Posted: Jul 23, 2010 10:56 am
CharlieM wrote:A three-dimensional structural similarity search using software DALI25 resulted in no match for domain D1, confirming its unique fold.
This is the kind of knowledge that is available to us these days. We see a complex structure such as this domain of protein FlgE and we know that this has to be inserted or developed from a similar protein to it and its homologs.
Wherefrom it doesn't logically follow that it was designed, at all. It doesn't even hint at it, all it says is that the protein fold, it's 3-dimensional structure, is unique among accessed protein folds by the software. The fact still remains that FlgE is homologous in it's sequence to the rod, cap and filament proteins.
There is of course also the fact that we have yet to sequence the entirety of bacterial genomes in their diversities, we have barely begun to scratch the surface.
For example, regarding the search for T3 export systems back in 2003 Matzke had these facts for digestion:
http://www.talkdesign.org/faqs/flagellum.html#origin
If type III virulence systems are derived from flagella, what is the basis for hypothesizing a type III secretion system ancestral to flagella? The question would be resolved if nonflagellar homologs of the type III export apparatus were to be discovered in other bacterial phyla, performing functions that would be useful in a pre-eukaryote world. That such an observation has not yet been made is a valid point against the present model, but at the same time serves as a prediction: the model will be considerably strengthened if a such a homolog is discovered. For the moment, it is easy enough to explain the lack of discovery of such a homolog on the basis of lack of data. Knowledge of microbial diversity is quite poor (Whitman et al., 1998): far less than 1% of bacteria extant in a particular environment are readily culturable (Hayward, 2000). Cultivation-independent surveys of prokaryote diversity based on environmental rRNA sequencing commonly discover deeply-branching microbes previously unknown to science (DeLong and Pace, 2001), and that certain groups are unexpectedly ubiquitous (Karner et al., 2001). In addition, only a fraction of cultured microbes have been studied in any substantial biochemical or genetic detail, and this subsample is heavily skewed towards pathogens and convenient model organisms. Of the ~112 complete bacterial genomes sequenced as of July 2003 (http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/eub_g.html), at least two-thirds are pathogens, mutualists, or commensals of multicellular eukaryotes. Many of the free-living bacteria that have been sequenced are extremophiles or are used in industrial applications
CharlieM wrote:It would take lots of mutations to achieve this unless we assume that it arrived fully formed and inserted itself in just the right place. Can random changes search through all the available combinations of forms and eventually hit a form that will do the job.
You are making the mistake of thinking that natural selection is working with some kind of goal in mind. Mutations happen. Most of them are neutral, some a beneficial, some are deleterious. Organisms that recieve deleterious mutations die out. Organisms that recieve beneficial mutations, whatever their nature, have increased chance of passing on to the next generation.
There is no end goal in mind. Whatever works, works and gets selected for. You are looking at the end product now, but it was never planned. Therefore, every single mutation is as impropable as the next... none of them are "special" and have to be "searched for".
To claim that the beneficial mutations are so impropable as to be virtually impossible implies you must know the total amount of beneficial, deleterious and neutral mutations. In addition to the total amount of relevant bacteria, and for how long they have existed. There is no reason to expect that the FlgE protein folds are the only possible protein folds capable of making a molecular universal joint.
Remember, natural selection was not selecting for mutations that would result in a modern bacterial flagellum. Natural selection simply selected anything that worked in a beneficial way. Intermediate steps were beneficial and that's why they stayed. Now it just so happens that the result we see today is a flagellum.
CharlieM wrote:You think yes, I think no, I would say its directed.
With no evidence whatsoever to back it up, making it completely unfalsifiable. You can of couse think anything you want, just don't expect it to be taught as science.
CharlieM wrote:I still don't think you are getting the universal joint thing.
I get it perfectly. All I have to do is look at this site to understand it's wonderful construction. http://molvis.sdsc.edu/flagellar_hook/index.htm
However, I don't think you get the difference between molecular sized object and macroscopic human-made tubes.
CharlieM wrote:Its no use just having a structure that is elastic in its longitudinal axis.
Molecules and their interactions are not really equal to macroscopic objects.
CharlieM wrote:Think of the hook like a muscle in your body, it can contract but it needs a nerve signal to do so. A protein in the hook won't just expand or contract on its own. It needs a signal or an outside force to do this and this signal or force needs to keep the expansions and contractions in time with the speed of the motor or the tail will be flailing all over the place. This is one more complexity of the system that I would very much like to see an explanation of. So if there are any experts out there with any ideas please share them.
Translation : It's so complex, I can't fathom how complex it is. See how complex it is? It's incredibly complex... how could that ever evolve? Surely it's so complex that it couldn't... therefore goddidit.
These are simply made-up hurdles of yours for us to ponder over and are entirely without substance.
CharlieM wrote:A protein in the hook won't just expand or contract on its own.
Well, no... but in the vicinity of other molecules it will.
CharlieM wrote:It needs a signal or an outside force to do this
Yes, those are the other molecules of the hook.
CharlieM wrote:and this signal or force needs to keep the expansions and contractions in time with the speed of the motor or the tail will be flailing all over the place.
Yeah it's called the electromagnetic force and it's propagating throuch a stack of molecules. The molecules have evolved in such a way as to respond to the one next to it. Nothing hugely complex about it I'm afraid. The molecules basically consist of two interacting ends with a joint between them. The interacting ends "stick" together, as is painfully obvious from that link I gave above, and they can bend across the joint. Viola!
This is also quite easy to infer from the structural comparisons between the hook protein FlgE and the Rod protein FlgG :
The differences mostly consist of changes to the two interacting "lumps" at either end of the protein, and the insertion of the "joint" in the middle. They even used the model of the FlgE hook protein as a basis for a model of the FlgG protein in this paper:
The mechanism of outer membrane penetration by the eubacterial flagellum and implications for spirochete evolution
http://genesdev.cshlp.org/content/21/18/2326.full.pdf+html
Modeling the FlgG structure based on homology with FlgE
Filamentous rod structures resulted from single amino acid substitutions in FlgG. This suggested a simple mechanism leading to the cessation of FlgG-rod growth and provided an important clue to the design of the flagellar structure. The FlgG amino acid sequence was shown to have a high degree of identity with the flagellar hook protein (FlgE), which is assembled just after FlgG-rod completion (Homma et al. 1990). Predicted secondary structure analysis shown in Figure 3A suggests that these proteins have a high degree of structural identity as well. This allowed the modeling of the filamentous rod mutations on a three-dimensional FlgG structure. There are two significant differences between the FlgG-rod and FlgE-hook sequences. First, the FlgG-rod has an insertion of 18 amino acids (residues 46–65 of FlgG) not present in FlgE, where the majority of the filamentous rod mutations occurred (amino acids 52–66). Second, FlgE-hook has two insertions of 16 amino acids and a stretch of 146 amino acids in the middle of the protein that is not present in FlgG (Fig. 3A). The structure of FlgE has been determined (Samatey et al. 2004). We modeled the FlgG-rod sequence onto the FlgE-hook structure that had previously been solved (Fig. 3B; Samatey et al. 2004). Unfortunately, the first 70 amino acids of FlgE-hook were not structured, which corresponds to the first 90 amino acids in FlgG, and where a number of filamentous rod mutations were located (amino acids 52–66 of FlgG). However, two filamentous rod mutant sites that include the G183R/G183W and S197L mutations, reside close to each other at the very bottom of the predicted FlgG structural model, and two other filamentous rod mutant sites that include the D117Y, G132R, and G133V mutations, are located close to each other in the middle of the structure (Fig. 3B). This allowed us to propose mechanisms for FlgG stop-polymerization. The 52- to 66-amino-acid region of one FlgG subunit could interact with the bottom region of a second FlgG subunit stacked on top of it at residues G183 and S197 to stop FlgG polymerization. The isolation of mutants at positions D117 and G132 would indicate an effect of these residues on this interaction.
Edit : Cleaned up the post a little.