THE PROCESS IN MOTION

How does the coffee plant make its caffeine, and what is it for?

Start the scene or choose a stage. The animation simplifies the mechanism; what follows gives the details and the available references.

▶ Play the process01XMT, first methylation02MXMT: theobromine03DXMT: caffeine04A duplicated gene family05A homemade pesticide06A memory for the bee

XMT, first methylation

The coffee plant makes its caffeine in three successive methylations starting from xanthosine. A methylation is the addition of a methyl group; each step is catalyzed by an N-methyltransferase. The first, XMT, turns xanthosine into 7-methylxanthosine.

Read the stages without animation

1. XMT, first methylationThe coffee plant makes its caffeine in three successive methylations starting from xanthosine. A methylation is the addition of a methyl group; each step is catalyzed by an N-methyltransferase. The first, XMT, turns xanthosine into 7-methylxanthosine.
2. MXMT: theobromine7-methylxanthosine becomes 7-methylxanthine, then the enzyme MXMT places a second methyl group: this is theobromine, the next-to-last molecule in the chain.
3. DXMT: caffeineThe third enzyme, DXMT, places the third methyl group: caffeine is made.
4. A duplicated gene familyThe canephora genome, published in 2014, shows that the gene family for these enzymes duplicated and specialized in the coffee lineage, independently of tea and cocoa: caffeine was invented at least three times. Canephora carries three highly expressed copies, arabica six less expressed copies, which explains part of the difference in content.
5. A homemade pesticideAt the concentrations found in leaves and seeds, caffeine and its relatives inhibit insect feeding and kill them: they block phosphodiesterase, and cyclic AMP accumulates in their cells (Nathanson, 1984).
6. A memory for the beeAt low dose in nectar, caffeine helps the bee: rewarded with caffeinated nectar, it remembers the scent of the flower three times better than with sugar alone (Wright and coauthors, 2013).

To remember: Repelling leaf eaters, keeping the foraging bees loyal: that the same molecule wakes up humans is, for the coffee plant, a side effect.

Read the full article and its sources ↓

The coffee plant makes its caffeine in three successive methylations starting from xanthosine: xanthosine, 7-methylxanthosine, 7-methylxanthine, theobromine, caffeine. Each step is catalyzed by an N-methyltransferase; in coffee they are called XMT, MXMT and DXMT. The genome of Coffea canephora, published in Science in 2014 by Denoeud and his coauthors, shows that this gene family duplicated and specialized in the coffee lineage independently of those of tea and cocoa: caffeine was invented at least three times by evolution, with different enzymes that end up at the same molecule.

The review by Yang and coauthors (2026) specifies that canephora carries three highly expressed copies of these genes and arabica six less expressed copies, which explains part of the difference in content between the two species.

Denoeud et al., The coffee genome provides insight into the convergent evolution of caffeine biosynthesis, Science 345 (2014); Yang et al. 2026, pp. 3-4, via digest; LC ch. 19

The molecule's role in the plant is twofold. Nathanson showed in 1984 in Science that caffeine and the neighboring methylxanthines inhibit insect feeding and kill insects at the concentrations naturally present in leaves and seeds, by blocking phosphodiesterase and causing cyclic AMP to accumulate in their cells: it is a pesticide that the plant synthesizes itself. Wright and coauthors showed in 2013, in the same journal, that the nectar of Coffea and Citrus contains caffeine at low dose and that bees rewarded with caffeinated nectar remember the scent of the flower three times better than those fed sugar alone, through antagonism of adenosine receptors in their mushroom bodies.

Repelling leaf eaters, keeping the foraging bees loyal: that the same molecule wakes up humans is, from the coffee plant's point of view, a side effect.

Nathanson, Caffeine and related methylxanthines: possible naturally occurring pesticides, Science 226 (1984); Wright et al., Caffeine in floral nectar enhances a pollinator's memory of reward, Science 339 (2013)