Hello, everyone!
So, I came across this post on X/Twitter. Interesting study. Surely creationist will say one thing or two about it. What are your thoughts on it?
[Mod edit to add a link that appeared in the original Tweet, but not here …]
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Hello @Joao_Rastodon, and welcome to Peaceful Science! 
I understood the part about Principle Components Analysis, but that’s about it. One of our Biochemists should be able to offer a more useful opinion.
I see the authors mostly publish on Materials Science? 1 2
That doesn’t automatically make them wrong, but it is going to raise a few eyebrows.
@Joao_Rastodon: Is this you?
https://www.researchgate.net/profile/Joao-Lucas-Da-Silva-2
Yep, that’s me!
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IT’S EFFICIENT THEREFORE IT CAN’T EVOLVE
God can they get some new material. Literally the same argument for decades.
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Are these authors disguised creationists? Their conclusion seems a bit rigid, but I can’t assess this topic. Is someone capable of doing so?
Richard Buggs gives no reasons or arguments why it can’t plausibly evolve by any suggested pathway, he just asserts it.
We have no good reason to accept his baseless opinion.
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There are organisms living without ATP synthase.
/thread
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So that’s a “not really ‘disguised’”
My thoughts
I don’t think the three hypotheses that the paper discusses are mutually exclusive (although the paper does not explicitly state otherwise). ATP synthase is inherently a bi-functional enzyme. Even if the enzyme mostly functions to one direction, either ATP synthesis (as in F-ATPases) or ATP hydrolysis (as in V-ATPases), they can do both depending on the conditions. Most straightforwardly, if the free energy present in the proton motive force is less than the free energy present in the ATP/ADP ratio, F-ATPases reverses. This is not ideal of course, but it’s still an important physiology process that maintains internal balance. So it’s not either “synthesis first” or “hydrolysis first”. Two directions of a chemical reaction are often two side of the same coin.
Secondly, regarding the “Co-option of earlier forerunners of FO and F1”, I think this is the most well-understood part of the evolution of ATP synthases: the FO and F1 sub-complexes have independent evolutionary histories before their integration into the ATP synthase complex.
- The FO sub-complex is a hydrophobic (water-insoluble) membrane-bound proton channel, which couples the transport of protons with mechanical rotation via Brownian and electrostatic (protonation / deprotonation) ratcheting. Viewed from above or below, the rotary component is composed of identical polypeptides (called c) arranged in a ring. The number of units in this c-ring varies from 8 to 17 depending on the organism.
- In contrast, the F1 sub-complex is hydrophilic (water-soluble) and protrudes into the cytoplasm (or matrix/stroma in the case of mitochondria/chloroplasts). It’s motion is not rotatory. It undergoes a mechanical cycle, consisting of six conformation states, which are 3-fold radially symmetric. The transitions from one state to the next is driven by ATP binding and hydrolysis, or it is driven by the ‘Axle’ (the central stalk subunit ‘gamma’ specifically) to drive the cycle in reverse which generates ATP. Corresponding to the 6 conformation stages, the F1 sub-complex is a hexamer consisting of 3 alpha and 3 beta subunits. Only the beta subunits are catalytic, so a full cycle will only hydrolyse/synthesize 3 ATP.
The assembly of FO and F1 is also modular. FO is assembled in the membrane separately from the soluble F1. It’s only after these are preformed that is when they will functionally integrate. They are functionally modular as well. Even when these sub-units are separated, FO is able to translocate protons across the membrane, and F1 is able to hydrolyse ATP. Then, by coupling the mechanical rotation of FO with the conformational cycle of F1… aaand… PRESTO!! Now you have coupled proton transport with ATP synthesis/hydrolysis. In other words, Chemiosmotic coupling. And this wasn’t without some issues. Remember that F1 is a hexamer with 6 different conformational states? The c-ring of FO has 8 to 17 units. That means you are dealing with a symmetric mismatch with FO-F1 coupling, which results in structural strains. These is resolved by some awkward contortions, distortions, and twists in several components. ATP synthase is a very wibbly wobbly, herky jerky protein… even by protein standards.
It’s also curious to note that, while F1 and FO are homologous across all life, but the protein subunits responsible for their integration (the axile / central stalk) is not. Archaea have the A-Type ATP synthase, which is homologous to the eukaryotic V-Type found in vacuoles. Bacteria have the F-type ATP synthse, the same type found in mitochondria and chloroplast. Mmmh… what an peculiar coincidence… Well in any case, this make me think whether this Chemiosmotic was established in the last universal common ancestor (LUCA) or whether LUCA possessed the F1 and FO precursors, but bacteria and Archaea managed to couple them independently. Alternatively, bacteria and/or archaea may have replaced the axle for some reason but I am not seeing exactly why this would be the case.
Another thing I am not sure about is what exactly the F1 and FO precursors were doing prior to ATP synthase. The straightforward functions is some type of ATP hydrolysis for F1 and some type of ion channel for FO, but for exactly what is less obvious. Long ago, I have seen this paper by Eugene Koonin and his colleagues proposing that the FO was initially a RNA translocase, and F1 was a RNA or DNA helicase (which also has a similar hexameric structure). The authors of the paper linked in the Top comment find it unlikely based on “phylogenetic considerations” such as the fact that hexameric helicases in bacteria and archaea are based on different protein folds. I am not sure if this argument holds up. Why can’t F1 be homologous to only one type of helicase? But there was one argument that raised my eyebrow:
A related difficulty for the co-option of a functioning ATPase and an ion channel involves the nontrivial coupling of the two complexes. An uncoupled FO motor would dissipate any proton gradient across the membrane, and an uncoupled F1-like motor would likewise dissipate ATP, causing such a protocell to drift rapidly toward equilibrium
I don’t buy this argument. What if the proton gradient is consistently renewed by the environment itself, such as in an alkaline hydrothermal vent? In this case, something like an uncoupled FO motor would be very convenient since dissipating any excesses is beneficial. This actually happens a lot even in modern cells, which use ‘uncoupling agents’ to dissipate the proton motive force (PMF) as heat. If the PMF gets too high, then that will inhibit the electron transport chain, which will produce reactive oxygen species. Likewise, an uncoupled F1 motor dissipating excess ATP can also be good. There are lot’s of so-called ‘futile cycles’ to do exactly this. One might even point out that all of life is rapidly drifting towards equilibrium, but the planet is constantly kept in a state of disequilibrium.
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It does not. It’s a misleading appeal to some differences in the exact structures among two major clades in the P-loop NTPases (some sub-domains don’t have the exact same orientation relative to the rest of the structure, some have small insertions, stuff like that) (probably they’ll be waffling about the meaning of the term ‘fold’), and in fact the individual subunits, and the overall structure of the catalytic hexamer are known to be homologous among all known ATPases, and hexameric RNA and DNA helicases.
Really, just find some sequences from different helicases and the catalytic hexamers of F, V, and A-type ATP synthases and do a simple protein sequence alignment, it’s immediately obvious they are all related but have simply diverged and further specialized towards their individual roles and functions. They all derive from a common ancestral protein that likely emerged first as an RNA helicase.
A great paper on these related proteins is:
And this thought-provoking set of experiements by the Tawfik lab on the plausible emergence of the entire superfamily:
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Buggs is.
Buggs isn’t an author here, he just tweeted it.
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