There are two principle ways to evolve related modern enzymes with specific activities. The first way postulates an ancestral enzyme that catalyzes a specific reaction (e.g. A1 → B1). Following a gene duplication event, one of the copies evolves an enzyme that catalyzes a completely different (but chemically related) reaction: A2 → B2.
Most people think that this is by far the most common pathway. That's because they are used to thinking that enzymes are highly specific—that's what's emphasized in most biochemistry courses. They think that it should be possible to reverse engineer the evolutionary pathway on the right-hand branch and thus transform one enzyme to another.
This works in some cases. For example, the enzymes shown in the figure are all members of the lactate dehydrogenase/malate dehydrogenase family. It's possible to take a modern lactate dehydrogenase enzyme and convert it to a malate dehydrogenase by changing only one amino acid [see Evolution and Variation in Folded Proteins, and Monday's Molecule #178]. It's likely that the ancestral enzyme was a malate dehydrogenase.
Imagine that the ancestral enzyme was promiscuous—it catalyzed a bunch of related reactions. This is not as far-fetched as you might imagine since most modern enzymes catalyze a variety of similar reactions even though the rate for one of them may be several orders of magnitude greater than that of the side reactions. Enzymes make "mistakes" quite often and their specificity is exaggerated. There are some classic examples: Fixing Carbon: Building a Better Rubisco.
When the gene for a promiscuous enzyme is duplicated, both of the daughter enzymes can each catalyze several reactions. However, now that there are two enzymes, each of them can evolve to become more specific without the cell losing the other function. The end result is two related enzymes with different specificities just as in the first scenario.
The difference is that in this scheme there never was a time when an enzyme with one specificity was transformed into an enzyme with a different specificity. The common ancestor could catalyze both reactions. This has implications for protein engineering and for those studies that try to mimic the evolutionary in the laboratory. You can't transform one enzyme into another without going through an intermediate with relaxed specificity [Evolution of a New Enzyme] [Evolution by Gene Duplication].
We'll return to this topic in a later post when I discuss the claims of creationists Douglas Axe and Ann Gauger.
It's difficult to decide between the two scenarios when dealing with gene duplication events that likely occurred two or three billion years ago. However, it should be much easier if you look at recent events.
Plants make a variety of obnoxious, sometimes toxic, compounds in order to discourage herbivores (i.e. vegetarians). Cilantro is a good example—no sane animal would eat a plant that makes cilantro [I Hate Cilantro/Coriander!]. I'm sure you're all aware of the most poisonous plants but you probably don't realize that almost all plants are trying to kill you (e.g. jalapeños).
Much of the chemical warfare being carried out by plants involves the relatively recent evolution of new enzymes with strange specificities. As you might expect, these enzymes evolve from related enzymes following a gene duplication. In many cases, the ancestral enzyme is promiscuous.
Most plants have an enzyme called HCT that catalyzes the fusion of two molecules of shikimic acid to produce p-coumaroyl shikimate (blue). Many herbs produce rosmarinic acid. One of the steps involves formation of p-coumaroyl-4′-OH-phenyllacate. This reaction (green) is a minor side reaction with HCT but the herbs have a related enzyme, RAS (rosmarinic acid synthase), that catalyzes it very efficiently. This is an example of the evolution of specificity from a promiscuous ancestor.
There are two other examples in the paper but I think you get the point. The evolution of enzymes with specific activities often involves a much less specific promiscuous ancestor.
Weng, J.K., Philippe, R.N., and Noel, J.P. (2012) The rise of chemodiversity in plants. Science 336:1667-1670. [PubMed] [DOI: 10.1126/science.1217411]