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Author
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Topic: IC and protein complexes
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Kirk Durston
Member
Member # 174
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posted 08. March 2002 11:37
I’ve been thinking about protein complexes and IC. “Proteins rarely act alone; rather, they interact with other proteins to perform particular cellular tasks. These assemblies represent more than the sum of their parts by having a new ‘function’” (Gavin et al., (2002) ‘Functional organization of the yeast proteome by systematic analysis of protein complexes’, Nature, vol. 415, 141-147). An example of such an assembly is provided by the polyadenylation machinery, which appears to be essential for eukaryotic mRNA cleavage and polyadenylation. In this case we have a complex of 20 different proteins.
It occurred to me that if there is at least one protein complex in the simplest life form, M. genitalium, and that complex has an irreducible core of multiple proteins necessary for the function the complex performs, and said function is essential, then we have a beautiful example of IC that would be difficult for opponents to challenge. Reason: if the simplest life form requires an IC protein complex, then it is difficult to invoke some of the Darwinian objections to IC. If a particular IC protein complex is essential to M. genitalium, then by minimal genome thinking, it is likely that the simplest theoretical organism would have required it as well.
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Frances
Member
Member # 169
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posted 09. March 2002 13:44
quote:
Originally posted by Kirk Durston:
I’ve been thinking about protein complexes and IC. “Proteins rarely act alone; rather, they interact with other proteins to perform particular cellular tasks. These assemblies represent more than the sum of their parts by having a new ‘function’” (Gavin et al., (2002) ‘Functional organization of the yeast proteome by systematic analysis of protein complexes’, Nature, vol. 415, 141-147). An example of such an assembly is provided by the polyadenylation machinery, which appears to be essential for eukaryotic mRNA cleavage and polyadenylation. In this case we have a complex of 20 different proteins.
It occurred to me that if there is at least one protein complex in the simplest life form, M. genitalium, and that complex has an irreducible core of multiple proteins necessary for the function the complex performs, and said function is essential, then we have a beautiful example of IC that would be difficult for opponents to challenge. Reason: if the simplest life form requires an IC protein complex, then it is difficult to invoke some of the Darwinian objections to IC. If a particular IC protein complex is essential to M. genitalium, then by minimal genome thinking, it is likely that the simplest theoretical organism would have required it as well.
An interesting approach that relies on M. genitalium to be the simplest life form possible
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The recently sequenced genome of the parasitic bacterium Mycoplasma genitalium contains only 468 identified protein-coding genes that have been dubbed a minimal gene complement [Fraser, C.M., Gocayne, J.D., White, O., Adams, M.D., Clayton, R.A., et al. (1995) Science 270, 397-403]. Although the M. genitalium gene complement is indeed the smallest among known cellular life forms, there is no evidence that it is the minimal self-sufficient gene set.
Mike Gene has suggested on ARN
that
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I, of course, think the F-ATP synthase is IC and I expect as advances in cell biology techniques continue, this will be easy to show. But for now, we can look to evolution, which represents a history of cell biology in action. What does it tell us?
When we look to eubacterial genomes, all eight subunits (a,b,c, alpha, beta, gamma, delta epsilon) are found in E. coli, Aquifex aeolicus, Mycobacterium tuberculosis, Bacillus subtilis, H. pylori, Neisseria meningitidis, Thermotoga maritima, and Vibrio cholerae. This is a very wide spread of bacterial types. Furthermore, all 8 subunits are even found in the reduced genome of Mycoplasma genitalium. In other words, where ever we find the F-ATP synthases, we find at least these eight subunits
Furthermore, the F-ATPase appears to be as ancient as eubacteria themselves. And bacteria are very good at stream-lining (or removing unnecessary genetic information). So the question is simply this: why is the F-ATPase so strongly conserved among these distantly related bacteria? There is a very simple hypothesis that explains this and that is the F-ATP synthase is IC:
Is strong conservation evidence of IC and if so is this evidence of ID?
Pgegen formulates my thoughts when stating that
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The ATP synthase is certainly an amazing enzyme, and one we should all be more excited about. However, I really think that we aren't getting anywhere with repeated recitations that the ATP synthase is "irreducibly complex," with no justification nor with any evidence that its components did not arise by normal evolutionary means.
[ 09 March 2002, 14:18: Message edited by: Frances ]
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Kirk Durston
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Member # 174
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posted 12. March 2002 20:34
M. genitalium may or may not be the simplest lifeform to examine for protein complexes, but it can give us an educated idea as to which proteins may be essential for the simplest hypothetical organism.
If F-ATP synthase is an essential protein complex, then the next step is to examine the individual proteins that make up the sub-units and determine for each one the fraction of sequence space that is functional. That will give us the probability that each unit could be derived through random assembly, which would enable us to calculate the probability that the entire ATPase could be assembled. Note that I say 'random' assembly because, with the simplest (first) life form, there would be, of course, no preceding biological evolution to help produce the first IC, essential protein complex.
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Doubting Thomas
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Member # 1214
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posted 26. March 2004 17:09
Kirk Durston wrote:
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M. genitalium may or may not be the simplest lifeform to examine for protein complexes, but it can give us an educated idea as to which proteins may be essential for the simplest hypothetical organism.
M. genitalium may have the smallest genome but it has attributes that make it less than ideal for studying protein systems. For one, it lacks a cell wall. And for two, it is parasitic.
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If F-ATP synthase is an essential protein complex, then the next step is to examine the individual proteins that make up the sub-units and determine for each one the fraction of sequence space that is functional. That will give us the probability that each unit could be derived through random assembly, which would enable us to calculate the probability that the entire ATPase could be assembled. Note that I say 'random' assembly because, with the simplest (first) life form, there would be, of course, no preceding biological evolution to help produce the first IC, essential protein complex.
As I posted recently, the F-ATP synthase is likely a chimera of two very different proteins that evolved from ancient ancestors and are now associated as a complex that can be disassociated and reconstituted with ease, as no covalent bonds are involved. The genes for Fo and F1 have been found separated in some primitive single-celled organisms. When found connected together in the unc operon, Fo domains are made first, followed by F1 domains. F1 domains are water-soluble, requiring the Fo membrane-associated hydrophobic domains to be present to bind the complete F1Fo-ATP synthase/ase complex. The recent work on the related A1Ao-ATPase that I posted is further evidence of the chimeric nature of these enzymes. And the fact that the alpha and beta subunits in the F1 domain show significant sequence homology is evidence that they likely resulted from a gene duplication followed by divergence. Taken together, these observations would tend to make the 'ICness' of F1Fo-ATP synthase a questionable issue.
[ 26. March 2004, 17:54: Message edited by: Doubting Thomas ]
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