Atrazine, watch out: There's a killer from the future tracking you down.
Scientists working in Georgia have engineered a common bacteria that will, in the lab, detect and seek out atrazine, a controversial herbicide sprayed over cornfields and sugar plantations across the United States.
And this bacteria, a genetically engineered version of E. coli, is no mere scout, mobile but powerless. It is armed -- specifically, equipped with a gene that allows the bacteria to strip atrazine of its punch, reducing it into a harmless chemical cousin.
Atrazine, banned in Europe, is one of the most common contaminants found in U.S. water supplies, though it remains uncertain at what concentration it begins damaging animal and human health. U.S. EPA is currently reviewing its risk assessment of the chemical after several studies linked low levels of atrazine to sexual defects in frogs and fish (Greenwire, March 2).
The atrazine-hunting bacteria remain far from real-world use. But the bleeding-edge techniques used to develop them point to a future where scientists will create designer microbes that can track and clean a wide variety of environmental contaminants, said Justin Gallivan, a synthetic biologist at Emory University and author of a report this week describing the seek-and-destroy bacteria in Nature Chemical Biology.
"This is a specific application in picking one target molecule [atrazine] and developing a way to sense this inside a cell and develop a predictable response," he said. But the methods used in developing the tracking could vastly expand the previously small number of chemicals that bacteria can be engineered to detect, Gallivan added.
There are other promising approaches to cleaning atrazine. Several years ago, scientists developed biotech alfalfa and tobacco lines that degraded the herbicide into a nontoxic relative. And after decades of use, natural selection, always working at a feverish pace in microbes, has allowed some bacteria to evolve robust talents to chew through the chemical, no human intervention required -- except for spraying vast amounts of weedkiller.
Previously, bacteria engineered to eat through atrazine was tested at the field scale, used on soil contaminated by a chemical spill. (Atrazine eventually degrades but can linger in soil for months on end.) While these tests were promising, the bacteria were dumb bombs compared to the precise munitions developed by Gallivan and his team of researchers.
Synthetic biology's promise
Programming bacteria to take on evolutionally unnatural tasks is one of the foundations of synthetic biology, the rapidly growing field that leverages recent strides in biotech that allow scientists to manufacture, if imprecisely, the building blocks of life. Few programmed bacteria have so far had feasible applications, and Gallivan's herbicide hunters represent the shape of things to come.
The Emory team's work depends, in effect, on a sensory back door. While it remains challenging to synthesize the protein-based sensors most commonly used by bacteria to detect amino acids or sugars, recent discoveries in an intermittently neglected realm of biology -- the role of RNA, the single-stranded sibling of DNA -- have allowed scientists to begin manipulating how bacteria observe and interact with their environment.
In particular, the atrazine hunters depend on messenger RNA, the chain of nucleotides previously thought only to carry instructions from genes, the body's architects, to proteins, its construction workers. Over the past two decades, scientists have discovered that these RNA strands can also independently act as switches -- called "riboswitches" -- to control whether genes are expressed.
Despite their single-strand backbone, riboswitches can possess three-dimensional structure, particularly the "nets" they use to catch and detect chemicals. These nets, called aptamers, are fitted to specific molecule shapes, and once filled, they flip a switch, in effect allowing the RNA to activate or smother the expression of a protein, among other functions.
While riboswitches were first created artificially, they are now known to play an active role in regulating some microbe behavior, perhaps as a sign of a previous time when, it is theorized, RNA determined the functions of life. Their influence on animal and plant behavior is less established. But what is clear is that these strands can be synthesized with high-tech lab equipment.
Still, manufacturing effective riboswitches is far from the construction-block analogies sometimes used to describe synthetic biology. The most challenging aspect is weaving nets that can catch a larger variety of chemicals than occurs in nature. Gallivan's team, following similar groundwork in Germany, combined two complex screening methods to eventually find a net shaped to catch atrazine.
After finding this net, which required sifting through far more than a trillion randomly generated sequences of RNA, Gallivan tied the net to a previously known gene that controls bacteria's ability to move. Since the bacteria are more likely to move when more atrazine is present, a seeking mechanism is created.
It is similar to "taking the foot off the brake when atrazine is around," Gallivan said.
In comparison, the weapon used by Gallivan's bacteria once they track down atrazine is far more prosaic. Thanks to widespread atrazine use, many bacteria have developed genes that convert the herbicide to hydroxyatrazine, which is not toxic and is easily absorbed into soils. Transfer that gene into E. coli -- it is easy compared to concocting ribosome switches -- and the herbicide hunter is armed.
Major hurdle looms
The bacteria are a rare example of a synthetic bacteria that could have a feasible use in the real world. Largely, scientists are focusing on ways to develop better aptamers and more foundational work, said Christina Smolke, a bioengineer at Stanford University who is working to apply riboswitch systems in immunotherapy.
"However, there will be more coming out in the future as researchers begin to link the riboswitches to the control of interesting cellular functions," Smolke said.
One great hurdle that remains will be programming bacteria to have more complex responses to their environment by switching more genes on or off, said Jason Micklefield, the head of chemical biology at the University of Manchester.
"A key challenge is to establish that the synthetic riboswitches can be used to control a larger range of different genes across a wider range of organisms," Micklefield said.
Once the limitations of creating riboswitches are overcome, Smolke added, the systems will have exciting applications in genetic medical therapy, agricultural biotech and synthetic biology.
Gallivan's herbicide hunter possesses great limitations. It is useful only for much higher concentrations than would be found in nature and, without the presence of atrazine, the bacteria grind to a halt. They are pampered creatures of the lab, and dumped into the wild, they would be outcompeted by native microbes.
"This isn't something that we're going to put into a field and solve all the world's problems," Gallivan said. This is often true in biotech, when engineered bacteria are weak compared to their natural counterparts.
"Our main challenge is developing systems that are much more robust," he said.