National Science Foundation.

While your last interaction with bacteria may have been unpleasant, to say the least, synthetic biologists can't get enough of these stomach bugs.

"Bacteria are great model systems for synthetic biology," says Chris Voigt, Ph.D., an associate professor in the Biological Engineering department at the Massachusetts Institute of Technology. "They are relatively simple organisms but we know so much about their genes."

Unlike traditional genetic engineering, which typically tweaks a few genes at a time, the field of synthetic biology is dedicated to rewiring and reprogramming cells, from the ground up. The result is a range of bacteria with unusual properties, from salmonella that produce spider silk, to E.coli that produce biofuels and target tumors.

Given half a chance by synthetic biologists, these bugs may ultimately redeem themselves for the mischief they occasionally make in your G.I. tract.

Engineering a bacterial cell, however, is not the same as tackling a traditional engineering problem. With funding from the National Science Foundation's Synthetic Biology Engineering Research Center (SynBERC), Voigt and his colleagues recently discovered solutions to two of the biggest challenges faced by synthetic biologists: consistency and space.

Creating "off-the-shelf" biological parts

The first challenge deals with one of the most basic assumptions synthetic biologists make about biological processes: that each step is driven by an individual genetic part that always behaves exactly the same way.

Think of each part as a word in an instructional sentence, such as "First, open the box." The idea is that the parts can be thought of as interchangeable, or off-the-shelf, such that the instructions could easily be modified to read, "First, open the envelope" or "First, close the box" or "Second, open the box."

But instead of letters and words, synthetic biologists use DNA and genes to tell the cell what to do. There's even a library, called the Registry of Standard Biological Parts, from which you can order over 3,400 "components" — things such as "on/off" switches, oscillators and pulse generators. The idea is that the parts can be combined to create the biological equivalent of an electrical circuit.

The problem is, in practice, these components don't always work the same way every time. Sometimes the act of combining certain parts leads to unexpected changes to the system as a whole.

"Unlike electrical parts, the genetic parts can interact with each other by a great diversity of biochemical interactions," says Chunbo Lou, a postdoctoral researcher in Voigt's lab.

What this means is that the behavior of individual parts can be influenced by surrounding parts much the way that adding an adverb such as "slowly" would influence the message in the example sentence above. As in the sentence, the modifying part sometimes comes before the part of interest (upstream), "First, slowly open the box" and sometimes comes after (downstream), "First, open the box slowly".

Chris Voigt is a synthetic biologist at the Massachusetts Institute of Technology, where he and his team are working to engineer bacteria with unique capabilities.
CREDIT: Martha Bruce.

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Because the parts are generally connected end to end — Firstopenthebox — you can also run into trouble when the junction of two separate components accidentally forms a new instruction: firstopen. The Voigt laboratory ran into this problem, which they call "part-junction interference," while trying to predict what would happen when multiple circuits were combined into one big circuit.

"I spent nearly a year and a half trying to develop an algorithm that could be used to predict how the circuits would perform when combined," says Lou.

The problem was that the measurements from the individual circuits didn't add up when the circuits were combined. Through a series of careful experiments, the investigators eventually determined that one of the parts in the first circuit was interfering with the activity of the second circuit.

To deal with this problem, they identified a number of potential "insulator parts," which they hoped would buffer the interference. These components are comparable to the spaces and punctuation that help define the message in our instructional sentence. In other words, "firstopenthebox" becomes "First, open the box." When the insulator parts were added, the result was a circuit that consistently generated the same response, a feature that Voigt says is critical for creating bacteria with more complex capabilities.

Making room for more circuits

But what about the fact that these complex circuits have to function within a tiny cell? In another recent study, Voigt and his colleagues sought a way to maximize the number of circuits that can be embedded in individual cells.

"A key limitation is that the circuits are based on biochemical interactions occurring in the confined volume of the cell, so the size of programs has always been limited to a few circuits," says Tae Seok Moon, Ph.D., an assistant professor in the Department of Energy, Environmental & Chemical Engineering at Washington University and former member of the Voigt laboratory.

The investigators mined their databases for parts that could serve double-duty. The result was a series of circuits that were effectively layered, with some components operating in more than one circuit at a time.

Importantly, while this strategy often results in delays, the investigators did not observe any problems with the layered circuit. Voigt believes that the success of this strategy will facilitate the development of large, integrated circuits in single cells.

By confronting these challenges, the Voigt laboratory is paving the way for the development of new technologies that will revolutionize how we produce fuel, clean up hazardous waste, interact with the environment and treat human disease.

The papers, "Ribozyme-based insulator parts buffer synthetic circuits from genetic context" and "Genetic programs constructed from layered logic gates in single cells" were published online in the journals Nature Biotechnology (October 3, 2012; DOI: 10.1038/nbt.2401) and Nature (October 7, 2012; DOI: 10.1038/nature11516), respectively.

Editor's Note: The researchers depicted in Behind the Scenes articles have been supported by the National Science Foundation, the federal agency charged with funding basic research and education across all fields of science and engineering. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author and do not necessarily reflect the views of the National Science Foundation. See the Behind the Scenes Archive.