Evolving the Bacterial Flagellum Through Mutation and Cooption

Evolving the Bacterial Flagellum Through Mutation and Cooption

By Mike Gene

The bacterial flagellum is a motility structure whose irreducible and specified complexity has been cited as evidence for its design (a good basic description can be found here). Several non-teleological mechanisms have been proposed to explain the origin of Irreducible Complexity (IC), each with its own difficulties [1]. Evolution through cooption is the most commonly cited mechanism, which would involve more than one protein, previously shaped by selection for one function, fortuitously coming together to interact and provide a novel, selectable function. Yet how plausible are such scenarios? Although there is no explanation for the origin of the flagellum in the scientific literature, various non-teleologists from the cyber-community have outlined a vague cooption scenario to explain its evolutionary origin. A detailed analysis of such an scenario might not only help us gage the plausibility of the story, but also help us appreciate what all cooption stories face when attempting to account for the origin of IC machines.

The basic cyber-story for the non-teleological origin of the flagellum is as follows:

We begin with a type III export system, given that several proteins of the flagellum's basal body are homologous to the secretory machinery of this export system (type III systems secrete various proteins to establish symbiotic relationships with eukaryotic cells). Thus, the flagellum began as a protein secretion system. Next, we hypothesize that some protein, that is normally secreted, is mutated such that it can stick to itself and the secretory system. This forms our proto-filament. Filament formation is not difficult, as a single point mutation in the beta globin gene, responsible for sickle cell anemia, converts soluble hemoglobin into a filament. This filament then could serve the function of anchoring the cell to some other substrate. In fact, if we survey living bacteria, we'll find that there are indeed many different forms of nonmotile filaments that provide benefits to the cell (thus allowing us to propose a selective advantage to this step in the flagellum's evolution). Next, we again invoke cooption, as some other membrane protein somehow associates with the type III/filament system and fortuitously causes it to wiggle in some fashion. This slight movement confers motility to the bacteria, which in turn, is selectively advantageous. From there, mutations are selected that improve the motility function and finally, another set of proteins are coopted to confer the switching of rotation and chemotaxis response. Thus, we have a step-by-step account that involves at least three different functional state: protein export system transformed into nonmotile filament transformed into flagellum. Let us refer to this scenario as the Export-Filament-Motility (EFM) Hypothesis.

Yet how well does such an account really explain the origin of the bacterial flagellum?

Philosophical Considerations

Before beginning a scientific analysis of this scenario, it is worth considering the larger philosophical picture. Many people labor under the impression that IC means "something that even a hefty dose of Darwinian imagination cannot possibly explain." That is, many seems to think that if they (or anyone else) can invent a vague scenario for how the flagellum (or something like it) could have possibly evolved, all the issues brought to the forefront by an IC analysis disappear. But keep in mind that whenever you are dealing with a machine, it is always going to be possible to imagine the various parts existing without the machine, as long as you keep your explanation vague and are free to imagine simpler states with imaginary selective benefits and ad hoc functions. Consider how Ken Miller explains the origin of the bacterial flagellum:

But Brown's Mr. Miller contends that the ID argument completely misunderstands how Darwinian evolution works. The various parts of the flagellum weren't destined to serve together as a motor when they first appeared piecemeal in the deep history of bacteria. Instead, the parts served different and separate purposes originally. Only later did they happen to come together to form a motor. Remnants of that process are still visible today in various lines of bacteria, he says. Yersinia pestis, the species that causes bubonic plague, produces a complex structure with 10 proteins closely related to the ones found in bacterial flagella. The deadly bug doesn't use those proteins to move; instead, they help Y. pestis inject its toxins into the cells of its host. Drawing on Mr. Behe's favorite analogy, Mr. Miller says that the various parts of a mousetrap have uses even on their own. Three out of the five components form a handy tie clip. Two of the five can serve as a clipboard. Nature is opportunistic, he says, cobbling together different molecules and reactions for entirely new purposes. [2]

What is interesting about this logic is that we already know that the mousetrap was intelligently designed. We also know that it did not first exist as a clipboard, then a tie clip. Thus, while it is logically possible to see the mousetrap as Miller does, that is, as a modified clipboard and tie clip, such perceptions are not tied to history nor the origin of the mousetrap. Thus, coming up with imaginary accounts that tap into our ability to imagine cooptional origins, by itself, is rather meaningless. If we can successfully come up with such explanations where they are known to be false(the mousetrap), how do we know that our ability to do likewise with things like the flagellum are not also inherently flawed? [3]

Before we turn our attention to the EFM Hypothesis, it is worth considering something that Julie Thomas posted to talk.origins back in 1997, since this hypothesis has all the characteristics of a just-so story:

Here's the recipe for making a just-so story. First, survey the biological world for structures/functions. Find those that seem useful for coming up with a precursor to the system in question and patch them together without much regard for biochemical and/or genetic details. Place the patchwork in an imaginary creature from the distant past that has conveniently gone extinct. Invoke a vague selective pressure that selects for the patchwork and then imagine it is plastic and amenable to further selective modification that just happens to arrive at the system in question.

Thus, if all we have is a just-so story that merely reflects our innate ability to imagine non-teleological causes for designed systems, the EFM Hypothesis can hardly be considered a serious rebuttal of the design inference stemming from the flagellum's IC essence. Let's now consider the hypothesis.

ASSUMING THE TRANSPORTER FROM THE START

The EFM hypothesis begins with the knowledge that a core subsystem of the flagellum is its protein secretion machinery and thus builds around this. That is, to explain the origin of the flagellum, the EFM hypothesis must start with the most complex subsystem that is part of the flagellum (called the type III export system, the machinery invoked by Miller above). However, that flagella have built-in sophisticated transport systems is no surprise from an teleological perspective.

With the construction of the flagellum comes a design problem. That is, how does one construct a complex and specific assembly of proteins outside the cell? The bacterial flagellum is quite unlike the eukaryotic flagellum in this regard, as the latter is in direct communication with the cytoplasm and bounded by the plasma membrane. The bacterial flagellum, in contrast, penetrates the cell membrane and wall and is housed outside of the cell membrane. Again, how can it be constructed? It's kind of like putting together a satellite dish on your roof without ever leaving the house.

One solution would be to construct the entire flagellum within the cytoplasm and move the whole thing outside. The problem? It would be far too large for such transport. Instead, the design problem has been solved as follows: the flagellum is hollow. This allows bacteria to construct flagella from the bottom up. To facilitate this construction, a significant chunk of the flagellar machinery functions as a protein secretion/export machine that channels components through the hollow space to distal ends where they attach (resulting in piecemeal growth of the flagellum). The interesting thing is that the mistakes in construction at any point actually shut down the expression of gene products that would be used in the later stages of flagellar construction, thus imparting a built in quality control mechanism for flagellar synthesis. Nevertheless, the export machinery solves a design problem entailed in the cell constructing a flagellum. Thus, we can see that an integral component of a flagellum is its modular export machinery needed to construct and maintain the flagellum. It's a clever solution to a clear design problem.

In the past, I have asked ID critics just what would the flagellum look like if it was not designed. After all, if you pay attention as I do, they commonly argue that this and that does not look like it was designed. Nevertheless, the critics have not answered this question. Yet if the transport/secretion system is a logical ingredient that solves a design problem entailed in making the flagellum, and the flagellum was indeed designed, those looking for non-teleological explanations would misinterpret the significance of such a subsystem and mistakenly impose an historical interpretation on an engineering solution.

Now, if someone wants to start this story with "any ol' transporter," I'm afraid that's not good enough. Remember, that we need to explain the origin of the bacterial flagellum (not some "flagellum"). That means we need to account for the flagellum's type III export machinery, which includes flhA, flhB, fliR, fliQ, fliP, fliI, and more. All of the other bacterial transport/secretion systems cited to support the EFM hypothesis merely illustrate that the majority of transport/secretion systems are dead-ends from a flagellar perspective, as none of them have spawned a eubacterial flagellum, despite them all being equally good starting material at this point in the EFM hypothesis.

It's important to keep in mind that there are indeed dead-ends in evolution. For just one example, consider the inverted retina of the vertebrate eye. As Ken Miller explained elsewhere:

Evolution, which works by repeatedly modifying preexisting structures, can explain the inside-out nature of the vertebrate eye quite simply. The verterbate retina evolved as a modification of the outer layer of the brain. Over time, evolution progressively modified this part of the brain for light-sensitivity. Although the layer of light-sensitive cells gradually assumed a retina-like shape, it retained its original orientation, including a series of nerve connections on its surface. Evolution, unlike an intelligent designer, cannot start over from scratch to achieve the optimal design. [4]

Evolution cannot start over and must work with what it is handed. We've heard much about the suboptimal retina. The reason why random mutations coupled to nature selection cannot "fix" it is because it is essentially hardwired in early embryological development. In other words, "choices" made early on in a progressive march of construction not only lack foresight, but constrain what can happen next. The blind watchmaker can box himself in with each new choice.

Thus, it would seem that we'd need to establish two things for the plausibility of the EFM hypothesis.

1. Would "any ol' transporter" really do? That is, could we take the framework of any ol' transporter and put the type of flesh on it that is exhibited by the bacterial flagellum? Or would most of these transporters be dead-ends in the sense that their transport mechanism entails a constraint that would prevent the evolution of something like the flagellum-as-we-know-it? Again, this latter point seems to be the case since none of the other transport systems evolved something comparable to flagellum among eubacteria.

2. Is there any reason to think the type III export system, complete with the ancestors of flhA, flhB, fliR, fliQ, fliP, fliI and others, existed as a "cooptable part." Thus far, the answer is no, as there are good reasons to think the type III system evolved from pre-existing flagella.

a. The bacterial flagellum is found in both mesophilic and thermophilic bacteria, gram-positive and gram-negative, high GC and low GC content bacteria, and spirochetes. Type III systems seem to be restricted to a few gram-negative bacteria. That is, if we look at the sequenced genomes from the various groups cited above, we can find the genes for the bacterial flagellum but not the type III system genes.

b. Independent evidence suggests the type III system is recent. It is not only restricted to gram-negative bacteria, but to animal and plant pathogens. In fact, the function of the system depends on intimate contact with these multicellular organisms. This all indicates this system arose after plants and animals appeared. In fact, the type III genes of plant pathogens are more similar to their own flagellar genes than the type III genes of animal pathogens. This has led some to propose that the type III system arose in plant pathogens and then spread to animal pathogens by horizontal transfer.

c. When we look at the type III system its genes are commonly clustered and found on large virulence plasmids. When they are in the chromosome, their GC content is typically lower than the GC content of the surrounding genome. In other words, there is good reason to invoke horizontal transfer to explain type III distribution. In contrast, flagellar genes are usually split into three or more operons, they are not found on plasmids, and their GC content is the same as the surrounding genome. There is no evidence that the flagellum has been spread about by horizontal transfer.

d. It's much easier to envision the evolution of the type III system from flagella than vice versa. For starters, evidence has surfaced that the basal body of the flagellum already works to secrete proteins other than the flagellar proteins, including virulence factors. Thus, the basal body is already poised to evolve into a type III system from the start. Evolution apparently would only have to duplicate and tweak the type III virulence protein secretion activity already existing in flagella. . In my opinion, this view is far more parsimonious than to propose that something like the type III system evolved long ago, was lost by all bacteria but gram-negative animal/plant pathogens and then was used to evolve the flagellum so that horizontal transfer could spread flagella far and wide (despite the lack of evidence for such transfer).

Thus, it should not be surprising that the scientific opinion has been converging on the notion that the export machinery evolved from the flagellar machinery [5-7].

Is there any evidence that supports transporting this system, or something like it, back in time? The type III system is one of at least four different bacterial protein transport systems. And it appears to be the most complex of the bunch. The key here is that the type III/flagellar cytoplasmic export system does not show clear homology with any of these other transport systems. But we also know that evolution builds on and modifies what already exists rather than create de novo. Thus, if these other transport systems were already in place (and they probably were), why didn't evolution simply build on one of the simpler versions rather than create a whole new method of protein secretion de novo? The type III-from-flagellum scenario better fits with what we know about evolution - that it uses what already exists rather than inventing de novo. Thus, not only is there no evidence to support putting this transporter (or something closely homologous) back in pre-flagella days, there is reason to think it wouldn't be there.

Another fundamental problem with the first step of the EFM hypothesis is that it assumes IC to explain IC. Consider that the flagellum is composed of about 20 different proteins. Of those twenty, ten are homologous to the type III export machinery. Thus, this hypothesis begins its attempt to explain the origin of a 20-part IC system by assuming the existence of half of it (10 parts).

Let's briefly consider the 10 parts of the type III export machinery, where I'll use the flagellar gene names. There is FliI, an ATPase that is anchored to cytoplasmic face of the inner membrane. It may provide energy for the synthesis of the export machinery or transport of secreted proteins. It is thought to capture proteins in the cytoplasm for transfer to the secretory apparatus. There are several proteins that span the inner membrane and probably make up the protein conducting channel, including FlhA, FliP, FliQ, FliR, and FlhB. There is FliF, which in flagella, form the MS ring. And there is FliN and FliG, which in flagella, make up the C ring (located beneath the MS ring). Finally, there is FliH, with an unknown function.