Selective Phosphonylation of 5′-Adenosine Monophosphate (5′-AMP) via Pyrophosphite [PPi(III)]
We describe here experiments which demonstrate the selective phospho-transfer from a plausibly prebiotic condensed phosphorus (P) salt, pyrophosphite [H2P2O52−; PPi(III)], to the phosphate group of 5′-adenosine mono phosphate (5′-AMP). We show further that this P-transfer process is accelerated both by divalent metal ions (M2+) and by organic co-factors such as acetate (AcO−). In this specific case of P-transfer from PPi(III) to 5′-AMP, we show a synergistic enhancement of transfer in the combined presence of M2+ & AcO−. Isotopic labelling studies demonstrate that hydrolysis of the phosphonylated 5′-AMP, [P(III)P(V)-5′-AMP], proceeds via nuceophilic attack of water at the Pi(III) terminus.
KeywordsPhosphorus Prebiotic Chemistry Origin of Life Nucleotides
We reported recently on a geologically plausible prebiotic ancestor to PPi(V), the closely related condensed P-material, pyrophosphite, PPi(III) [H2P2O52−; Fig. 1; Bryant et al. 2013a, b] and have selected to examine the phosphorus(P)-transfer behaviour of this compound in selected chemical processes of potential value in prebiotic contexts. We envisage PPi(III) to possess a strong prebiotic provenance as this condensed P-compound is found to be readily prepared from H-phosphonate [also called phosphite, Pi(III)] by dehydration under relatively mild conditions (Bryant et al. 2013a, b). We have also recently demonstrated that both Pi(III) and PPi(III) can be readily produced within hot, acidic hydrothermal environments, both lab simulations and in the field at the Hveradalur geothermal site; Kverkfjöll volcanic system, Iceland (Cousins et al. 2013). Amongst such processes are the ability to promote P-transfer leading to both condensed phosphates and organophosphorus species. In our previous paper (Bryant et al. 2013a, b) we described how PPi(III) was capable of phosphonylating phosphate [Pi(V)] in aqueous solution under ambient temperature conditions to afford the mixed-valance condensed P-compound, isohypophosphate, PPi(III-V). We described further how divalent metal ions such as Ca2+ and Mg2+ had acceleratory effects upon this P-transfer process. Here we expand upon the potential of PPi(III) to function as a P-transfer reagent and report on the selective phosphonylation of 5′-AMP at the 5′-phosphate terminus, mediated by PPi(III). In addition, we ouline how divalent metal ions influence this process, in a similar manner to that observed with PPi(III-V) formation (Bryant et al. 2013a, b) but how also there appear to be synergistic effects in that P-transfer is accelerated when these divalent metal ions are accompanied by carboxylate-containing organic molecules.
Materials and Methods
Water was purified by ion exchange on a Purite Select Analyst (PSA) reverse osmosis-deionisation system (Purite Ltd., Oxford UK). D2O (99.9 % atom D) for NMR analyses and H-phosphonic acid were used as received from Sigma-Aldrich. Isotopically-enriched H218O (98.5 %:1.0 %:0.5 % 18O:17O:16O) was purchased from Cambridge Isotope Laboratories). Solution pH measurements were made on a Schochem pH meter calibrated to pH 4 and 7 with commercial (Fisher Chemicals) standards. 31P-NMR analyses were performed on a Bruker Avance 500 MHz instrument operating at 202.634 MHz for 31P internally referenced to 85 % H3PO4. Molecular modelling was performed using PC Spartan Pro v1.03. Approximate transition structures were produced using the TS approximation feature within the software. These structures were then optimized using PM3 semi-empirical calculations and a gradient following approach. The resulting transition structures were analyzed using vibrational mode analysis and were characterized as each having a single negative vibrational frequency (shown within Fig. 4).
Production of Pyrophosphite, Na2-PPi(III)
H-Phosphonic acid (16.4 g, 0.2 mols) was dissolved in H2O (30 ml). NaOH(s) (8.1 g, 0.2 mols) was added slowly with stirring until all solid had dissolved. The solution was evaporated to dryness under reduced pressure and the residue heated (160 °C) under a dynamic flow of dinitrogen gas for 3 days. A sample was subsequently dissolved in D2O for 31P-NMR and 1H-NMR spectroscopic analysis which revealed a mixture of only starting material and product, PPi(III), pyrophosphite, both as dissociated sodium salts, usually in a 5:95 % ratio respectively. 1H-NMR (D2O, 27 °C, 300.13 MHz): δ 6.97 (AA’XX’ spin system, 1JPH = 666 Hz, 2JPH = 9 Hz, 3JHH = 8 Hz). 31P-NMR (D2O, 27 °C, 121.49 MHz): δ -4.98 (AA’XX’ spin system, 1JPH = 666 Hz, 2JPH = 9 Hz, 3JHH = 8 Hz).
Phosphonylation of 5′-AMP Mediated by Na2-PPi(III)
5′-Adenosine monophosphate (5′-AMP) was phosphonylated in the presence of Na2-PPi(III) using a procedure modified from that reported (Yamamoto et al. 1988) to afford a range of products which could be identified and quantified by 31P-NMR spectroscopy (See SI). Thus, a mixture of Na2-PPi(III) (0.29 g, 1.5 mmol) and 5′-AMP (0.037 g, 0.1 mmol) was dissolved in deionized water, the pH of solutions was adjusted to 7 using aqueous NaOH solution (1 M) and the solution made up to 1 mL total volume to arrive at solutions with PPi(III) and 5‘-AMP at 1.5 M and 0.1 M respectively. Solutions were then treated with appropriate additives to achieve the final concentrations as indicated (glycine, G1, 0.1 M; diglycine G2, 1.0 M; MgCl2, 0.1 M; MgCl2-G1, 0.1-1.0 M; MgCl2-G2, 0.1-1.0 M) and left to incubate at ambient temperature (ca. 20°C) and aliquots removed (0.6 mL) at various time intervals, added to D2O for NMR locking purposes (ca. 0.1 mL) and reaction progress monitored by 31P-NMR spectroscopy at 202.634 MHz operating frequency. 31P-NMR (H2O; 25°C; pH 7): PPi(III-V)-5‘-AMP: δ -5.5 (dd, 2JPP = 20 Hz, 1JPH = 666 Hz, Pi(III)]; δ -10.5 [dm, 2JPP = 20 Hz, P(V)]. 3‘/2‘-P(III)-5’AMP: δ = 6.1 [dd, 1JPH = 652 Hz, 3JPH = 10 Hz, Pi(III)]; δ 2.3 [s, br, Pi(V)]. 2′/3′-P(III)-5’AMP: δ = 4.9 [ddd, 1JPH = 652 Hz, 3JPH = 10 Hz, 3JPH = 7 Hz, Pi(III)], δ 2.3 [s, br, Pi(V)]. Full measured compositional data for PPi(III), Pi(III), 5′-AMP, PPi(III-V)-5′-AMP, 2′-P(III)-5′-AMP and 3′-P(III)-5′-AMP are collected in accompanying spread-sheet file and were assigned by 31P-NMR spectroscopy and by comparison to previously reported data (Yamamoto et al. 1988): 5’AMP KK45–52 Collated Results.xlsx.
Hydrolysis of PPi(III-V)-5′-AMP Using isoptopically Enriched H218O
An aqueous (1 mL) solution containing sodium pyrophosphite, Na2-PPi(III), (0.29 g, 1.5 mmol), 5‘-AMP (0.037 g, 0.1 mmol) and MgCl2 (0.02 g, 0.1 mmol), was adjusted to pH 7 by slow addition of solid NaOH. This solution was allowed to stand for 24 hrs at ambient temperature before analysis by 31P-NMR spectroscopy which reveals the following speciation by integration of peaks: unreacted 5’AMP: 21.5 %; 3′/2′-P(III)-5’AMP: 11.0 % & P(III)P(V)-5‘-AMP: 67.4% (The percentages here refer to only the products of 5’-AMP reaction referenced to total 5’-AMP present. The sum of these products is 5 % of total solution P with 13 % as Pi(III) and unreacted PPi(III) 82 %). This solution was transferred to a micro-distillation apparatus connected to a Schlenk line and the D2O removed under reduced pressure. Subsequently, the apparatus was filled with dry dinitrogen gas and H218O (1.0 g) added to the residues by syringe. After standing at room temperature for 6 days hydrolysis was found to be complete with the bulk PPi(III) hydrolyzing to Pi(III) and the P(III)P(V)-5′-AMP hydrolyzing back to 5′-AMP. The 3′/2′-P(III)-5’AMP products are relatively more resistant to hydrolysis. Additionally some hydrolysis of the phosphate ester linkage within 5′-AMP generated some Pi(V) which has reacted with PPi(III) to afford PPi(III-V). Excess H218O was removed under reduced pressure and replaced with D2O (1 mL) and the pH adjusted to 12 via slow addition of solid NaOH. Analysis of the Pi(III) resonances by 31P-NMR shows that 18O has been incorporated and with a Δδ value of 20 ppb which is consistent with isotopic incorporation.
Results and Discussion
The second model proposes that G1 and G2 react with PPi(III) to afford acylphosphonates, the key intermediate in PPi(III)-mediated G1 coupling. As both 5′-AMP (Bock et al. 1991) and acylphosphonates (Kluger et al. 1975) are known to bind, albeit relatively weakly, to Mg2+, binding of both at the same metal centre could facilitate effective phosphonylation of 5′-AMP. An example of this is the simple Spartan PM3 model in which a acetylphosphonate phosphonylates 5′-AMP at a Mg2+ centre (Fig. 5c). Whilst not directly comparable to the system reported here we have independent evidence for acylphosphonate formation upon dissolution of Pi(III) in Ac2O/AcOH solvent. Both experimental and more detailed computational studies to differentiate between these mechanistic possibilities are currently on-going in our laboratory.
The peaks due to the P(III) in PPi(III-V) have isotopomers but the peak due to Pi(V) does not appear to show any 18O incorporation (Fig. 6b). Close analysis of the 5′-AMP signal, in the 31P-NMR spectrum, after hydrolysis (Fig. 6c) reveals a larger (at δ 3.97) and smaller set (at δ 3.90; 3JPH = 4 Hz, 4JPH = 2 Hz) of what appears to be triplets of doublets (td). We believe that the difference between the sets of triplets of 70 ppb is too large to be explained as isotopomers of 5‘-AMP (which would indicate incorporation of three 18O-atoms) but that the larger td-pattern is due to unreacted 5’-AMP together with the 5′-Pi(V) nucleus of either 3′/2′-P(III)-5’AMP isomers and that the smaller td-pattern is the remaining 3′/2′-P(III)-5’AMP isomer (Fig. 6c).
Whilst we recognize that many of the concentration ranges and chemical environments used in this study likely map only poorly to early earth geological scenarios (Sleep 2010), much is now known about P-cycling within geological environments (Pasek and Block 2009). We believe this work demonstrates further that condensed P-oxyacids derived from Pi(III) have potential as primitive energy currency molecules. We find that P-transfer from PPi(III) to 5′-AMP appears to be markedly accelerated by divalent cations such as Mg2+ and Ca2+ and organic co-factors containing acyl-functionalities, scenarios reminiscent of those employed within contemporary biochemistry. The major product of this P-transfer process is the functionalized isohypophosphate, PPi(III-V)-5‘-AMP. In attempting to ascertain whether this condensed P-compound could be considered as an activated form of 5’-AMP, isotopic exchange studies reveal that hydrolysis of PPi(III-V)-5′-AMP via H218O takes place preferentially at the Pi(III) rather than Pi(V) terminus, arguing for a greater inherent reactivity at Pi(III). Further studies are continuing to better place some of the above chemistry within putative Hadean geological environments.
We thank the EPSRC (grant EP/F042558/1), the Leverhulme Trust (grant F07112AA) and the UK Space Agency (Aurora Fellowship to TPK, 2009-12) for financial support of this work. This work was also supported by COST Action TD 1308 ORIGINS (life-origins.com).
- Bock J-L, Crull G-B, Wishnia A, Springer C-S Jr (1991) 25Mg NMR Studies of magnesium binding to erythrocyte constituents. J Inorg Biochem 44:79–87Google Scholar
- Bryant DE, Greenfield D, Walshaw RD, Johnson BRG, Herschy B, Smith C, Pasek MA, Telford R, Scowen I, Munshi T, Edwards HGM, Cousins CR, Crawford IA, Kee TP (2013a) Hydrothermal modification of the sikhote-alin iron meteorite under low pH geothermal environments. A plausibly Prebiotic Route to Activated Phosphorus on the Early Earth Geochim et Cosmochim Acta 109:90–112Google Scholar
- Cousins CR, Gunn M, Crawford IA, Carrivik JL, Harris J, Kee TP, Karlsson M, Thorsteinsson T, Carmody L, Herschy B, Ward JM, Cockell C, Joy KH, White OL (2013) Glaciovolcanic hydrothermal environments in Iceland and implications for their detection on Mars. J Volcanol Geotherm Res 256:61–77CrossRefGoogle Scholar
- Harold F-M (1986) The vital force: A study of bioenergetics. W. H. Freeman & Co., New YorkGoogle Scholar
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