Biotechnology

Predicting the past

GENES YIELD CLUES TO ANCIENT EVOLUTIONARY PRESSURES

MOST PROGNOSTICATORS TRY TO PAINT PICTURES OF THE FUTURE

Antony Dean, associate professor in the Department of Ecology, Evolution, and Behavior and the Biotechnology Institute, predicts
the past instead. He and colleagues use molecular-level analysis, genetic engineering,
and experimentation to study selection pressures that gave rise to modern-day biochemical traits.

“We’ve been involved in reconstructing an adaptive event that occurred 3.5 billion years
ago,” Dean says. “We’re finding a way to make historical adaptation an experimental science.”

Dean and colleagues study a family of enzymes known as isocitrate dehydrogenases (IDH), which bacteria use to extract energy from glucose. To do their job, these enzymes require a helper molecule, or coenzyme. For most bacteria, the coenzyme is a substance known as NAD. But about 3.5 billion years ago, at least three distinct lines of IDH began using a coenzyme called NADP instead. What was happening, Dean asked, that made a preference for NADP evolve three separate times? And how did IDH change in the process?

To find out, he and colleagues altered the IDH found in Escherichia coli,a bacterium that uses the NADP system today but which had evolved from an NAD-using ancestor. The researchers strategically switched six amino acids that shape the cubbyhole in IDH into which NADP normally fits. In the process, they produced an E. coli IDH molecule into which NAD fit even better—the equivalent, Dean says, of re-creating the enzyme function as it existed before the mystery conditions caused it to evolve NADP preference.

With both NAD-binding and NADP-binding versions of E. coli in hand, Dean set out to test
conditions that might favor one or the other. He suspected that an environment in which acetate had to be used for food might favor the NADP based system. To test that, he grew IDH-NADP E. coli and engineered IDH-NAD E. colion acetate and on glucose. As predicted, the NAD using bacteria grew best on the glucose, while the NADP-using ones grew best on the acetate.

Dean and colleagues also engineered an IDH like molecule, IMDH, which normally uses NAD as its coenzyme, to use NADP instead. As before, they chose replacement amino acids based on their knowledge of molecular structures. “So we not only engineered it, we engineered it the way nature did it,” he says.

Dean and colleagues have now engineered E. coli that can’t grow on acetate in hopes of seeing if they can get the IDH-NADP system to re-evolve in the face of acetate-based selection pressure.

“We’re going to try to rerun the tape of life,” he says. Dean says the U of M is a perfect place to pursue work at the interface of evolution and biochemistry because of the way the biological sciences disciplines are organized.

“This is a very unusual place to be,” he says.

—MARY K. HOFF