Coffee: Millions of Years of Poison and Brain Manipulation

Many people think of coffee simply as an absolute necessity in the morning. But it’s also a fascinating piece of natural history. Here we have a plant that produces a potent chemical–caffeine–that can snap our brains to attention in low doses and kill us in big doses. Why on Earth would some Ethiopian bean go to such great lengths? For my Matter column this week in the New York Times, I take a look at a new study that offers some answers.

The study is, in fact, the sequencing of the coffee genome. Normally, I’m very leery of genome papers–I come down with a disorder I’ve dubbed YAGS. But sometimes the scientists who sequence a genome also discover some interesting things in it. Such is the case with coffee: the scientists were able to test some hypotheses for how caffeine evolved. The scenario they propose is an elegant combination of gene duplication and convergence. And it can help scientists to figure out exactly what kind of benefits caffeine offers plants that could fuel its evolution not just in coffee, but in other species like tea and cacao as well. Check it out.

16 thoughts on “Coffee: Millions of Years of Poison and Brain Manipulation

  1. The “Check it out link” is to the YAGS article instead of the coffee article. (Feel free to delete this comment.)

    [CZ: Fixed. Thanks!]

  2. “Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.”

    If I got this straight this means that the caffeine genes in Coffea, in Camelia Sinensis, in Ilex Paraguayensis, and in Cocoa are:

    * different
    * placed on different loci


    [CZ: Yes. The genes in the different plants evolved from different ancestral genes. And during gene duplication and recombination, those genes have also moved around a bit.]

  3. “The principal caffeine biosynthetic pathway. Three methylation steps are necessary to produce caffeine from xanthosine, involving the successive action of three NMTs: xanthosine methyltransferase (XMT), theobromine synthase [7-methylxanthine methyltransferase (MXMT)], and caffeine synthase [3,7-dimethylxanthine methyltransferase (DXMT)]. SAM, S-adenosylmethionine; SAH, S-adenosylhomocysteine.”

    Specifically this one:

    “Three methylation steps are necessary to produce caffeine from xanthosine”

    Is xanthosine even being synthesised outside the caffeine bearing plants itself?

    If not, one would also want to know why there is xanthosine in them in the first place.

    [CZ: Xanthosine is a very common compound–it’s a base, similar to the bases that make up DNA–which has many uses aside from being turned into caffeine in plants like coffee.]

  4. It was my understanding that cacao does not actually make caffeine. Rather, it makes theobromine, a caffeine analog. Because of the similarity, are they simply referring to theobromine as caffeine, starting from an initial hypothesis that the genes for caffeine and theobromine originated from a common gene or does cacao make both (not to say that these two possibilities are mutually exclusive, because I see no reason they would be)?

    [CZ: Theobromine is produced on the pathway to caffeine. So coffee makes theobromine too, but converts a lot of it to caffeine. Cacao leaves a lot of it as theobromine. Nevertheless, cacao does have a special enzyme for converting theobromine to caffeine.]

  5. CZ : “Xanthosine is a very common compound”

    Deutsche Wiki: “Xanthosin ist ein seltenes Nukleosid und entsteht bei der Desaminierung von Guanosin der RNA. Es besteht aus der β-D-Ribofuranose (Zucker) und dem Xanthin.”

    Common or selten (uncommon)?

    Specifically: in grapes and tomatoes, supposedly relatives of coffee (according to the cladogram), do we see either xanthosine or some non-caffeine direction derivative of it?

  6. OK, should have looked up before asking.

    Vitis vinifera Reaction:

    “Enzyme Commission Synonyms: xanthosine-5′-phosphate-ammonia ligase, guanylate synthetase, XMP aminase, xanthosine 5′-monophosphate aminase”

    Changing Metabolites for Ripe Tomato Introgression Lines (with Possible Identification)

    3476 Chromosome 1-1

    283 (Changing Bin=locus?) xanthosine (Possible ID) C10H12N4O6 (Formula) 284.0757 (Accurate Mass)

    So, answering question myself, answer was yes.

  7. In your NYT article, I found the following statement.

    ‘When coffee leaves die and fall to the ground, they contaminate the soil with caffeine, which makes it difficult for other plants to germinate. Coffee may thus use caffeine to kill off the competition.

    Coffee plants also use caffeine to ward off insects that would otherwise feast on their leaves and beans. At high doses, caffeine can be toxic to insects. As a result, insects have evolved taste receptors that help them avoid ingesting caffeine.’

    Living in the midst of Kona coffee growing region, both of them do not seem to hold. Weeds grow like crazy on coffee land unless weeding is done. Also the CBB, the coffee bean borer beetles infest the inside of the beans quite rampantly. Easily 20-30% of beans have to be discarded to avoid excessive bitterness. Some beans get half black with the tiny beetles. How we wish these beetles to learn that coffee beans are toxic and they should stay away.

  8. What contribution does caffeine have on the coffee plants ability to fend off molds and other attacking species? I ask this as coffee grouts have a tendency to quickly attract mold, whereby tea seems more robust. I am refering to it’s “used” state, it has been roasted and then cooked.

  9. Mitzi: That one species of beetle infests coffee fruit to the exclusion of others argues for caffeine deterring other insects from munching on an otherwise good source of nutrition. The one species that evolves a resistance to caffeine’s effects has the field to itself, so to speak. If coffee beans were subject to attack from many different types of insects, that would argue that caffeine doesn’t protect them.

  10. I stopped reading when you said caffeine “evolved”. Anyone who is a proponent of evolution is obviously an idiot who knows nothing about science and is unable to think for themselves, since evolution goes against all the known laws of physics.

    That said, coffee is poison…

  11. John, while the mechanisms inside evolving organisms are inorganic, evolution itself is an organic phenomenon not DIRECTLY based on laws of physics. At first I thought your comment was silly, but it certainly got me thinking. However, evolution is alive and well because now genomic and epigenetic data clearly show it in action. And epigenetic data (transgenerational epigenetic imprinting etc.) get us closer to accepting how complex biological systems could have evolved in as short a time as they have, and how a chimp can have a genome 98.X% the same as that of a human. This has always been the one thing that I can’t figure out.

  12. Here’s a follow-up comment. Think about it: the human genome is less complex and smaller than that of some plants and mutations – permanent changes in the genome – only occur in less than 1% of the population, and are often not random. If you look at this in purely mathematical terms, how can this mechanism generate enough within-species variation to allow natural selection to drive the amount of change that has evolved. It just doesn’t work.
    BUT, when you add epigenetics to the mix, and you have layer upon layer of control systems, overlying the genome, now there is an enormous capacity for variation. A 64-bit chip can be at the center of a modern computer based upon 2 to the 64th different binary numbers. Scale that up to 20,000 or more genes turned on or off and you have 2 to the 20,000th different numbers. Actually, this is faulty mathematics but still it creates a basis for a principle that works. There must be enough possible variation, both random and otherwise, for natural selection to do its thing and create the miraculous variety of life on Earth….and thus I came to the conclusion that there is a God!

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