Ruminations on how enzymes evolved.

It's not quite Jurassic Park, but researchers are getting closer to recreating extinct life -- or at least extinct molecules. Working backwards from the molecular structures of digestive enzymes in cattle and their modern relatives, a Swiss research team claims to have synthesized ancestral forms of these enzymes from millions of years ago.

In the process, they have found biochemical clues to the evolution of the molecules.

The team, led by Steven A. Benner of the Swiss Federal Institute of Technology (ETH) in Zurich, is among the first to recreate possibly ancient molecules in the laboratory and to compare the results with fossil evidence.

"It's kind of like using a DNA synthesizer [a machine that can assemble genes] as a time machine," says Clyde A. Hutchison III of the University of North Carolina at Chapel Hill. "It's just one molecule, but this is really exciting."

Benner and his colleagues studied a protein, a form of the enzyme ribonuclease, that breaks down bacterial RNA in the digestive systems of cows, sheep, deer, giraffes, and other ruminants.

The fossil record shows that these creatures' common ancestor, a small, deerlike animal, branched off from nonruminants 40 million years ago by developing the rumen, a stomach chamber that holds cellulose-chomping bacteria. With these bacteria, and with enzymes such as ribonuclease to digest the bacteria, ruminants can thrive on fibrous plants such as grass.

The 124 amino acids that make up this ribonuclease vary slightly among modern ruminants. By correlating these variations with the evolutionary tree, Benner's group deduced the likely amino acid sequence of ancestral enzymes at 13 points in the animals' evolution. They then put suitably mutated forms of the genes for the modern enzymes into bacteria to make them crank out old-style enzymes.

Finally, as they report in the March 2 Nature, the researchers showed that their reconstructed enzymes can work on RNA in a test tube.

Their most striking finding was the change of a single amino acid in ribonuclease at the point when the ruminants' ancestor emerged. This tiny alteration helped the enzyme resist heat, thus enabling it to prosper in the digestive system, but also made it one-fifth as efficient at processing double-stranded RNA. This ability is of little importance for digesting bacteria, but it hints at a different function of the more primitive enzyme, the group suggests.

The idea of recreating ancient molecules from modern organisms originated with Linus Pauling and Emile Zuckerkandl in 1963, long before anyone had the techniques to do it, notes Caro-Beth Stewart of the State University of New York in Albany in a comment accompanying the work.

"It was a very visionary idea," Stewart says. "I think we're at the very preliminary stages of what this can be used for." By combining the sequences of molecules from many more species, she notes, "we should be able to reconstruct ancestral molecules going further back in time, perhaps -- in the future -- to the very root of the 'tree of life'."