Promiscuity in Evolution
No, this is not another post about the sexual habits of female apes. This is about enzymes, and their ability to catalyze different reactions with different substrates, even those that aren’t found in nature. It’s a property known as “promiscuity”, one that’s being increasingly recognized as important in enzymology and enzyme evolution.
The usefulness of enzymes derives in part from their specificity, in that they don’t just catalyze any old reaction with any old substrate. It would be hard for cells to maintain homeostasis if enzymes were highly nonspecific; helpful reactions would be coupled with harmful side reactions, regulation would be impossible, and things would get messy real quick. So it’s useful for enzymes to specialize in certain functions so that they can be applied for specific tasks at specific times. But because nature is a bit sloppy, enzymes are often able to catalyze many reactions weakly in addition to the “native” functions that they specialize in. These additional weak activities are referred to as promiscuous activities, and they’re potentially very important in enzyme evolution. Now a recent study (subscription required) published in Nature Genetics by Amir Aharoni and coworkers sheds some light on why enzymes are promiscuous, and what it means for their evolvability. (There is some good non-technical commentary on the paper here and here.) It also badly knocks down some bold claims made by leading ID proponents.
Enzyme promiscuity facilitates evolution because new catalytic functions can evolve from those that already exist weakly in existing enzymes. One notable example is TCHQ dehalogenase, an enzyme involved in PCP degradation, which evolved very recently from maleylacetate isomerase. Even though TCHQ, which is a breakdown product of PCP, does not exist in nature, bacteria quickly evolved an enzyme that digests it.
Aharoni and coworkers decided to look at three enzymes that weakly catalyze extra reactions, and apply a technique known as “directed evolution” to see if these promiscuous activities could be increased. Directed evolution is just Darwinian evolution in a test tube – you apply random mutagenesis to a gene, apply selection criteria to the results, and repeat. DNA shuffling, which mimics the natural process of recombination, is also frequently added in. The enzymes they used are serum paraoxonase (PON1), a bacterial phosphotriesterase (PTE) and carbonic anhydrase II (CAII). Each one can catalyze a variety of promiscuous activities in addition to its native activity. The researchers attempted to evolve improved activity towards different substrates for each, using 9 substrates total.
What the authors discovered isn’t too surprising: they were able to substantially improve the level of activity for each of the promiscuous functions they studied. Lots of other directed evolution experiments have done the same. What is somewhat surprising, however, is what happened to the native functions. It’s important to note that in each of their experiments, the researchers only selected for a given promiscuous activity – they did not select for other promiscuous activities nor did they select for the maintenance of the native activity. This is crucial because they found that in some cases, activity had substantially improved for other promiscuous activities (indicating plasticity), but had not decreased by a large amount for the native activity (indicating robustness). Or to put it another way, the promiscuous activities were easily perturbed (increased or decreased) through a few mutations, but the native function was not so easily perturbed. This may seem rather fortuitous, but aside from structural considerations, there is one simple explanation for this phenomenon: native functions have been under selection, which should favor robustness. Promiscuous activities, however, have not been selected for, so they tend to be more plastic. While plenty of previous studies have demonstrated the prevalence of promiscuity among various enzymes, it is not well established that the native function can remain undisturbed while the promiscuous functions are greatly improved. Aharoni and coworkers looked through the literature and found many other examples of this phenomenon. (I’ll toss in yet another example which was just published.)
When it comes to evolvability, these two properties – robustness of native function and plasticity towards promiscuous functions – are great facilitators. When an organism is faced with new challenges, an enzyme can improve its activity towards a new substrate (or new reaction) while maintaining a high level of native function. This greatly increases the chances of successfully achieving a novel function without disrupting the old one. As the simplified graph below shows, an enzyme evolving a new function must maintain a high level of fitness throughout its evolution otherwise it will be constrained by selection. Selection will keep the enzyme near the “peaks” in sequence space and away from the “valleys”. If the old function must be lost or severely degraded before the new one can evolve, then protein evolution is limited by negative trade-offs.
But the results of Aharoni et al show that enzymes can indeed maintain their old functions while adapting to new ones. So they need never enter a valley before finding a new peak. When coupled with gene duplication, this presents us with a generalized model of how new functions are continuously added to the genome. The authors give a simple account in their text:
The divergence of new proteins could follow this route: initially, a gene acquires a beneficial mutation that renders it generalized by increasing the protein’s promiscuous activity to a level sufficient for survival while maintaining the original activity largely intact. Gene duplication, and the divergence of a completely new gene (with respect to sequence and function), then follow.
This is likely to be a fairly general method of novel protein evolution, and quite interesting in its own right. But it also refutes some key claims made by ID advocates. In particular, it pertains to our previous critique of a paper written by ID advocates Michael Behe and David Snoke, which attempted to model the evolution of gene duplication using a simple “neo-functionalization” assumption. Their model assumes that gene duplication occurs first, and then it’s a race against time for beneficial mutations to appear before the duplicate gene is rendered nonfunctional by deleterious mutations. But as we see here, a likely route towards novel gene evolution, which they did not account for, is one in which the new activity exists prior to gene duplication, with duplication simply allowing specialization. Hence, there is no race against the clock, since the selectable function is already present.
More strikingly, however, is how this research flies in the face of a prediction made by William Dembski:
In section 5.10 of NFL [No Free Lunch], I indicated how perturbation probabilities apply to individual enzymes and how experimental evidence promises shortly to nail down the improbabilities of these systems. The beauty of work being done by ID theorists on these systems is that they are much more tractable than multiprotein molecular machines. What’s more, preliminary findings of this research indicate that islands of functionality are not only extremely isolated but completely surrounded by a sea of nonfunctionality (not merely polypeptides having different functions but polypeptides incapable of function on thermodynamic grounds – in particular, they can’t fold). For such extremely isolated islands of functionality, there is no way for [Richard] Wein’s method of co-evolving functions to work.
Prediction: Within the next two years work on certain enzymes will demonstrate overwhelmingly that they are extremely isolated functionally, making it effectively impossible for Darwinian and other gradualistic pathways to evolve into or out of them. This will provide convincing evidence for specified complexity as a principled way to detect design and not merely as a cloak for ignorance.
William Dembski, Obsessively Criticized but Scarcely Refuted: A Response to Richard Wein (Emphases original)
Well it’s been over two years since Dembski wrote this, and not only has the evidence for “isolated functionality” of enzymes not materialized, the precise opposite has been discovered – protein functions overlap. (Note that the “preliminary” findings that Dembski refers to are not cited, and most protein chemists wouldn’t have bought this claim in the first place.) So we have here a bold yet failed prediction, the sort of thing we’ll undoubtedly be seeing lots more of.
Notice also that Dembski is positing this property of “isolated functionality” in order to shore up his concept of “specified complexity”. Richard Wein has written a lengthy critique of specified complexity as presented by Dembski in No Free Lunch, and the above quote is part of Dembski’s reply. As Wein points out in response, Dembski is hanging his grand method of detecting design in biology on the speculative outcome of future research, which basically proves the point that specified complexity is indeed an argument from ignorance. Here we see the dangers of making revolutionary claims based on what might be discovered some time in the future – you often end up being wrong.
Reference:
Aharoni A, et al. Nat Genet. 2005 Jan;37(1):73-6.