Retuning Bacteria

Gene-silencing techniques for bacteria could mean better treatments for infections and more-efficient biofuel production.

Silencing bacteria: Duke University graduate student Sara Morey and civil- and environmental-engineering professor Claudia Gunsch are developing a method for silencing genes in bacteria.
Credit: Duke University

Researchers at Duke University are hoping to develop methods to reversibly turn off harmful or unwanted genes in bacteria. If they succeed, gene silencing could be used to treat persistent infections by turning off antibiotic resistance genes in bacteria and in environmental and industrial applications, including water filtration. The technique could also make it possible to engineer bacteria to more efficiently make biofuels and other industrial products.

The Duke researchers, led by environmental engineer Claudia Gunsch, hope that gene silencing in bacteria will be as useful as it has been in so many other organisms. Gene silencing by a pathway called RNA interference has proved a powerful tool for biologists, who have used the technique to silence particular genes in order to study their functions in development and disease in animals from yeast to worms to mice. And RNA-interference-based therapies that work by shutting down genes involved in macular degeneration and other diseases have shown great promise in clinical trials. But RNA interference doesn't work in bacteria, which don't have the necessary molecular pathways.

Although still in very early stages, Gunsch's work has shown hints of success. Instead of the short pieces of RNA used to induce RNA interference, Gunsch used short single strands of DNA to silence a test gene in yeast. She is now testing the technique in bacteria.

In one promising application of the Duke work, the gene-silencing methods could be used in water filters. Gunsch presented proof-of-concept data for this application at the American Society for Microbiology meeting last week. For gene-silencing water filters, DNA would be embedded in a gel that would filter the water right at the sink. Waterborne pathogens, including bacteria, often mutate and become resistant to the existing treatment methods, ultraviolet light and chlorination. "Chlorine-resistant bacteria are starting to show up," says Gunsch. The advantage of gene-silencing filters would be that the genes they target could be changed as the pathogens mutate.

If Gunsch can get bacterial gene silencing to work, says James Collins, a biomedical engineer at Boston University, metabolic engineering of microbes to produce biofuels and drugs would be a good application. Designing organisms to efficiently make a particular end product, such as ethanol, without wasting energy and fuel making side products is challenging. Most metabolic engineering is binary: researchers give a microbe a gene or delete it. "But in many cases, the better way to go would be to tune down the expression of a gene, then allow it to come on at other stages," says Collins.

However, Gunsch and her coworkers face enormous challenges. Bacteria do have gene-silencing mechanisms, but they're different from those in other cells, says Susan Gottesman, chief of the biomedical genetics section at the National Cancer Institute's laboratory of molecular biology. Gottesman says that it could be possible to draw on bacterial pathways to induce gene silencing, but previous attempts have not met with much success. And Gottesman is skeptical that the Duke researchers will be able to overcome the hurdles that have prevented other labs from developing gene-silencing techniques for bacteria.

Gunsch acknowledges that the work is in its early stages. The Duke researchers will have to prove that they can target bacterial genes and get the silencing agent, whether RNA or DNA, into bacterial cells efficiently. "Our results seem to indicate that it's possible," says Gunsch.

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