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      Divergent prebiotic synthesis of pyrimidine and 8-oxo-purine ribonucleotides

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          Abstract

          Understanding prebiotic nucleotide synthesis is a long standing challenge thought to be essential to elucidating the origins of life on Earth. Recently, remarkable progress has been made, but to date all proposed syntheses account separately for the pyrimidine and purine ribonucleotides; no divergent synthesis from common precursors has been proposed. Moreover, the prebiotic syntheses of pyrimidine and purine nucleotides that have been demonstrated operate under mutually incompatible conditions. Here, we tackle this mutual incompatibility by recognizing that the 8-oxo-purines share an underlying generational parity with the pyrimidine nucleotides. We present a divergent synthesis of pyrimidine and 8-oxo-purine nucleotides starting from a common prebiotic precursor that yields the β-ribo-stereochemistry found in the sugar phosphate backbone of biological nucleic acids. The generational relationship between pyrimidine and 8-oxo-purine nucleotides suggests that 8-oxo-purine ribonucleotides may have played a key role in primordial nucleic acids prior to the emergence of the canonical nucleotides of biology.

          Abstract

          While mechanisms have been proposed for the prebiotic nucleotide synthesis, these require separate (and potentially incompatible) routes for pyrimidines and purines. Here the authors show that both of these classes of molecules can be formed by a divergent synthesis from a common prebiotic precursor.

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          Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions.

          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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            Endogenous production, exogenous delivery and impact-shock synthesis of organic molecules: an inventory for the origins of life.

            Sources of organic molecules on the early Earth divide into three categories: delivery by extraterrestrial objects; organic synthesis driven by impact shocks; and organic synthesis by other energy sources (such as ultraviolet light or electrical discharges). Estimates of these sources for plausible end-member oxidation states of the early terrestrial atmosphere suggest that the heavy bombardment before 3.5 Gyr ago either produced or delivered quantities of organics comparable to those produced by other energy sources. Which sources of prebiotic organics were quantitatively dominant depends strongly on the composition of the early terrestrial atmosphere. In the event of an early strongly reducing atmosphere, production by atmospheric shocks seems to have dominated that due to electrical discharges. Organic synthesis by ultraviolet light may, in turn, have dominated shock production, but only if a long-wavelength absorber such as H2S were supplied to the atmosphere at a rate sufficient for synthesis to have been limited by ultraviolet flux, rather than by reactant abundance. In the apparently more likely case of an early terrestrial atmosphere of intermediate oxidation state, atmospheric shocks were probably of little importance for direct organic production. For [H2]/[CO2] ratios of approximately 0.1, net organic production was some three orders of magnitude lower than for reducing atmospheres, with delivery of intact exogenous organics in interplanetary dust particles (IDPs) and ultraviolet production being the most important sources. At still lower [H2]/[CO2] ratios, IDPs may have been the dominant source of prebiotic organics on the early Earth. Endogenous, exogenous and impact-shock sources of organics could each have made a significant contribution to the origins of life.
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              Prebiotic chemistry and the origin of the RNA world.

              The demonstration that ribosomal peptide synthesis is a ribozyme-catalyzed reaction makes it almost certain that there was once an RNA World. The central problem for origin-of-life studies, therefore, is to understand how a protein-free RNA World became established on the primitive Earth. We first review the literature on the prebiotic synthesis of the nucleotides, the nonenzymatic synthesis and copying of polynucleotides, and the selection of ribozyme catalysts of a kind that might have facilitated polynucleotide replication. This leads to a brief outline of the Molecular Biologists' Dream, an optimistic scenario for the origin of the RNA World. In the second part of the review we point out the many unresolved problems presented by the Molecular Biologists' Dream. This in turn leads to a discussion of genetic systems simpler than RNA that might have "invented" RNA. Finally, we review studies of prebiotic membrane formation.
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                Author and article information

                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group
                2041-1723
                19 May 2017
                2017
                : 8
                : 15270
                Affiliations
                [1 ]Department of Chemistry, University College London , 20 Gordon Street, London WC1H 0AJ, UK
                [2 ]Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, USA
                [3 ]Department of Molecular Biology and Center for Computational and Integrative Biology, Howard Hughes Medical Institute, Massachusetts General Hospital , 185 Cambridge Street, Boston, Massachusetts 02114, USA
                Author notes
                [*]

                These authors contributed equally to this work.

                Author information
                http://orcid.org/0000-0002-6368-3190
                Article
                ncomms15270
                10.1038/ncomms15270
                5454461
                28524845
                984a1742-ae99-4dc4-b0ca-9d80df99c9e1
                Copyright © 2017, The Author(s)

                This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

                History
                : 20 December 2016
                : 15 March 2017
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