UCSF bioengineering graduate student Alvin Tamsir places E.coli bacteria onto a petri dish in the lab. (Credit: Susan Merrell, UCSF)

Reported for KQEDnews.org.

Researchers at the University of California-San Francisco have hacked into the genetic wiring of billions of individual bacteria and outfitted them with the kind of on/off switches normally found in computer chips, not living organisms.

The switches, which are built out of genes, allow the bacteria to listen for chemical signals and respond, much like computer chips that can perform powerful tasks.

The switches may one day help the development of biofuels that are cheaper and more powerful than gasoline, or a new suite of pharmaceuticals that could more effectively target and kill tumor cells with fewer side effects.

“Scientists have been trying to engineer bacteria to be more programmable, to do various things, but biology is hard to program” said Alvin Tamsir a doctoral student at UCSF. “I want to generate the technology so that bacteria can be more programmable in a more predictable way.”

Tasmir was the lead author of a study on the subject that was published last week in the journal, Nature.

UCSF bioengineering graduate student Alvin Tamsir. (Credit: Susan Merrell, UCSF)

By building new molecular circuits into bacteria, Tamsir and his team can now make the bacteria perform specific tasks, much like the millions of wires which comprise the electrical circuitry of a modern computer chip enable the dizzying array of complex calculations and tasks a computer can do in micro-seconds.

It’s all part of the new field of synthetic biology, where principles from computer science, electrical engineering and genetics, along with other sciences, mix together to reveal the tools and strategies for reprogramming the cellular machinery of living organisms like bacteria and yeast. Scientists and companies in the Bay Area and elsewhere, working on other synthetic biology project, already are developing a new generation of drugs and biofuels with bionic bacteria and yeast.

“Some of these drugs that we are working on right now require 40 genes. And you have to control when those genes turn on and for how long and in what order, and for all that, you need a circuit,” said Christopher Voigt, an associate professor at UCSF’s Department of Pharmaceutical Chemistry and the senior author of the study.

Tamsir and Voigt looked to the world of electrical engineering, where circuits bring the necessary level of control to millions of precisely timed calculations that a computer chip must complete to execute any task, like spellchecking a document or surfing the web.

To do these tasks, microscopic switches called “logic gates” are etched into the silicon of computer chips. The logic gates function according to a set of rules and are connected with wires that make up a circuit on the chip. Each of these logic gates receives an input, such as an electrical current, from the wires, and responds based on the kind of gate it is. For example, if it’s an “AND” gate, it will turn on and send its output of an electrical signal to the gate next to it, but only if it is getting inputs from the two wires that feed into it. If it’s an “OR” gate, it will turn on even if it is getting a signal from just one of the wires connected to it.

“In computers, complex tasks like opening a document or performing a calculation can be boiled down to simpler calculations performed by these logic gates,” said Tamsir. A modern Pentium chip can have more than a million logic gates, each one performing a tiny piece of the calculation or task at hand.

“But you don't have an engineer at Intel that is choosing exactly where each wire goes,” said Voigt. Instead, programming languages have automated the process, quickly and reliably reproducing on the computer chip the precise circuits of logic gates needed to carry out functions specified by a computer engineer.

“We are trying to create a programming language for cells,” Voigt added, “and ultimately have it so you can take any function you can imagine and convert that into a DNA sequence that carries out that function.”

Four colonies of E. coli bacteria cells plated onto a petri dish. Each colony contains a billion cells. (Credit: Susan Merrell, UCSF)

But scientists can’t exactly take the hardware of tiny gates and wires on computer chips and insert them into living bacteria like E. coli. So Tamsir and his team had to engineer genes that would reprogram the DNA of E. coli, instructing it to make logic gates out of proteins that would help the bacteria perform more like a computer to carry out a specific task – in this case, to make a fluorescent yellow protein.

In computer chips, the metal wires that feed into a logic gate are physically separated so that the inputs going into one logic gate don’t cross with the wires of a nearby logic gate. But this isn’t the case with living bacteria. “Every gate is a molecule and they're all being run based on molecules and they're all crammed together in the bag that is the cell,” Voigt said.

Although the scientists created eight different colonies of bacteria, each with their own discrete logic gate, only four colonies were used at a time to see if they could link up to form a circuit that would yield the fluorescent protein.

One logic gate in one of the bacteria colonies may need two inputs, like a sugar and an antibiotic, to release its molecular output, such as an enzyme, that would then act as an input for a second set of logic gates. But this next set of logic gates may have been designed so that it produces its own molecular output only if it doesn’t receive the sugar and antibiotic inputs that triggered the activity of the first logic gate.

“It’s by combining multiple gates together that you get different behavior. And that's how electrical circuits behave – they use a lot of logic gates and combine them in various ways to get various functions,” said Tamsir. Similarly, the scientists were able to modify the behavior of their bacterial circuits by simply moving the location of the bacteria colonies in the petri dish, since each colony operated with its own set of logical rules for responding to the chemical inputs feeding into it.

An illustrated wiring diagram showing two different kinds of logic gates (NOR and Buffer) operating in four bacteria colonies on a petri dish. The last bacteria colony, indicated in brown, completes the circuit to make fluorescent yellow protein. (Credit: Alvin Tamsir, UCSF)

Tamsir built 16 different kinds of genetic logic gates to program the bacterial 'computers'. Each one successfully suppressed or promoted the production of the fluorescent yellow protein depending on how it was linked together in the bacteria.

“The hard part,” said Tamsir, who has worked for more than two years on this research, “was combining different genetic parts so that when they are put together, they function as you want them to.”

Other researchers are taking note.

“They have begun the process of creating a characterized library of elements which can be used by other labs to build more complex systems,” said Douglas Densmore, an assistant professor of computer and electrical engineering at Boston University who read the Nature paper describing the UCSF team’s research.

Tamsir and his team now want to increase the complexity of their bacterial circuits by building even more sophisticated logic gates.

Voigt added that there are roughly 200 to 300 circuits that regulate different biological activities in E. coli bacteria.

“And that’s the good news – that it’s not millions,” he said. Unlike a computer chip, “the bacteria don’t require a lot of gates and if we had 100 gates, we could do some pretty amazing things,” Voigt said.

By designing more complex gates and more of them, he said a scientist could be “in full control of programming bacteria.” This arsenal of expanded logic gates could then coax the bacteria to produce more than just a biofuel or a low-cost malaria drug, like the one developed using synthetic biology by Amyris Biotechnologies in Emeryville.

“Everything you see in biology — such as a corn plant growing — those complex processes are being implemented by natural circuitry,” said Voigt. “And one of the reasons that we can't access those functions is because we don't have that refined level of control.”

With the new system of logic gates snapping together to form synthetic circuits, the UCSF scientists have expanded that level of control and consequently, what bacteria or yeast could be programmed to do, like some day make synthetic wood, silk or antibiotics.

UCSF bioengineering graduate student Alvin Tamsir handles test tubes containing E. coli bacteria. (Credit: Susan Merrell, UCSF)

Life Technologies, a biotech firm based in Carlsbad, has partnered with Voigt’s lab to generate a software package that would allow other scientists to specify the kind of logic gates they want to run in the bacteria being used in their experiments. After a few keystrokes and some processing by the computer, the scientists would receive a recipe for making those logic gates, which could then be sequenced from the sugars and phosphates which make up genes, and inserted into their bacteria.

For Tamsir, the research is incredibly challenging but also extremely rewarding, a vital part of his doctorate degree in bioengineering which he hopes to complete in May. The 26 year-old scientist grew up tinkering with circuit boards and even derived programming inspiration from Lego Mindstorms, a line of robotic toys.

“I found out about the field of synthetic biology through Chris Voigt's lab. Right then, I knew that this was the right field of study for me,” he said. “It combines my love for computer programming with my love for biology.”

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UCSF biologist Jeff Tabor holds up an ecoli culture designed to display the shape of a squid.

Synthetic biology portends big changes in our lives by ushering in a dizzying array of applications in everything from medicine to biofuels, environmental remediation to agriculture. Though many of these applications haven’t yet come on line, researchers are hard at work to synthesize new drugs and devices made from genetic parts.

For example, there’s an enzyme that exists in plants which makes methyl halides, a molecule which can be catalytically converted into gasoline and other chemicals. Imagine if you could put this enzyme-making gene into yeast, then you could brew the yeast to churn out the methyl halides and after some optimization of the production pathway, you could scale up production to pump out this carbon neutral gasoline precursor for use in today’s automobiles. This is the idea behind an innovative biofuels project that has taken off in the lab of Chris Voigt at UCSF’s School of Pharmacy.

Voigt and his team surveyed the genetic database for the presence of the gene that encodes for the enzyme that makes methyl halides. Lo and behold, the gene exists in plants as diverse as ice plant, which dots the northern California coast, bok choy and pinot noir grapes. After building a library of about 100 enzymes from these diverse plants, the researchers had to determine which of these would function best in the yeast. They zeroed in on an enzyme from ice plant and then used the tool of DNA synthesis to translate the gene for the enzyme that makes methyl halides into something that would work in yeast.

The remarkable thing about this project is that the researchers never actually touched any of the plants. They simply “Googled” a genetic database to find all the genes out there in plants that produce the enzyme that makes methyl halides. As Professor Voigt says, “it’s incredible that synthetic biology is something that could really unlock the potential of using organisms in order to produce fuels.”

Watch the video made by the Voigt Lab demonstrating the combustible property of their synthetically derived methyl halides:

QUEST on KQED Public Media. Video courtesy of
Prof. Chris Voigt, UCSF School of Pharmacy

Watch the Decoding Synthetic Biology television story online.

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Companies like GenoCAD allow users to piece together
their own designer DNA.

“Synthetic biology” seems like a contradiction in terms, doesn’t it? I mean, if it’s biological, it’s natural, right? And if it’s natural, then it’s not synthetic.

Sure. Except that modern science has sorta blurred all those nice convenient boundaries.

Nothing has demonstrated this more clearly than Craig Venter’s latest feat of building out an entire bacterial genome from scratch. It’s the second episode of a three-part plan, devised by the venerable entrepreneur who brought the world its first look at the human genome, to create an organism with a manmade DNA sequence. First, he took a genome from one bacterium, stuck it into an empty cell, and then got it going. Now he’s pieced together a copy of the DNA of Mycoplasma genitalium, the second-smallest known bacterial genome. The last in this troika of tricks will be to combine these two steps, inserting the manufactured genome into a cell and starting it up.

Some scientists believe that success in this endeavor will soon lead to the creation of organisms with new, artificial genomes. Couple that idea with the announcement that researchers at Scripps have devised two new molecules that can function as DNA bases and the question of what’s alive, even what counts as biology, gets a little fuzzy.

I first heard about synthetic biology several years ago, at a lecture for science writers. The speaker had culled together sections of DNA that he hoped would produce a medically useful enzyme, inserted the sequences into a bacterial genome, then let the bug do its work copying the gene and producing the chemical, which the speaker could then harvest.

This seemed to me to be a fundamentally different way of thinking about biology. Here was a scientist who wasn’t asking: “How does this work?” or “Isn’t the living world amazing?” He was asking: “How can I employ this system to manufacture a specific product for my benefit?” He was harnessing the ingenious mechanisms of biology as tools. Being able to put together sequences of DNA seemed akin to the invention of movable type, a letter here, a letter there, till you spell the words (or in this case, genes) you want.

At some level, I was offended by this, though I’m still not exactly sure why. It seemed like a disrespectful exploitation of life. Who are we to manipulate the code defining living things and make them do our bidding? And how far will we go with this? Will the precious genomes of my plants, or my pets, or even me for Godsakes be manipulated one day, ordered to pump out some substance that a distant researcher has deemed desirable?

On the other hand, I was fascinated. The potential this technique held for research was enough to send a geek’s mind reeling. What amazing ingenuity. What creative thinking. How wholly human, actually, to devise a new purpose for knowledge we’d gained. This engineering feat struck me as demonstrating a deep appreciation—almost a reverence for—the power within the systems that the living world has evolved.

So there I was, conflicted.

Since then, this process of connecting DNA bits together has become more commonplace. So common, in fact, that a variety of companies, like Gene Design and GenoCad invite you design a gene online and have it sent to you (Go ahead, try it. It’s easy to make up valid sequences.). This is, in fact, what Venter did: ordered sequences of DNA and pieced them together, discovering that he could make an exact copy of the genome he desired.

Synthetic biology’s proponents promise microbes that can clean up pollution, produce drugs, signal changes in the environment, help with medical diagnoses, and a slew of other useful tasks. Its detractors fear the creation of new biological weapons, and new organisms that aren’t well understood but which may be able to reproduce and evolve.

Since this sort of talk makes a sci-fi world of ready-made critters seem like it’s just around the corner, it’s easy to forget how much work remains before our best (or worst) dreams come true. Just because we can string functional bits of DNA together, even whole (though relatively small) genomes, doesn’t mean that we actually know much about how they work. Venter, after all, didn’t invent a new genome, he just put an already-known one together. The goal, of course, is to be able to someday make new genes that do specific things. But for the moment, synthetic biologists hope to use the technologies they’re developing to learn much more about how genes work in the first place.

What does wait for us around the corner is a set of questions similar to those that accompany all new and emerging technologies. How do we create policy to protect ourselves from the risk but not quash research? Who decides what research directions and questions are most important to pursue? How do we create profit incentives for technology that benefits the common good?

And will I ever resolve my mixed feelings about this new science? Is it better off that I don’t?

Robin Marks is a journalist and science writer who current serves as a Multimedia Projects Developer for the Exploratorium in San Francisco, CA.

latitude: 39.1067, longitude: -77.1623