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Topic: Archaeal ATPase indicates these enzymes evolved as chimeras
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Doubting Thomas
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posted 25. March 2004 14:07
A very recent publication in the Journal of Biological Chemistry (see next post for bibliographic info. pdf file requires use of free Adobe Acrobat reader. The article itself can be downloaded for free from JBC's web site.) brings out some very interesting information about the archaeal A1Ao ATPase that is evidence that ATPases both evolved from simpler proteins and are chimeric in nature, i.e. consisting of a complex of two proteins with different functions and origins.
In the article entitled Three-dimensional organization of the archaeal A1 ATPase from Methanosarcina mazei Gdelta1 by workers at several universities in Germany and the United States and just published last month, the authors state as follows on page 4:
quote:
INTRODUCTION - Methanogenic, halophilic and thermophilic archaea synthesize adenosine 5'-triphosphate (ATP) by means of ion gradient-driven phosphorylation. Although it was speculated for some time, due to the lack of in-depth information, that the ATP synthases of archaea may be either F1Fo- or V1Vo-like enzymes, it is now clear that they evolved as a sewparate class of ATPases/ATPsynthases, the A1Ao ATPsynthases/ases (1-4). This class of enzyme is different from F1Fo- or V1Vo-ATPases by function, subunit composition, regulation and structure (1). The A1Ao ATPase has at least nine subunits (A3:B3:C:D:E:F:H:I:Ksubx), but the actual subunit stoichiometry, especially regarding the proteolipid subunits K in A-ATPases (subunits c in F1Fo-ATPases) is different in various organisms (12, 6, 4 or, as suggested by genomic data, only 1 (5). As suggested by its bipartite name, the A1Ao ATPase is composed of a water-soluble A1 ATPase and an integral membrane complex, Ao. ATP is synthesized or hydrolyzed on the A1 headpiece, consisting of an A3B3 domain, and the energy provided for or released during that process is transmitted to the membrane-bound Ao domain (1). The energy coupling between the two active domains occurs via the so-called stalk part, an assembly proposed to be composed by the subunits C, D and F (2). The archaeal A1Ao ATP synthase/ase is regarded as a chimeric (italics mine) protein in which the membrane domain is closely related to the F1Fo ATP synthases but the catalytic subunits closely to V1Vo ATPases (3-4).
As I posted in another thread, the various ATP synthases that we see today are not examples of primordial systems from the beginning of life but instead the result of their modification and adaptation through subsequent billions of years of evolution. The '1' domains started out as simple soluble ATPases, then became more efficient hexameric A3B3 ATPases via gene duplication and divergence, such as we see in the globins. The 'o' domains started out as ion channels. In the genetics of these organisms, the 'o' domains are made first, before the '1' domains. The '1' domains are made after the 'o' domains are completed, and 'pop' into them and stay put through hydrophobic bonding. If this were not the case, the water-soluble '1' domains would simply (and ineffectively) diffuse off into the cytoplasm. The 'o's and the '1's started out as separate entities with different functions but ultimately linked up to result in an efficient producer of ATP.
The rotary action of these enzymes is powered by and is the inevitable result of the proton flux through the enzyme. A simple analogy is the familiar rotary lawn sprinkler. High pressure water goes in and the thing spins. Not quite the same mechanism in the ATPases, but you get the general idea. The force of the proton flux (the 'proton motive force') causes the '1' domain to spin by converting an electrical potential into rotational movement.
The example discussed in this paper is clear evidence of a much more complex evolutionary history for these proteins than is usually assumed. The scenario outlined above is a reasonable explanation of how a supposedly IC protein could have evolved in a stepwise Darwinian manner.
[ 25. March 2004, 18:10: Message edited by: Doubting Thomas ]
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Doubting Thomas
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posted 25. March 2004 14:12
That web page URL doesn't work for some reason, so here is the bibliographic info for the paper I cited:
J Biol Chem. 2004 Feb 26 [Epub ahead of print]
Three-dimensional organization of the archaeal A1 ATPase from methanosarcina mazei Gdelta 1.
Coskun U, Radermacher M, Muller V, Ruiz T, Gruber G.
Fachrichtung 2.5 - Biophysik, Universitt des Saarlandes, Homburg D-66421.
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posted 25. March 2004 19:00
This post is being moved to "Literature Review"
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Jurie
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posted 29. March 2004 07:18
I always wonder how the fact that the same components are used elsewhere in cells can be clear evidence of evolution. At most it is not refuting evolution, but it can't be clear evidence for evolution if an alternative hypothesis (ID) requires the same type of evidence.
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The rotary action of these enzymes is powered by and is the inevitable result of the proton flux through the enzyme. A simple analogy is the familiar rotary lawn sprinkler. High pressure water goes in and the thing spins. Not quite the same mechanism in the ATPases, but you get the general idea
This model of how the torque is produced is very far off the mark. It is much more a case of the potential energy of a proton being converted to binding energy, and subsequent passing on until it exits with almost no potential energy left, the energy having been converted into torque as it is passed on. A very complex mechanism far removed from a simple rotary sprinkler. While rotation is inevitable, the mechanism for producing it is not. It is not just a cork-screw-shaped protein in a hole as you seem to suggest. Putative pre-existing proton pores could hardly have been more complex than this.
[ 29. March 2004, 07:30: Message edited by: Jurie ]
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Doubting Thomas
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posted 29. March 2004 10:12
Jurie wrote:
quote:
I always wonder how the fact that the same components are used elsewhere in cells can be clear evidence of evolution. At most it is not refuting evolution, but it can't be clear evidence for evolution if an alternative hypothesis (ID) requires the same type of evidence.
Please reread my earlier posts in Brainstorms regarding this. The ATP synthases are highly evolved chimeras, complexes made up of two very different sorts of proteins having very different functions and properties. Their genes are found apart in some simple organisms, but linked in the unc operon in more advanced cells. But that doesn't mean that they are used elsewhere in the cell today. They may have been in this distant past but today form ATP-producing complexes.
A number of different facts indicate that the ATP synthases evolved. The alpha and beta subunits in the '1' domains show significant sequence homology, an indication that they evolved by gene duplication and divergence into the present A3:B3 hexameric structures. And in the unc operon, the 'o' domains, which are hydrophobic and sit in the membrane, are made first. Only after they are in place are the water-soluble '1' domains made, which 'pop' into the hydrophobic channel of the 'o' domains. If it weren't this way, the '1' domains would just diffuse uselessly off into the cytoplasm. And the connection between the 'o' and '1' domains is only caused by hydrophobic bonding. It can be disrupted with detergent and the active enzymes restored later on simply by adding the two back together.
The authors of the paper I posted on the A1Ao-ATPases concluded that these enzymes were chimeras (structures made up of parts with different origins). If they came from different origins, they obviously evolved and were not 'designed.'
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The rotary action of these enzymes is powered by and is the inevitable result of the proton flux through the enzyme. A simple analogy is the familiar rotary lawn sprinkler. High pressure water goes in and the thing spins. Not quite the same mechanism in the ATPases, but you get the general idea
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quote:
This model of how the torque is produced is very far off the mark. It is much more a case of the potential energy of a proton being converted to binding energy, and subsequent passing on until it exits with almost no potential energy left, the energy having been converted into torque as it is passed on. A very complex mechanism far removed from a simple rotary sprinkler. While rotation is inevitable, the mechanism for producing it is not. It is not just a cork-screw-shaped protein in a hole as you seem to suggest. Putative pre-existing proton pores could hardly have been more complex than this.
I agree that I used an overly simplistic model, but not everyone on this board is a physical biochemist specializing in enzyme bioenergetics. Bottom line, proton flux energy is converted into rotation via a mechanism. I used a model that was simple enough that anyone could understand it. I thought I made that clear.
But please keep in mind that these ATP synthases we see today are highly evolved and are separated from the original state of life by billions of years of evolution. So any complexity we see today in their structure is only the result of evolution rather than design. I would not jump to use our lack of exact knowledge as to how the rotary motion is produced to invoke the design inference. It's unwarranted and is called the God of the Gaps argument. There are plenty of models and discussions of this on the web and in the literature. How rotary motion is obtained is not the key point here. The key point is that these enzymes evolved from different ancestral proteins to form complexes and therefore cannot be IC by definition.
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Doubting Thomas
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posted 29. March 2004 10:26
Jurie wrote:
quote:
This model of how the torque is produced is very far off the mark. It is much more a case of the potential energy of a proton being converted to binding energy, and subsequent passing on until it exits with almost no potential energy left, the energy having been converted into torque as it is passed on. A very complex mechanism far removed from a simple rotary sprinkler. While rotation is inevitable, the mechanism for producing it is not. It is not just a cork-screw-shaped protein in a hole as you seem to suggest. Putative pre-existing proton pores could hardly have been more complex than this.
Rather than risk the ire of the Moderator by 'literature bombing,' here is a highly edited paper on the subject from an authority on the subject of this mechanism with most of the unneeded verbiage edited out:
quote:
The Rotary Mechanism of ATP Synthase
John E Walker
Medical Research Council-Dunn Human Nutrition Unit
Hills Road, Cambridge
CB2 2XY, UK
In F1-ATPase, the central stalk, which is asymmetrical, rotates during ATP hydrolysis [7,8] with an anticipated frequency of 100-200 Hz. The rotation of the central stalk, which proceeds in 120° steps [9], changes the affinities of the catalytic sites taking each through cycles of “open”, “loose” and “tight” states. Therefore, in ATP synthase, the rotating central stalk is the key coupling element in the enzyme, involved in transferring energy from the F0 membrane domain, where rotation is generated from the transmembrane proton motive force, into the catalytic sites some 100 Å above the membrane surface. A peripheral stalk linking the surface of F1 to F0 probably acts as a stator to counter the tendency of the (ab)3 domain to follow the rotation of the central stalk [3,10].
A major unanswered question is: how is rotation of the central stalk generated by the passage of protons through the F0 membrane domain? Two F0 subunits known as subunits a and b are involved in proton translocation. An electron density map of a complex of F1 with associated c-subunits shows 10 c-subunits arranged in a ring, with the foot of the central stalk standing on the ring [11]. The large area of contact between the foot of the stalk and the ring suggests that the stalk-c ring subcomplex rotates as an ensemble. It is likely that the protons are translocated through the interface between the single a-subunit and the c-ring and that protonation and deprotonation of buried carboxyls in the c-subunits are involved in generation of rotation. The number of c-subunits in the ring has profound mechanistic implications. With 10 c-subunits in the ring, the number of protons translocated for each ATP synthesised is likely to be 10/3 = 3.3. There is evidence that chloroplast ATP synthase has 14 subunits in its ring [12] and so the corresponding H+/ATP value is 14/3. It is unlikely that the mechanism of rotation will be understood fully until accurate models of the entire ATP synthase in different conformational states have been established. Determination of these structures requires either the crystallization of the intact enzyme, or the establishment of an accurate low resolution model by electron microscopy of single complexes, which can then be used as a framework for building a molecular model from structures of subcomplexes and individual subunits.
I didn't include the URL for this but you can find it by doing a Google search on 'atp synthase rotary.' There probably is a great deal of research available on this mechanism but exploring it further doesn't interest me at the moment.
[ 29. March 2004, 10:28: Message edited by: Doubting Thomas ]
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