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Author
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Topic: Are type III virulence systems really derived?
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yersinia
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Member # 324
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posted 24. August 2003 14:35
Nelson wrote in the eukaryotic flagellum thread:
quote:
If [axostyles] are truly derived then I would say it is something similar to the bacterial flagella ---> Type III secretory system (the latter evolved from the former and not the other way around).
Similarly, Dembski supported this position some time ago.
But actually, this is a matter of some debate.
quote:
Gophna U, Ron EZ, Graur D. Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events. Gene. 2003 Jul 17;312:151-63.
Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Ramat Aviv, Israel
Type III secretion systems (TTSS) are unique bacterial mechanisms that mediate elaborate interactions with their hosts. The fact that several of the TTSS proteins are closely related to flagellar export proteins has led to the suggestion that TTSS had evolved from flagella. Here we reconstruct the evolutionary history of four conserved type III secretion proteins and their phylogenetic relationships with flagellar paralogs. Our analysis indicates that the TTSS and the flagellar export mechanism share a common ancestor, but have evolved independently from one another. The suggestion that TTSS genes have evolved from genes encoding flagellar proteins is effectively refuted. A comparison of the species tree, as deduced from 16S rDNA sequences, to the protein phylogenetic trees has led to the identification of several major lateral transfer events involving clusters of TTSS genes. It is hypothesized that horizontal gene transfer has occurred much earlier and more frequently than previously inferred for TTSS genes and is, consequently, a major force shaping the evolution of species that harbor type III secretion systems.
I'm not going to say that the flagellum-->type III virulence notion is dead, various lines of evidence still seem to support it (such as the current restriction to eukaryote virulence and the presence of homologs of proteins like FliG that only have a (obvious) function in the flagellum). But it appears that sequence phylogeny is not one of them.
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Nel
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posted 24. August 2003 16:25
The data that contradicts the t3ss ---> bacterial flagella is not just the phylogenetic evidence:
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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.
source
[ 24. August 2003, 16:25: Message edited by: Nelson-Alonso ]
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Nel
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posted 24. August 2003 16:26
That paper seems to say that the flagella and t3ss evolved independantly. They even invoke HGT. This is another nail in the coffin of Miller's scenario, if the paper is correct.
quote:
Our analysis indicates that the TTSS and the flagellar export mechanism share a common ancestor, but have evolved independently from one another. The suggestion that TTSS genes have evolved from genes encoding flagellar proteins is effectively refuted. A comparison of the species tree, as deduced from 16S rDNA sequences, to the protein phylogenetic trees has led to the identification of several major lateral transfer events involving clusters of TTSS genes. It is hypothesized that horizontal gene transfer has occurred much earlier and more frequently than previously inferred for TTSS genes and is, consequently, a major force shaping the evolution of species that harbor type III secretion systems.
[ 24. August 2003, 17:26: Message edited by: Nelson-Alonso ]
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yersinia
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posted 24. August 2003 20:22
Nelson quotes,
quote:
Our analysis indicates that the TTSS and the flagellar export mechanism share a common ancestor, but have evolved independently from one another.
But one could just as well quote it like this:
quote:
Our analysis indicates that the TTSS and the flagellar export mechanism share a common ancestor, but have evolved independently from one another. The suggestion that TTSS genes have evolved from genes encoding flagellar proteins is effectively refuted.
They specifically go after Nguyen et al.'s conclusions in the article. Nguyen et al. is Mike's reference 5 in that long quote from Mike you provide. Nguyen et al. is also Dembski's main authority.
Look, I'm not saying that Gophna et al. are necessarily right. Too early to tell IMO.
My point is that statements like this from Mike, which you quoted:
quote:
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.
Ain't so anymore. Opinion is not converging, rather the two major studies on the topic are split.
yersinia
[ 24. August 2003, 20:23: Message edited by: yersinia ]
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Nel
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posted 24. August 2003 20:26
I think the main point, Nic, is that Miller's scenario, even if those guys are correct, and Nguyen is wrong, is completely out of the arena. Not even the t3ss evolved step by Darwinian step, but through HGT.
Also, the common ancestor may be more complex than both. In other words, both scenarios that are currently in the literature are "ID friendly".
[ 24. August 2003, 20:55: Message edited by: Nelson-Alonso ]
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Mike Gene
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posted 24. August 2003 20:57
Yersinia: They specifically go after Nguyen et al.'s conclusions in the article.
Yeah, but their arguments are weak. Also, their main motivation for skepticism was outlined in their introduction and seems rather strange to me:
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Second, the suggestion that a simpler system (TTSS) is derived from a more complex system (flagella) is quite odd in an evolutionary context since it runs against the progressionist grain that pervades evolutionary thought since the days of Jean-Baptiste Lamarck. As was pointed out by Aizawa (2001): “The flagellum is a beautifully designed architecture almost completed in evolution. Why should those sophisticated skills be abandoned to go back to boring soluble proteins?”
Our evolutionary context was set by Lamarck? And Aizawa’s argument is actually quite weak. Have these guys heard of microsporidia and myxozoa? Anyway, to their results……
The abstract of the paper asserts: The suggestion that TTSS genes have evolved from genes encoding flagellar proteins is effectively refuted.
That’s a rather strong claim. Yet their whole argument effectively boils down to this: Branch lengths indicate that the levels of diversity are similar in the TTSS and flagella subtrees implying a similar degree of antiquity for both groups.
In other words, let’s imagine the TTSS evolved from the flagellar export system in chlamydiae (as JF Kim argues). Gophna et al. are (for example) then assuming that the TTSS machinery should thus nest with the chlamydiae flagellar export system. That doesn’t seem like a very good assumption to me.
Like I said elsewhere, time is very limited right now.
More later…..
[ 24. August 2003, 21:04: Message edited by: Mike Gene ]
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yersinia
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posted 24. August 2003 20:59
The next time you can identify ID causing HGT in the wild, Nelson, please be so good as to point it out to us...its a perfectly natural mechanism.
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Nel
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posted 24. August 2003 21:04
Nic,
Thats like saying if I claim assembly of eukaryotic flagella is designed, that I have to see the designer doing it manually everytime it happens out in the wild.
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yersinia
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posted 24. August 2003 21:35
OK, so I guess when the PCP degradation genes were laterally transferred at PCP-polluted sites, that was an ID intervention that occurred? To help us deal with humanity's pollution problems, I guess?
C'mon, Nelson, if evolution can explain something using natural mechanisms that are observed to operate today, then ID is unnecessary. You can't just take one of those currently-operating mechanisms and assert that IDdidit if evidence shows that that mechanism was operating in the past.
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yersinia
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posted 24. August 2003 21:44
Mike, I have some of the same concerns as you. Citing Lamarkian progressivism and not discussing the common cases of reduction in parasites are both worrisome.
However, probably the most important point in favor of the flagella-->TTSS hypothesis was that TTSS sequences nested within flagellar sequences (That was my impression at least, Gophna et al. say that Nguyen et al's data never supported that idea). But that has been called into question.
Again, my point: still controversial, still too early to tell.
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Nel
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posted 24. August 2003 21:51
Nic writes:
quote:
OK, so I guess when the PCP degradation genes were laterally transferred at PCP-polluted sites, that was an ID intervention that occurred? To help us deal with humanity's pollution problems, I guess?
Why did it have to be a manual ID intervention? I think HGT was designed at the origin of life and that such things were useful for the transfer of packages of genes.
Nic writes:
quote:
C'mon, Nelson, if evolution can explain something using natural mechanisms that are observed to operate today, then ID is unnecessary.
That makes no sense. Assembly of eukaryotic flagella is "natural" in the same sense and yet I think it's origin lies in intelligent agency. Same with HGT.
Nic writes:
quote:
You can't just take one of those currently-operating mechanisms and assert that IDdidit if evidence shows that that mechanism was operating in the past.
All mechanisms we talk about operate in the past and is currently operating. Want to see some cells divide? One can either say chancedidit or iddidit. I say the latter.
[ 24. August 2003, 21:53: Message edited by: Nelson-Alonso ]
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yersinia
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posted 24. August 2003 22:04
Nelson, I don't even care if HGT mechanisms (diverse as they are, including everything from conjugation apparati to viruses to near-random DNA uptake) were IDed. Start another thread if you want to argue that.
What you can't do is say that if HGT was involved in the evolution of X, therefore X was IDed. That's like saying (using your analogy) that if eukaryotic flagella were involved in the evolution of X (say, the evolution of the ear), then X was IDed. Or, to use your other analogy, if cell division was involved in the origin of X, then X was IDed. It's either outright illegitimate and you just don't realize it, or you just like to raise HGT as a smokescreen to distract a discussion if it's going a direction you don't like.
Unless you're going to tell us that invoking cell division in an evolutionary scenario makes it "ID-friendly" also...
[ 24. August 2003, 22:07: Message edited by: yersinia ]
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Nel
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posted 24. August 2003 22:08
Nic writes:
quote:
Nelson, I don't even care if HGT mechanisms (diverse as they are, including everything from conjugation apparati to viruses to near-random DNA uptake) were IDed. Start another thread if you want to argue that.
Umm, you brought it up.
Nic writes:
quote:
What you can't do is say that if HGT was involved in the evolution of X, therefore X was IDed.
Sure I can. If I transfer an entire gene package into a bacterium, I have designed something new in that organism. HGT is basically genetic engineering.
[ 24. August 2003, 22:12: Message edited by: Nelson-Alonso ]
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yersinia
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posted 24. August 2003 22:42
OK, so then you *do* think that PCP degradation ability in bacteria, which originated in the last few decades, was Intelligently Designed.
Fine with me, Nelson, I just want you to be consistent.
(And by the way, are you now saying that diseases using type III secretion were IDed? That is the implication of your statements. Perhaps the Bubonic Plague really was due to the wrath of God?)
[ 24. August 2003, 22:43: Message edited by: yersinia ]
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Pim van Meurs
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posted 25. August 2003 00:50
nelson: If I transfer an entire gene package into a bacterium, I have designed something new in that organism. HGT is basically genetic engineering.
Seems to me that Nelson is arguing that natural processes can be 'designers' after all. HGT, the natural intelligent designer :-)
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