Secondary metabolism and Metacyc

Metabolism is a concept we generally think about in terms of diet pills and exercise: the process of burning the complex chemical fuels we need to survive or, on the plant side, turning sunlight and carbon dioxide into those same tasty fuels. Ask a biochem student what metabolism is and (s)he'll have a flashback to a huge org chart of hundreds of small molecule chemical intermediates stemming from just a few enzymatic pathways. Many of which had to be copied out by hand on one term paper or the other, like this.

(Thanks, Steven Hsu!)

 Luckily, we live in the future, and we have the internet. There is a wonderful tool for exploring these pathways which is called MetaCyc. Load it up, and type in a tasty metabolite, like capsaicin, the spicy part of chili peppers.

You get a site with a lot of gibberish and a nice SVG of capsaicin

Under the heading "Reactions known to produce the compound:" you'll see capsaicin biosynthesis.
 
Click on it! 

Now we're in business: those yellow words on the right are the enzymes that the plant uses to transform one chemical intermediate (red) into another. So here is something interesting: capsaicin, a profoundly spicy chemical, is made from the conjugation of a long chain that looks like a fatty acid chain to vanillylamine, which is one step off vanillin. Vanillin is just like it sounds: the main taste component of vanilla beans, a strong taste in a totally different direction. So here is where your artisan transgenic foodie ears should prick up: if one of those genes upstream of the final product were knocked out, would you get a pepper that tasted like vanilla?


In a word, maybe. The reality of enzyme kinetics in a plant are very different from this well organized chart. We know, for example, that many peppers are not pungent at all, while the ones that produce capsaicin produce it only in some tissues (the placenta around the seeds), and at levels that vary hugely: from the relatively tame Jalapeno to the current record holder, the Bhut Jolokia, you have a difference in capsaicin from 200 - 50,000 ppm.

Scrolling down to the bottom of the page, you see the academic papers the curator used to create this graph. If you really want to knock some of these enzymes out and see what happens, you should read those first. Especially the one that talks about "capsaicin synthase", which is the missing enzyme that connects the two main precursors at the bottom.

Metacyc is great to troll around before getting into the nitty gritty of how to modify, but in the end you should read the papers that people have published about actually intervening in those genomes, or what mRNA transcripts come out of pungent / non-pungent peppers. We can wait.