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Fahrenbach AC, Giurgiu C, Tam CP, Li L, Hongo Y, Aono M, Szostak JW. Common and Potentially Prebiotic Origin for Precursors of Nucleotide Synthesis and Activation. J Am Chem Soc 2017. [PMID: 28640999 PMCID: PMC6326526 DOI: 10.1021/jacs.7b01562] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
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We
have recently shown that 2-aminoimidazole is a superior nucleotide
activating group for nonenzymatic RNA copying. Here we describe a
prebiotic synthesis of 2-aminoimidazole that shares a common mechanistic
pathway with that of 2-aminooxazole, a previously described key intermediate
in prebiotic nucleotide synthesis. In the presence of glycolaldehyde,
cyanamide, phosphate and ammonium ion, both 2-aminoimidazole and 2-aminooxazole
are produced, with higher concentrations of ammonium ion and acidic
pH favoring the former. Given a 1:1 mixture of 2-aminoimidazole and
2-aminooxazole, glyceraldehyde preferentially reacts and cyclizes
with the latter, forming a mixture of pentose aminooxazolines, and
leaving free 2-aminoimidazole available for nucleotide activation.
The common synthetic origin of 2-aminoimidazole and 2-aminooxazole
and their distinct reactivities are suggestive of a reaction network
that could lead to both the synthesis of RNA monomers and to their
subsequent chemical activation.
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Affiliation(s)
- Albert C Fahrenbach
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital , 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Earth-Life Science Institute, Tokyo Institute of Technology , 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Constantin Giurgiu
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital , 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Chun Pong Tam
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital , 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Li Li
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital , 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Yayoi Hongo
- Earth-Life Science Institute, Tokyo Institute of Technology , 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Masashi Aono
- Earth-Life Science Institute, Tokyo Institute of Technology , 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.,Faculty of Environment and Information Studies, Keio University , 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital , 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States.,Earth-Life Science Institute, Tokyo Institute of Technology , 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
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Adam ZR. Temperature oscillations near natural nuclear reactor cores and the potential for prebiotic oligomer synthesis. ORIGINS LIFE EVOL B 2016; 46:171-87. [PMID: 26680444 DOI: 10.1007/s11084-015-9478-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 12/04/2015] [Indexed: 12/01/2022]
Abstract
Geologic settings capable of driving prebiotic oligomer synthesis reactions remain a relatively unexplored aspect of origins of life research. Natural nuclear reactors are an example of Precambrian energy sources that produced unique temperature fluctuations. Heat transfer models indicate that water-moderated, convectively-cooled natural fission reactors in porous host rocks create temperature oscillations that resemble those employed in polymerase chain reaction (PCR) devices to artificially amplify oligonucleotides. This temperature profile is characterized by short-duration pulses up to 70-100 °C, followed by a sustained period of temperatures in the range of 30-70 °C, and finally a period of relaxation to ambient temperatures until the cycle is restarted by a fresh influx of pore water. For a given reactor configuration, temperature maxima and the time required to relax to ambient temperatures depend most strongly on the aggregate effect of host rock permeability in decreasing the thermal expansion and increasing the viscosity and evaporation temperature of the pore fluids. Once formed, fission-fueled reactors can sustain multi-kilowatt-level power production for 10(5)-10(6) years, ensuring microenvironmental longevity and chemical output. The model outputs indicate that organic synthesis on young planetary bodies with a sizeable reservoir of fissile material can involve more sophisticated energy dissipation pathways than modern terrestrial analog settings alone would suggest.
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Affiliation(s)
- Zachary R Adam
- Department of Earth and Planetary Sciences, Harvard University, 26 Oxford Street, Room 51, Cambridge, MA, 02138, USA.
- Blue Marble Space Institute of Science, 1001 4th Ave, Suite 3201, Seattle, WA, 98154, USA.
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López de la Osa J, Bateman DA, Ho S, González C, Chakrabartty A, Laurents DV. Getting specificity from simplicity in putative proteins from the prebiotic earth. Proc Natl Acad Sci U S A 2007; 104:14941-6. [PMID: 17855563 PMCID: PMC1986592 DOI: 10.1073/pnas.0706876104] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Indexed: 11/18/2022] Open
Abstract
Can unique protein structures arise from a limited set of amino acids present on the prebiotic earth? To address this question, we have determined the stability and structure of KIA7, a 20-residue polypeptide containing chiefly Lys, Ile, and Ala. NMR methods reveal that KIA7 tetramerizes and folds on the millisecond time scale to adopt a four-helix X-bundle structure with a tightly and specifically packed core. Denaturation studies and hydrogen exchange measurements of KIA7 and several variants demonstrate that ridges-into-grooves packing of Ala and Ile side chains and the packing of a C-terminal aromatic group into the hydrophobic core are sufficient to give rise to a rather stable, well folded protein structure, with no favorable electrostatic interactions or tertiary or quaternary hydrogen bonds. Both modern proteins and RNAs can adopt specific structures, but RNAs do so with a limited "alphabet" of residues and types of stabilizing interactions. The results reported here show that specific, well folded protein structures can also arise from a highly reduced set of stabilizing interactions and amino acids that are thought to have been present on the prebiotic earth.
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Affiliation(s)
- Jaime López de la Osa
- *Instituto de Química Física “Rocasolano,” Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain; and
| | - David A. Bateman
- Departments of Medical Biophysics and Biochemistry, University of Toronto, Toronto, ON, Canada M5G-2M9
| | - Sylvia Ho
- Departments of Medical Biophysics and Biochemistry, University of Toronto, Toronto, ON, Canada M5G-2M9
| | - Carlos González
- *Instituto de Química Física “Rocasolano,” Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain; and
| | - Avijit Chakrabartty
- Departments of Medical Biophysics and Biochemistry, University of Toronto, Toronto, ON, Canada M5G-2M9
| | - Douglas V. Laurents
- *Instituto de Química Física “Rocasolano,” Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain; and
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Lahav N, White DH. A possible role of fluctuating clay-water systems in the production of ordered prebiotic oligomers. J Mol Evol 1980; 16:11-21. [PMID: 7441778 DOI: 10.1007/bf01732066] [Citation(s) in RCA: 74] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A model is proposed for the intermediate stages of prebiotic evolution, based on the characteristics of the adsorption and condensation of amino acids and nucleotides on the surface area of clay minerals in a fluctuating environment. Template replication and translation of adsorbed oligonucleotides and catalytic effects by peptide products on further condensation are proposed, due to specific properties of hypohydrous clay surfaces as well as the biomolecules themselves. Experimental evidence supports some of the proposed interactions, and all of them can be tested experimentally.
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Abstract
Recent experimental work suggests a possible cyclical pathway for early prebiotic oligonucleotide formation that involves (i) dry-state (nontemplate) synthesis of random copolymers with mixed 2',5' and 3',5' bonds, (ii) passage of these oligomers into solution at low temperatures, and (iii) a preferential hydrolysis of the 2',5' bond in any short helices that have formed. This early system could have selected for complementary sequences that were largely 3',5'-linked, but may not have selected efficiently for a single enantiomer of ribose.
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