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Problems with the Cooption Scenario

September 25, 2011

Problems with the Cooption Scenario

Introduction

To explain the origin of the intricate protein-based machinery of the cell, non-teleologists will often invoke cooption. If system X requires components ABC to maintain that function, how does Darwinian evolution explain the origin of system X? By cooption. In the cooption scenario, components A, B, and C start out with different functions, and then A and B happen to associate with each producing function AB. Next, C is associated with function AB, forming function ABC.

I have just a few problems with the cooption scenario, especially when the cooption scenario is invoked to explain the origin of biological systems that have a large number of essential components. First of all, as I have pointed out earlier, the foundation of the cooption model is rooted in chance:

Ultimately, the cooption scenario is based on chance. Natural selection does play a role, but the primary mechanism is chance. This is because in the cooption scenario: (a) chance alone determines that proteins currently performing vastly different functions will have just the right shape so that they can fit snuggly together with other proteins (that also just happened to have just the right shape) and form a novel IC structure; (b) it is primarily chance that determines that these proteins will happen to associate with each other to form the novel IC structure. Natural selection only kicks in once these proteins have associated with each other to produce new function.

Since the cooption model is rooted in chance, the cooption model should be invoked with caution. But there are other problems with non-teleological cooption as an explanation for the origin of certain protein-based systems. How likely is it that a large number of proteins with independent functions will have just the right interfaces so that they will fit snuggly with another protein to form a novel function?

There are thousands of different types of proteins in one cell, each of them performing vastly different functions. To explain the origin of the flagellum, the cooption scenario suggests that an inner membrane pore protein complex, an ATP synthase, an outer membrane pore protein complex, an ion pump complex, an adhesin, and a signal transduction protein (to name a few) all gradually associated with each other to form the bacterial flagellum. This is like suggesting that a contractile protein like actin, a motor protein like kinesin, a tubular protein like tubulin, and a transport protein like cytochrome, could all be coopted to form an entirely novel function. This isn’t likely at all, because the above proteins almost certainly don’t have the right complementary shapes to associate with the other proteins, thereby forming a novel function. In fact, it’s quite likely that random association of a random protein with another random protein won’t result in any beneficial function at all.

Now, what exactly do I mean by “right complementary shapes” and what does it mean when I talk about proteins “fitting snuggly with each other”? Perhaps the best way to explain this is by example.

In “Your Weekly Dose of Proteins” I discuss the YscJ/FliF ring complex. This complex provides a nice example of proteins that snuggly fit with each other to form a functional structure (see below figure).

YscJ Ring Complex

Figure 1. A 3D model of the YscJ ring complex. Note the areas encircled by a red squares. These are areas where the YscJ monomer fits with other YscJ monomers to form a functional complex.

An example of a protein complex where two different types of proteins fit with each other to perform a function is the FliM/FliG complex. Both FliM and FliG function as part of the bacterial flagellum. Both of these proteins associate with each other and are involved in rotation and switching of the bacterial flagellum.

The interesting thing about these two flagellar proteins is that their shapes are complementary to each other so that they can snuggly fit together. This is illustrated below in the space-fill 3D model of this protein complex, and further illustrated by the tube model.

FliM/FliG Complex

Figure 2. Space-fill model of the FliM/FliG complex, which forms part of the bacterial flagellum. The pink protein represents FliM, and the blue protein represents FliG. Note how the two proteins nicely fit together – their shapes are complementary.

Tube Model

Figure 3. Tube model of the same FliM/FliG complex.

A Teleological Prediction

I would predict that the interfaces of these two proteins would be highly conserved. In other words, I suspect that the areas in with these proteins associate – that is, the actual surfaces of these proteins where they fit together – are highly conserved in sequence identity. Is this a teleological prediction or is this just a prediction that stems from the way proteins work? This is an interesting question, but I’ll try to add some insight to that question: firstly, Darwinian evolution doesn’t exactly predict that those regions will be highly conserved. This is because, in the Darwinian model, protein complexes are probably expected to fit loosely with each other. The Darwinian model doesn’t predict that specific proteins will be tightly matched with each other because Darwinian evolution doesn’t exactly predict that a structure will demonstrate the (appearance) of rational design. If proteins are tightly matched with each other, this is an example of rational design. The better the fit (and therefore, the higher the conservation of sequences at the surfaces of the proteins where they fit with each other), the more efficient the function. And efficiency is a hallmark of rational design – efficiency is not a hallmark of Darwinian evolution.

Let me put it this way: Darwinian evolution does not explicitly predict that the sequences in the  region where two proteins fit together will be tightly conserved. But, at the same time, if these regions were well conserved, this would not mean that Darwinian evolution could not explain it. Rather, the observation that the regions would be well conserved means that it provides yet another clue – albeit a minute one – that perhaps teleology was involved in the origin of the molecular systems. Certainly, Darwinian evolution could explain that observation; Darwinian evolution could also explain the reverse observation (namely, that those regions are not well conserved). However, the teleological hypothesis would only predict that those regions will be well conserved, since, if those regions were well conserved, this would mean that the function is carried out efficiently, and I have already noted that efficiency is a hallmark of rational design, which in turn is a signature of teleology.

I decided to test the teleological prediction. I downloaded the FliM/FliG complex from MMDB Structure, and viewed the complex in 3D using the program Cn3D. Next, I determined what part of the FliG structure corresponds to what part of the FliG protein sequence. Having done that, I determined which sequences represented the region where FliG interacts with FliM. One of these regions is highlighted in yellow in the below figure.

Figure 4. Tube model of a region (highlighted in yellow) in FliG that fits with FliM.

The highlighted section of FliG represents the amino acid sequence “EHPQ.” To determine the level of conservation of this sequence, I aligned 5 different FliG sequences (using ClustalW) belonging to a wide range of organisms, from the deep-branching Thermotoga to the late-branching Escherichia coli. The results confirmed the teleological prediction. Amazingly, the sequence “EHPQ” is 100% conserved throughout all five bacteria lineages. Not only that, but it is one of the few 100% conserved patches in FliG. In other words, all of the sequences around “EHPQ” aren’t entirely conserved. It looks like the teleological prediction is tentatively confirmed.

Figure 5. Space-fill model of the same region, highlighted in yellow. The region highlighted in yellow represents the amino acid sequence “EHPQ.”

Now, I don’t expect that every single time there will be 100% conservation. That’s not what is needed to fully confirm the teleological hypothesis. What is needed is a higher than usual level of conservation in these regions – with few exceptions.

 

 

Back to the Cooption Scenario

Aside from the teleological predictions that we can glean from protein-protein complexes, protein-protein complexes are interesting because they demonstrate the problems with the cooption model. The non-teleological cooption model suffers from the very serious problem that it is very unlikely for proteins to exist that have just the right complementary shapes so that they can be joined with other proteins which also happened to have the right complementary shapes to form a beneficial function. This problem especially comes into play when we look at protein-based functions that have a large number of components, all of which have just the right complementary shapes to associate with several different types of proteins, all of which have just the right 3D shapes.

But there is another problem. If protein A can fortuitously associate with protein B to form function AB, then component A can also associate with protein W, to form a non-functional system. It can associate with protein R, T, and S, for example, and all these associations would result in a non-functional system. Similarly, protein B can associate with proteins W, R, T, and S, again, resulting in a non-functional system. Of all the possible combinations of associations that protein A can do, only a small fraction will be functional. This is a problem that I will investigate in a later article.

Conclusion

The cooption scenario suffers from two difficulties, as described in this article. Thus, the cooption scenario is a shaky foundation on which to build a non-teleological explanation for the origin of protein machines that are composed of a large number of tightly integrated components.

In other news, this website now has a twitter account. The twitter account is called GenomeTale. So, follow my twitter account and spread the news, ‘cause we all know that my website rox!

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