Why ATP? Abiotic chemistry provides an answer

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Why ATP? Abiotic chemistry provides an answer

#1  Postby Rumraket » Oct 12, 2021 5:55 pm

Nick Lane's research group as UCL has found an answer to one of the most fundamental mysteries about the chemistry of life: Why do cells use ATP rather than any one of the other, equally capable nucleotide triphosphates? It turns out the answer is found uniquely in abiotic chemistry.

The ion Fe3+ will catalyze the phosphorylation of only ADP to ATP with acetyl-phosphate(AcP) under mild and anoxic conditions in water, whereas the reaction does not occur for any of the other nucleotides, and no other common ion or metabolic cofactor seems able to catalyze the reaction.

https://www.biorxiv.org/content/10.1101/2021.10.06.463298v1.full
Silvana Pinna, Cäcilia Kunz, Stuart Harrison, Sean F. Jordan, John Ward, Finn Werner, and Nick Lane1*
A prebiotic basis for ATP as the universal energy currency

Abstract
ATP is universally conserved as the principal energy currency in cells, driving metabolism through phosphorylation and condensation reactions. Such deep conservation suggests that ATP arose at an early stage of biochemical evolution. Yet purine synthesis requires six phosphorylation steps linked to ATP hydrolysis. This autocatalytic requirement for ATP to synthesize ATP implies the need for an earlier prebiotic ATP-equivalent, which could drive protometabolism before purine synthesis. Why this early phosphorylating agent was replaced, and specifically with ATP rather than other nucleotide triphosphates, remains a mystery. Here we show that the deep conservation of ATP reflects its prebiotic chemistry in relation to another universally conserved intermediate, acetyl phosphate, which bridges between thioester and phosphate metabolism by linking acetyl CoA to the substrate-level phosphorylation of ADP. We confirm earlier results showing that acetyl phosphate can phosphorylate ADP to ATP at nearly 20 % yield in water in the presence of Fe3+ ions. We then show that Fe3+ and acetyl phosphate are surprisingly favoured: a panel of other prebiotically relevant ions and minerals did not catalyze ADP phosphorylation; nor did a number of other potentially prebiotic phosphorylating agents. Only carbamoyl phosphate showed some modest phosphorylating activity. Critically, we show that acetyl phosphate does not phosphorylate other nucleotide diphosphates or free pyrophosphate in water. The phosphorylation of ADP monomers seems to be favoured by the interaction between the N6 amino group on the adenine ring with Fe3+ coupled to acetyl phosphate. Our findings suggest that the reason ATP is universally conserved across life is that its formation is chemically favoured in aqueous solution under mild prebiotic conditions.


Thus prebiotic chemistry that would have almost certainly existed on the primordial Earth(high iron contents in water, no oxygen) answers this most fundamental question about the basic metabolic process of all known cellular life. This then, incidentally, also constitutes evidence that the metabolic processes of life on Earth began with prebiotic chemistry in an aqueous setting. And is thus evidence for a natural, physical and chemical origin of life, rather than any direct intelligent design, since in all extant life the phosphorylation of nucleotides is catalyzed by enzymes rather than abiotic chemistry.

Introduction
ATP is casually referred to as the ‘universal energy currency’ of life. Why it gained this ascendency in metabolism, in place of many possible equivalents, is an abiding mystery in biology. There is nothing particularly special about the ‘high-energy’ phosphoanhydride bonds in ATP. Rather, its ability to drive phosphorylation or condensation reactions reflects the extraordinary disequilibrium between ATP and ADP – about 10 orders of magnitude in modern cells, pushed by free energy derived from respiration [1]. ATP drives intermediary metabolism through the coupling of exergonic to endergonic reactions via phosphorylation and hydrolysis, but other phosphorylating agents (including GTP and CTP) could be pushed equally far from equilibrium, and accomplish equivalent coupling. In fact, the centrality of ATP goes far beyond phosphorylation, as emphasised by the ubiquity of ATP derivatives in intermediary metabolism, including the ancient cofactors NADH, FADH and Coenzyme A (which all derive from ATP rather than AMP or adenine). ATP-coupled monomer activation also promotes the polymerisation of macromolecules, including RNA, DNA and proteins. Protein synthesis requires the activation of amino acids by adenylation (using ATP) before binding to tRNA, while the nucleotide triphosphates used for RNA and DNA synthesis are phosphorylated by ATP. So what, if anything, is special about ATP?



Notice how only ATP formation from ADP and AcP is catalyzed above the uncatalyzed rate by Fe3+:

F4.large.jpg
F4.large.jpg (85.41 KiB) Viewed 139 times

Figure 4
Phosphorylation of nucleotide diphosphates by AcP.
HPLC chromatogram of the resulting NTP of the phosphorylation of (a) adenosine diphosphate (ADP), (b) inosine diphosphate (IDP), (c) guanosine diphosphate (GDP), (d) cytidine diphosphate (CDP) and (e) uridine diphosphate (UDP) by AcP catalysed by Fe3+ at 30°C and pH ∼5.5–6 at the beginning of the reaction (0 h, broken line, blue) and after 3 hours (solid line, red). The molecular structure of each base forming the nucleotides is shown. (f) 31P–NMR spectrum of PPi (bottom, blue), PPPi (middle, red) and the reaction PPi (1 mM) + AcP (4 mM) + Fe3+ (500 μM) at 30°C and pH ∼5.5–6 after 3h (top, green).


The discovery that AcP can phosphorylate ADP to ATP in the presence of Fe3+ was serendipitous: while studying the electrolysis of ADP in the presence of AcP, Kitani et al . noted a ∼20 % conversion of ADP to ATP as the iron electrode they were using in their setup corroded [32]. But the fact that substrate-level phosphorylation of ADP to ATP can be accomplished by AcP in water says nothing about whether this mechanism actually holds prebiotic relevance. We have therefore explored the phosphorylation of ADP more systematically using a range of prebiotically plausible and biologically relevant phosphorylating agents, and a panel of metal ions as possible catalysts. We find that the combination of Fe3+ and AcP is unique: no other metal ions or phosphorylating agents are as effective at phosphorylating ADP. Equally striking, we find that ADP is also unique: the combination of AcP and Fe3+ will phosphorylate ADP but not GDP, CDP, UDP or IDP, nor free pyrophosphate. We use these data and the reaction kinetics to propose a possible mechanism. Our results suggest that ATP became established as the universal energy currency in a prebiotic, monomeric world, on the basis of its unusual chemistry in water.


Discussion
Our results support the following conclusions: (i) acetyl phosphate (AcP) efficiently phosphorylates ADP to ATP, but only in the presence of Fe3+ ions as catalyst (Fig. 1); (ii) the reaction takes place in water and can occur in a wide range of aqueous environments (Fig. 2); (iii) no other phosphorylating agent tested was as effective as AcP (Fig. 3); and (iv) adenine is unique among canonical nucleobases in facilitating the phosphorylation of its nucleotide diphosphate to the triphosphate (Fig. 4). Taken together, these findings suggest that the pre-eminence of ATP in biology has its roots in aqueous prebiotic chemistry. The substrate-level phosphorylation of ADP to ATP by AcP is uniquely facilitated in water under prebiotic conditions and remains the fulcrum between thioester and phosphate metabolism in bacteria and archaea today [2]. This implies that ATP became the universal energy currency of life not as the endpoint of genetic selection or some frozen accident, but for fundamental chemical reasons, and probably in a monomer world before the polymerization of RNA, DNA and proteins.

The work presented here provides a compelling basis for each of these statements, but also raises a number of questions. Why ferric iron? Unlike AcP or ATP itself there is no clear link with biology in this case; we had expected other ions more commonly associated with nucleotides, notably Mg2+ or Ca2+ [39,40], to play a more clear-cut role. In fact, their catalytic effect was only noticeable in the presence of Fe3+, as has been reported before, whereas higher concentrations, equivalent to modern ocean conditions, precluded ATP synthesis. We infer that the reason Fe3+ plays a unique role relates in part to its high charge density and small ionic radius. The fact that only ADP could be phosphorylated among canonical nucleobases suggests that Fe3+ interacts directly with the N6 amino group on the adenine ring as well as the N7 previously noted by others [60–63]. But the interactions between Fe3+ and the N7 moiety alone cannot explain our results, as no triphosphate was formed in the absence of the N6-amino group, for example in the case of GDP. The fact that ADP is phosphorylated more readily than AMP (SI Fig. 5) indicates that Fe3+ also interacts with the diphosphate tail of ADP. And the fact that the optimal stoichiometry of Fe3+ to ADP is 1:1, coupled with the absence of evidence for stacking of bases by MALDI-ToF (Fig. 5), indicates that a single Fe3+ ion interacts with a single ADP, and necessarily also with a single AcP.
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Re: Why ATP? Abiotic chemistry provides an answer

#2  Postby Macdoc » Oct 13, 2021 5:27 am

Thus prebiotic chemistry that would have almost certainly existed on the primordial Earth(high iron contents in water, no oxygen) answers this most fundamental question about the basic metabolic process of all known cellular life. This then, incidentally, also constitutes evidence that the metabolic processes of life on Earth began with prebiotic chemistry in an aqueous setting. And is thus evidence for a natural, physical and chemical origin of life, rather than any direct intelligent design, since in all extant life the phosphorylation of nucleotides is catalyzed by enzymes rather than abiotic chemistry.


Damn what a wonderful discovery ...I suppose one could argue still for panspermia just taking origin back an iteration but Occam would say ...yeah primordial soup what brewed it. :thumbup:
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Re: Why ATP? Abiotic chemistry provides an answer

#3  Postby hackenslash » Oct 13, 2021 9:59 pm

Super cool.
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