E. coli caught in the act of evolving

Long-term lab experiment traces a trait's reappearance

Big leaps in evolution are the products of tiny genetic changes accumulated over thousands of generations, a new study shows.

DIET BREAKTHROUGH A flask of bacteria in an experiment at Michigan State University in East Lansing turned cloudy when the E. coli within evolved the ability to eat a chemical called citrate. A new study describes the three-step process that led to the ability. Brian Baer and Neerja Hajela

E. coli bacteria growing in a flask in a lab for nearly 25 years have learned to do something no E. coli has done since the Miocene epoch: eat a chemical called citrate in the presence of oxygen. Evolutionary biologists Zachary Blount and Richard Lenski of Michigan State University in East Lansing and their colleagues describe the molecular steps leading to the feat online September 19 in Nature.

The work demonstrates that although new traits seem to emerge in the blink of an eye evolutionarily speaking, those traits are actually the product of thousands of generations of genetic tweaks.

“The ability to be able to not just talk about how genes evolve, but to see it in action is just awesome,” says Bruce Levin, a population and evolutionary biologist at Emory University in Atlanta. “This is really getting at the nitty-gritty of evolution.”

Teasing out the molecular details behind the evolution of citrate-eating E. coli may help researchers better understand evolution in other organisms.

Learning to eat citrate, also called citric acid, is as big an innovation for E. coli as developing eyes or wings would be for multicellular creatures, says evolutionary geneticist Paul Rainey of Massey University in Auckland, New Zealand, and the Max Planck Institute for Evolutionary Biology in Plön, Germany.

Ancestors of E. coli and other bacteria may once have been able to eat citrate when oxygen is around, but E. coli lost the ability at least 13 million years ago, Blount says. In fact, the inability to grow on citrate in oxygen-rich conditions is a defining characteristic of E. coli that helps distinguish them from other types of bacteria.

Twelve flasks, each containing an independently evolving population of E. coli, have been growing in Lenski’s lab for more than 56,000 generations. A low concentration of E. coli’s favorite food, the sugar glucose, keeps most of the populations in check. But around generation 33,000, one flask, designated Ara–3, suddenly became cloudy as the bacteria within developed the ability to gobble citrate, an acid-controlling chemical that is abundant in the growth solution.

The ability of the Ara–3 E. coli to chow down on the alternative food source took at least three steps to develop, carried out over more than 13,000 generations. That’s the equivalent of a quarter-million years worth of human evolution in just five to six years of growth time in the lab. Step one, which the researchers call potentiation, set the stage for developing the citrate-eating ability. Bacteria as far back as generation 20,000 had the potential to evolve into citrate eaters, Blount found in earlier experiments. After thoroughly examining genetic blueprints of multiple generations of bacteria for the new study, Blount and colleagues found that at least two mutations arose before generation 20,000 that set the stage for the citrate-eating ability to evolve, and those mutations probably interact with each other.

Step two, called actualization, was much more obvious; a stretch of DNA containing a dormant gene for moving citrate into cells was copied and the copy was inserted near the original gene. The copied and pasted version of the gene started producing the citrate-pumping protein again. Before the duplication, E. coli couldn’t bring citrate into their cells to eat it.

Even though the initial duplication happened sometime between generation 31,000 and 31,500, those bacteria only nibbled citrate. Step three, refinement, took another 1,500 to 2,000 generations (about a year in the lab, or 30,000 to 40,000 years worth of human evolution) before the bacteria could make full use of the new food source. Some of those refinements included making even more copies of the citrate-transporter gene. Four copies of the gene appears to be the ideal number.

Tina Hesman Saey is the senior staff writer and reports on molecular biology. She has a Ph.D. in molecular genetics from Washington University in St. Louis and a master’s degree in science journalism from Boston University.

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