Emory chemists develop bacteria that may help decaffeinate coffee

Chemists at Emory University have made an important advance in harnessing the ability of bacteria to make new molecules, and their discovery could eventually lead to the creation of naturally decaffeinated coffee plants. The research, by Emory chemist Justin Gallivan and graduate student Shawn Desai, is scheduled to appear in the Oct. 27 edition of the Journal of the American Chemical Society.

Bacteria are terrific chemists, but they normally synthesize only molecules they need for their own survival, says Gallivan. His research team is interested in making bacteria synthesize molecules that they would otherwise not make on their own, resulting in molecules that may someday benefit humans. The Emory team reasoned that if a bacterium needs a particular molecule to survive, it has a strong incentive to help make it, so the goal was to make bacteria depend on a molecule that they wouldn’t normally need.

In their first major breakthrough, the Emory researchers have coupled the life of a bacterium to the presence of theophylline, a compound that is used to treat asthma, and is produced by the breakdown of caffeine in both coffee and tea plants. One of the reasons that coffee has a high level of caffeine is that in the plant, caffeine is synthesized very quickly, but breaks down to theophylline very slowly.

“We know that there is an enzyme that breaks caffeine down into theophylline, but we don’t know much about it,” says Gallivan, an assistant professor of chemistry. “What we do know is that it works very slowly. Ideally, we would like to speed it up a bit so that we could create coffee plants that are low in caffeine. That’s where the bacteria come in. They now need the breakdown product of the enzyme (theophylline) for survival, but they can’t do much with caffeine.”

Gallivan says that the idea is to supply these bacteria with caffeine, and give each bacterium a piece of DNA from coffee plants that may encode the enzyme that will allow the bacterium to convert the caffeine to the theophylline it needs to survive.

“At the end of the day, we will know that all of the surviving bacteria have ’learned’ to convert caffeine to theophylline, and thus have the enzyme that we’re interested in. We can then learn about the enzyme and how it works,” Gallivan says. “We hope to use a process known as ’directed evolution’ to help speed up the enzyme to break down caffeine faster. Since the bacteria need theophylline for their survival, they’re partners in the whole process.” Eventually, the faster enzyme could be introduced into coffee plants to produce decaffeinated coffee, he says.

To develop bacteria that are addicted to theophylline, Gallivan and Desai used a piece of the genetic material RNA, known as an aptamer, which was known to bind to theophylline tightly. The remaining challenge was to couple this binding to a vital function of the bacteria — the production of a protein. To do this, the Emory team created a new sequence of RNA known as a “riboswitch.”

In bacteria, riboswitches normally recognize essential molecules, such as vitamin B12, and switch the production of proteins on or off. The Emory team created a synthetic riboswitch that recognizes theophylline, and turns on the production of a protein known as “cat” which allows the cells to survive in the presence of an antibiotic known as chloramphenicol. Most bacteria die when exposed to chloramphenicol. However, bacteria containing the synthetic riboswitch survive when exposed to chloramphenicol as long as theophylline is present because theophylline turns on the production of the “cat” protein.

Gallivan says not to expect good-tasting, naturally decaffeinated coffee anytime soon. “We’re still at the earliest stages of this work. There are many hurdles to overcome,” he says. “As a scientist, I’m excited about the future. As a caffeinated coffee addict, part of me is not in a hurry to solve this one.”