Because plants can’t get up and run away, they’ve had to be clever instead. They are the chemists of the living world, producing hundreds of thousands of small molecules that they use as sunscreens, to poison plant eaters, to scent the air, to color flowers, and for much other secret vegetative business.
Historically these chemicals, called “secondary metabolites,” have been distinguished from “primary metabolites,” which are the building blocks of proteins, fats, sugars and DNA. Secondary metabolites smooth the way in life, but the primary metabolites are essential, and the failure to make them correctly and efficiently is fatal.
Secondary metabolism is thought to have evolved to help plant ancestors to deal with living on dry land rather than the more hospitable oceans. The idea is that the genes for enzymes in the molecular assembly lines of primary metabolism were duplicated. The duplicates were more tolerant of mutations that might have destabilized the primary pathways because the originals were still on the job. With evolutionary constraints thus relaxed, synthetic machinery was able to accumulate enough mutations to do new chemistry.
Primary metabolism, however, is widely conserved, meaning that it remains unchanged across many different groups of organisms because it has been fine tuned to operate correctly and efficiently, and because its products are necessary for life. Or so the textbooks say.
But now, a collaborative team of scientists has caught primary metabolism in the act of evolving. In a comprehensive study of a primary-metabolism assembly line in plants, they discovered a key enzyme evolving from a canonical form possessed by most plants, through noncanonical forms in tomatoes, to a switch-hitting form found in peanuts, and finally committing to the novel form in some strains of soybeans.
This feat, comparable to pulling the tablecloth out from under the dishes without breaking any of them, is described in the June 26 issue of Nature Chemical Biology. It is the work of a collaboration between the Maeda lab at the University of Wisconsin, which has a longstanding interest in this biochemical pathway, and the Jez lab at Washington University in St. Louis, which crystallized the soybean enzyme to reveal how nature changed how the protein works.
“The work captures plants in the process of building a pathway that links the primary to the secondary metabolism,” said Joseph Jez, the Howard Hughes Medical Institute Professor in the Department of Biology in Arts & Sciences. “We’re finally seeing how evolution creates the machinery to make new molecules.”
It also may have practical importance because the old and the new pathways make the amino acid tyrosine, which is a precursor for many secondary metabolites with biological and pharmaceutical activity — everything from vitamin E to opioids. But the old pathway makes only tiny amounts of these compounds, in part because they must compete for carbon atoms with the greedy process for making lignin, the tough polymers that let plants stand tall.
The discovery of the new pathway for making tyrosine is much less constrained than the old one. This raises the possibility that carbon flow could be directed away from lignin, increasing the yields of drugs or nutrients to levels that would allow them to be produced in commercial quantities.