In the past, I have floated the hypothesis of molecular threaders, which are ring structures that can interact with polymers to unfold them, in essence translating the rotary motion inherent in a wheel to the linear unfolding (and thus threading) of a polymer. As I explained:

What all these proposed wheels have in common is that they form ring structures and handle polymers in an ATP dependent fashion. I’ll label these machines as the molecular threaders. In a sense, cells do have “cog wheels,” only they are more sophisticated than Paley’s watch.

Above, I noted the advantage of a rotary motion device is that it can carry out such work indefinitely with minimal rearrangement of the surrounding structural architecture. Yet the cell is also very good at coordinating internal structural rearrangements, as its order is dynamic. Thus, the advantage of the wheel inside the cell may be minimal and restricted to certain functions. This is one reason why I propose the molecular threaders. The rapid threading of polymers is something a wheel could do very well.

A good candidate for expression of this common design theme is the FliI component of the bacterial flagellum and the alpha/beta hexamer of the F-ATPase:

While it is true for many years that scientists thought FliI functioned as a single copy, more sophisticated experimental work showed that it too forms a six-member ring, using six copies of FliI [2]. Suddenly, the theme of common design resurfaces. Might the sequence and domain similarity be tied to the shared structure of a ring? The FliI ring sits at the very base of the flagellum, where it acts as the intermediary between the cytoplasm and the embedded protein secretion apparatus, recruiting flagellar proteins. Since many flagellar proteins are probably unfolded as they enter the secretion apparatus, one can envision FliI snagging and threading the amino acids chains of flagellar proteins into the flagellum while it is under construction [3]. The explanatory balances now levels off, where it appears that both common descent and common design are plausible explanations.

This theme has been recently supported by new research, where Imada et al. have solved the crystal structure of FliI (Katsumi Imada, Tohru Minamino, Aiko Tahara, and Keiichi Namba. 2007. Structural similarity between the flagellar type III ATPase FliI and F1-ATPase subunits. PNAS 104: 485-490). What they find is that the structure of the the FliI subunits is essentially the same as the alpha and beta subunits of the F-ATPase, allowing them to model the hexameric structure of FliI. Interestingly, FliI appears to be a mosaic of the alpha and beta subunits. Since the alpha/beta subunit function by interacting sequentially with the central gamma subunit, this raises the question of what would function analogously in the FliI ring. The researchers comment as follows:

InvC, the FliI homolog in Salmonella virulence type III secretion system, has been shown to act as an ATPase-dependent unfoldase that interacts with the chaperone-substrate complexes and unfold the substrates. Based on the FliI structure, the potential chaperone-binding site of the InvC is mapped on the C-terminal region of the C1 alpha helic, which corresponds to the region of the beta subunit with which the gamma subunit interacts. This observation suggests that those chaperones are one of the candidates for the “gamma subunit.” It may also well be that the FliI hexamer is a linear motor, unfolding and threading export substrates through its central channel by cooperative conformational changes of the subunits, just as speculated for AAA ATPase complexes.

Thus, it appears that the chaperone may hand off its substrate to one member of the ring to initiate the process of unfolding. In essence, this would mean that the chaperone, combined with the extended polypeptide in the act of being secreted, would mimic the structure of the gamma subunit. What at first seemed to be quirky similarities between FliI and the alpha/beta subunits best explained through common descent are turning out to reflect a similar mechanism and design plan.