At the University of Massachusetts (UMass) Institute for Cellular Engineering (ICE), Gregory Tew’s group is using synthetic protein transduction domain mimics, which were developed in their lab, to help an ICE immunology group deliver certain reagents into their cells of interest.

“They have very different problems than we do, but we can sit down and talk, and these kinds of lunch table discussions lead to solutions,” says Tew, an associate professor of polymer science and engineering at UMass.

Nearly fifty ICE faculty members from ten academic departments are investigating different aspects of cell biology using a common approach, cell engineering. By pooling their expertise of cellular mechanisms in plants, animals, and microbes, the ICE researchers hope to address questions that have long fascinated the science community.

Within this unifying approach, the ICE researchers have a variety of methods and techniques. Some build upon nature’s diversity. Others are thinking outside Mother Nature’s box. Either way, they both have social and technical challenges before their research will impact our lives.

Fall of the plant cell wall

Cellular engineering—one approach within the synthetic biology field—aims to harness knowledge of these intricate cellular structures and functions to create new technologies in human therapeutics, biomanufacturing, and alternative energies.

Less than one-tenth of 1% of soil bacteria has been identified, according to Leschine. But within this small percentage, researchers have discovered microbes with highly evolved skills to get past thick plant cell wall defenses. Once these defenses have been broken down, the microbes can uptake plant cell components essential for survival. These mechanisms that turn plant biomass into microbial chemicals produce waste materials, like ethanol, which could be used by humans. And since there are already manmade sources of plant biomass ripe for microbial recycling—paper, cardboard, and other cellulose items make up 50% of global municipal solid waste—it would kill two environmental problems with one microbe.

But before these environmental problems can be solved, Leschine must first identify good candidates for certain consumption or production of wanted product and then develop them for industrial-scale use. Industrial microbiology already relies heavily on Escherichia coli as standard laboratory equipment, so it would seem an obvious place to start. But because the natural history of E. coli does not include significant interaction with plants, it does not have the innate mechanisms for plant biomass degradation.

To create efficient microbial machines that carry out a greater range of functions than preexisting ones, Leschine identifies microbes that already have the complex machinery required to break down plant biomass. Since evolution has already created microbes with these functions, all Leschine has to do is encourage the microbe to do what it already does, just faster and with a greater output. This encouragement comes in the form of directed evolution, an approach that uses natural selection to evolve microbes with desirable functions.

In Leschine’s directed evolution approach, microbes are raised in a medium that lacks a key nutrient. Only colonies that have a mutation that does not require the nutrient from the environment will grow. These mutations have either removed the need for the nutrient or developed a pathway to produce the nutrient internally.

Researchers then select these colonies and raise more generations, each time encouraging the growth of these desirable mutants. In this way, an organism with a novel or heightened mechanism is created, often without the need for outright genetic modification or foreign DNA.

In Leschine’s lab, directed evolution helps her raise colonies of microbes that breakdown cellulose more efficiently than those found in nature. “When you first recognize that there’s all this incredible diversity out there, waiting to be discovered, it’s really exciting,” says Leschine. "We discover new microbes, develop novel technologies through directed evolution and cellular engineering, and this leads to innovation." One such discovery led to a technology for cellulosic ethanol production currently being commercialized by Qteros in Marlborough, Massachusetts (formerly, SunEthanol) (1).

Mimicry: The highest form of flattery

But Tew has a different approach to cell engineering; his approach involves taking an organic mechanism and applying it to an inorganic subject. His ICE lab is trying to coax synthetic polymers to behave like proteins.

After Tew earned a Ph.D. in chemistry and material science, he applied for a postdoc position in biochemistry and biophysics. “It was clear to me that the interface between biology and materials chemistry was going to be a frontier,” says Tew. At ICE, Tew’s group works at the interface of biology, materials science, and biochemistry to change the way protein construction is done.

While other researchers are attempting to build proteins with amino acid building blocks, Tew’s methods focus on the novel synthesis of biological parts. “I want to build a protein from scratch, but I don’t want it to be a protein; I want it to be a synthetic polymer,” he says. And, according to Tew, his methods have been quite successful: “We’ve been able to do things in a decade with polymers that others haven’t been able to do in 25 years in proteins.”

Coming from a materials science background, Tew wondered if small, synthetic polymer scaffolds could be built and taught to act like these mercurial antimicrobial peptides. The answer was yes. Tew’s lab created synthetic antibiotics, which are now in human clinical trials (2,3).

Now, the lab is focusing on a class of proteins called protein transduction domains, which facilitate the transport of biological specimens across cell membranes. “In a side-by-side comparison of a natural protein and our synthetic polymer mimics, the synthetic polymers have been shown to enter the cells more consistently,” says Tew; in vitro studies have demonstrated the ability of mimics to deliver functional siRNA, functional proteins, and plasmid DNA. Tew is looking forward to testing their range of applications in primary human cells.

Shutting a door, but opening a window

Despite bringing together cell engineers to collaborate, many of the ICE’s successes stories may end at the discovery stage. One reason for these premature ends is the public perception of cellular engineering and synthetic biology. “I think that we need new terminologies,” says Leschine. “One of the problems with ‘synthetic biology’ is that it does sort of evoke that image of monster movies.”

"We're already on our way, but the advanced biofuels industry is just developing," says Leschine. "It's going to be hard to get the investment to fund new projects until there are some breakthroughs and success stories."

Likewise, Tew remains uncertain about the future of his polymer antimicrobial peptides. Although his lab can build molecules that behave like antimicrobial peptides, whether these synthetic antimicrobials become a drug is another story. “We’ve learned how to scientifically create polymer peptides, but whether or not our method will translate into a pharmaceutical has lots of other problems,” admits Tew.

But for now, the ICE researchers believe that they are writing only the first chapter of the history of cellular engineering, looking to the next generation of synthetic biologists to write the endings of their research. “We need more of the smarter people looking at this interface; we need to train up more of these students who are willing to be excellent in their core discipline but cross the boundaries,” says Tew. “That’s something that’s beginning to happen, but it needs to happen more.”

References:

1. Gorham, J., S. Parekh, S. Leschine. 2008. Single-step production of cellulosic ethanol. Biofuels Technology 1(Q4):37-44.

2. Scott, R.W., W.F. DeGrado, and G.N. Tew. 2008. De novo designed synthetic mimics of antimicrobial peptides. Current Opinion in Biotechnology 19:620-627

3. Tew, G.N., R.W. Scott, M.L. Klein, and W.F. DeGrado. 2009. De novo design of antimicrobial polymers, foldamers, and small molecules: from discovery to practical applications. Accounts of Chemical Research 43:30-39