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U.S. Department of Energy | Office of Science | Office of Biological and Environmental Research

Pulling the Tablecloth Out from Under Essential Metabolism

June 26, 2017

Feature Story

For the first time, scientists have caught a vital cell machinery molecule in the process of evolving. A key enzyme plants use to make tyrosine, an amino acid necessary for life, was thought to be conserved across the plant kingdom, but the scientists found a mutated form in legumes. In cherry tomatoes, the basic canonical form of the enzyme dominates; peanuts can switch hit; and some strains of soybeans (lumpy beans at right) have lost the canonical form. [Courtesy Jez laboratory, Washington University in St. Louis]

Plants caught in the act, changing chemistry thought to be immutable because necessary for life

Plants are the chemists of the living world, producing hundreds of thousands of small molecules that provide protection—to screen sunrays, to poison plant eaters, to scent the air, to color flowers, and for much other vegetative business.

Called “secondary metabolites,” these chemicals are distinguished from “primary metabolites,” which are the essential building blocks of proteins, fats, sugars, and DNA. Secondary metabolites just smooth the way in life, but failure to make primary metabolites correctly and efficiently is fatal. Genes for enzymes in the molecular assembly lines of primary metabolism have duplicates, allowing more tolerance 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.

Widely conserved, primary metabolism it was thought to remain unchanged across many different groups of organisms because it operates correctly and efficiently and because its products are necessary for life. 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 is comparable to pulling the tablecloth out from under the dishes without breaking any of them. A collaborative study of this biochemical pathway resulted in the crystallization of the soybean enzyme to reveal how nature changed the way the protein works, also capturing plants “building a pathway that links the primary to the secondary metabolism,” to reveal evolutionary machinery that creates new molecules.

A new pathway discovered for making tyrosine is much less constrained than the old one, raising the possibility that carbon flow could be directed away from lignin to increase the yields of drugs or nutrients to levels that would allow them to be produced in commercial quantities. Though the scientists have found two different assembly lines for tyrosine, they have not determined why except in general terms. This work is important because it demonstrates that primary metabolism does evolve.

Schenck, C. A., et al. “Molecular Basis of the Evolution of Alternative Tyrosine Biosynthetic Routes in Plants.” Nat. Chem. Biol. 13, 1029–1035 (2017). [DOI:10.1038/nchembio.2414].

Instruments and Facilities Used: X-ray macromolecular crystallography; diffraction data collected at beamline 19-ID of the Advanced Photon Source at Argonne National Laboratory Structural Biology Center.

Funding Acknowledgements: Work supported by the National Science Foundation (NSF; IOS-1354971 to H.A.M. and MCB-1614539 to J.M.J.). C.K.H. support: NSF Graduate Research Fellowship Program (DGE-1143954). Portions of research carried out at Argonne National Laboratory (ANL) Structural Biology Center (SBC) of the Advanced Photon Source (APS), a national user facility operated by the University of Chicago for the Office of Biological and Environmental Research (OBER), U.S. Department of Energy (DOE) Office of Science (DE-AC02-06CH11357).