Prebiotic Phosphorylation of Uridine using Diamidophosphate in Aerosols

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Abstract

One of the most challenging fundamental problems in establishing prebiotically plausible routes for phosphorylation reactions using phosphate is that they are thermodynamically unfavorable in aqueous conditions. Diamidophosphate (DAP), a potentially prebiotically relevant compound, was shown to phosphorylate nucleosides in aqueous medium, albeit at a very slow rate (days/weeks). Here, we demonstrate that performing these reactions within an aerosol environment, a suitable model for the early Earth ocean-air interface, yields higher reaction rates when compared to bulk solution, thus overcoming these rate limitations. As a proof-of-concept, we demonstrate the effective conversion (~6.5–10%) of uridine to uridine-2′,3′-cyclophosphate in less than 1 h. These results suggest that aerosol environments are a possible scenario in which prebiotic phosphorylation could have occurred despite unfavorable rates in bulk solution.

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Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions.

Matthew W Powner, Béatrice Gerland, John Sutherland (2009)

At some stage in the origin of life, an informational polymer must have arisen by purely chemical means. According to one version of the 'RNA world' hypothesis this polymer was RNA, but attempts to provide experimental support for this have failed. In particular, although there has been some success demonstrating that 'activated' ribonucleotides can polymerize to form RNA, it is far from obvious how such ribonucleotides could have formed from their constituent parts (ribose and nucleobases). Ribose is difficult to form selectively, and the addition of nucleobases to ribose is inefficient in the case of purines and does not occur at all in the case of the canonical pyrimidines. Here we show that activated pyrimidine ribonucleotides can be formed in a short sequence that bypasses free ribose and the nucleobases, and instead proceeds through arabinose amino-oxazoline and anhydronucleoside intermediates. The starting materials for the synthesis-cyanamide, cyanoacetylene, glycolaldehyde, glyceraldehyde and inorganic phosphate-are plausible prebiotic feedstock molecules, and the conditions of the synthesis are consistent with potential early-Earth geochemical models. Although inorganic phosphate is only incorporated into the nucleotides at a late stage of the sequence, its presence from the start is essential as it controls three reactions in the earlier stages by acting as a general acid/base catalyst, a nucleophilic catalyst, a pH buffer and a chemical buffer. For prebiotic reaction sequences, our results highlight the importance of working with mixed chemical systems in which reactants for a particular reaction step can also control other steps.

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Volcanic production of polyphosphates and its relevance to prebiotic evolution.

G Yamagata, T Namba, R L H Watanabe … (1991)

Phosphates would probably have been essential compounds for prebiotic evolution on the primitive Earth. In this context, there have been several studies of condensation of water-soluble phosphates to polyphosphates and phosphorylation and condensation or polymerization of biomolecules with polyphosphates. But most of the phosphorus on the early Earth would have been in the form of water-insoluble apatite, and the origin of the water-soluble polyphosphates required for prebiotic evolution has therefore been a mystery. Here we show, both from experiments that simulate magmatic conditions and from analysis of volatile condensates in volcanic gas, that volcanic activity can produce water-soluble polyphosphates through partial hydrolysis of P4O10. This mechanism seems to be the only viable route identified so far for the production of these species on the primitive Earth.

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Fine-particle water and pH in the southeastern United States

R. Weber, A. Nenes, N. L. Ng … (2015)

Particle water and pH are predicted using meteorological observations (relative humidity (RH), temperature ( T )), gas/particle composition, and thermodynamic modeling (ISORROPIA-II). A comprehensive uncertainty analysis is included, and the model is validated. We investigate mass concentrations of particle water and related particle pH for ambient fine-mode aerosols sampled in a relatively remote Alabama forest during the Southern Oxidant and Aerosol Study (SOAS) in summer and at various sites in the southeastern US during different seasons, as part of the Southeastern Center for Air Pollution and Epidemiology (SCAPE) study. Particle water and pH are closely linked; pH is a measure of the particle H + aqueous concentration and depends on both the presence of ions and amount of particle liquid water. Levels of particle water, in turn, are determined through water uptake by both the ionic species and organic compounds. Thermodynamic calculations based on measured ion concentrations can predict both pH and liquid water but may be biased since contributions of organic species to liquid water are not considered. In this study, contributions of both the inorganic and organic fractions to aerosol liquid water were considered, and predictions were in good agreement with measured liquid water based on differences in ambient and dry light scattering coefficients (prediction vs. measurement: slope = 0.91, intercept = 0.5 μg m −3 , R 2 = 0.75). ISORROPIA-II predictions were confirmed by good agreement between predicted and measured ammonia concentrations (slope = 1.07, intercept = −0.12 μg m −3 , R 2 = 0.76). Based on this study, organic species on average contributed 35% to the total water, with a substantially higher contribution (50%) at night. However, not including contributions of organic water had a minor effect on pH (changes pH by 0.15 to 0.23 units), suggesting that predicted pH without consideration of organic water could be sufficient for the purposes of aqueous secondary organic aerosol (SOA) chemistry. The mean pH predicted in the Alabama forest (SOAS) was 0.94 ± 0.59 (median 0.93). pH diurnal trends followed liquid water and were driven mainly by variability in RH; during SOAS nighttime pH was near 1.5, while daytime pH was near 0.5. pH ranged from 0.5 to 2 in summer and 1 to 3 in the winter at other sites. The systematically low pH levels in the southeast may have important ramifications, such as significantly influencing acid-catalyzed reactions, gas–aerosol partitioning, and mobilization of redox metals and minerals. Particle ion balances or molar ratios, often used to infer pH, do not consider the dissociation state of individual ions or particle liquid water levels and do not correlate with particle pH.

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Author and article information

Contributors

N. L. Ng: ng@chbe.gatech.edu

T. M. Orlando:

ORCID: http://orcid.org/0000-0002-2422-4506

thomas.orlando@chemistry.gatech.edu

Journal

Journal ID (nlm-ta): Sci Rep

Journal ID (iso-abbrev): Sci Rep

Title: Scientific Reports

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2045-2322

Publication date (Electronic): 19 September 2019

Publication date PMC-release: 19 September 2019

Publication date Collection: 2019

Volume: 9

Affiliations

[1 ]ISNI 0000 0001 2097 4943, GRID grid.213917.f, School of Chemistry and Biochemistry, , Georgia Institute of Technology, ; Atlanta, GA 30332 USA

[2 ]ISNI 0000 0001 2097 4943, GRID grid.213917.f, School of Earth and Atmospheric Sciences, , Georgia Institute of Technology, ; Atlanta, GA 30332 USA

[3 ]ISNI 0000000122199231, GRID grid.214007.0, Department of Chemistry, , The Scripps Research Institute, ; La Jolla, CA 92037 USA

[4 ]ISNI 0000 0001 2097 4943, GRID grid.213917.f, School of Chemical and Biomolecular Engineering, , Georgia Institute of Technology, ; Atlanta, GA 30332 USA

Article

Publisher ID: 49947

DOI: 10.1038/s41598-019-49947-8

PMC ID: 6753121

PubMed ID: 31537885

SO-VID: f4f44a8f-a576-4505-b26e-0446b440266b

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Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

Funding

Funded by: FundRef https://doi.org/10.13039/100000001, National Science Foundation (NSF);

Award ID: CHE‐1004570

Award ID: CHE‐1504217

Award Recipient : N. L. Ng

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ScienceOpen disciplines: Uncategorized

Keywords: origin of life,mass spectrometry,atmospheric chemistry

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ScienceOpen disciplines: Uncategorized

Keywords: origin of life, mass spectrometry, atmospheric chemistry

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Prebiotic Phosphorylation of Uridine using Diamidophosphate in Aerosols

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Most cited references 26

Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions.

Volcanic production of polyphosphates and its relevance to prebiotic evolution.

Fine-particle water and pH in the southeastern United States

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