1
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Moroz LL, Nikitin MA, Poličar PG, Kohn AB, Romanova DY. Evolution of glutamatergic signaling and synapses. Neuropharmacology 2021; 199:108740. [PMID: 34343611 DOI: 10.1016/j.neuropharm.2021.108740] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/13/2022]
Abstract
Glutamate (Glu) is the primary excitatory transmitter in the mammalian brain. But, we know little about the evolutionary history of this adaptation, including the selection of l-glutamate as a signaling molecule in the first place. Here, we used comparative metabolomics and genomic data to reconstruct the genealogy of glutamatergic signaling. The origin of Glu-mediated communications might be traced to primordial nitrogen and carbon metabolic pathways. The versatile chemistry of L-Glu placed this molecule at the crossroad of cellular biochemistry as one of the most abundant metabolites. From there, innovations multiplied. Many stress factors or injuries could increase extracellular glutamate concentration, which led to the development of modular molecular systems for its rapid sensing in bacteria and archaea. More than 20 evolutionarily distinct families of ionotropic glutamate receptors (iGluRs) have been identified in eukaryotes. The domain compositions of iGluRs correlate with the origins of multicellularity in eukaryotes. Although L-Glu was recruited as a neuro-muscular transmitter in the early-branching metazoans, it was predominantly a non-neuronal messenger, with a possibility that glutamatergic synapses evolved more than once. Furthermore, the molecular secretory complexity of glutamatergic synapses in invertebrates (e.g., Aplysia) can exceed their vertebrate counterparts. Comparative genomics also revealed 15+ subfamilies of iGluRs across Metazoa. However, most of this ancestral diversity had been lost in the vertebrate lineage, preserving AMPA, Kainate, Delta, and NMDA receptors. The widespread expansion of glutamate synapses in the cortical areas might be associated with the enhanced metabolic demands of the complex brain and compartmentalization of Glu signaling within modular neuronal ensembles.
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Affiliation(s)
- Leonid L Moroz
- Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, FL, 32080, USA; Departments of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA.
| | - Mikhail A Nikitin
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia; Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127994, Russia
| | - Pavlin G Poličar
- Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, FL, 32080, USA; Faculty of Computer and Information Science, University of Ljubljana, SI-1000, Ljubljana, Slovenia
| | - Andrea B Kohn
- Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, FL, 32080, USA
| | - Daria Y Romanova
- Cellular Neurobiology of Learning Lab, Institute of Higher Nervous Activity and Neurophysiology, Moscow, 117485, Russia.
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2
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Bizzarri BM, Saladino R, Delfino I, García-Ruiz JM, Di Mauro E. Prebiotic Organic Chemistry of Formamide and the Origin of Life in Planetary Conditions: What We Know and What Is the Future. Int J Mol Sci 2021; 22:ijms22020917. [PMID: 33477625 PMCID: PMC7831497 DOI: 10.3390/ijms22020917] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/14/2021] [Accepted: 01/17/2021] [Indexed: 11/18/2022] Open
Abstract
The goal of prebiotic chemistry is the depiction of molecular evolution events preceding the emergence of life on Earth or elsewhere in the cosmos. Plausible experimental models require geochemical scenarios and robust chemistry. Today we know that the chemical and physical conditions for life to flourish on Earth were at work much earlier than thought, i.e., earlier than 4.4 billion years ago. In recent years, a geochemical model for the first five hundred million years of the history of our planet has been devised that would work as a cradle for life. Serpentinization processes in the Hadean eon affording self-assembled structures and vesicles provides the link between the catalytic properties of the inorganic environment and the impressive chemical potential of formamide to produce complete panels of organic molecules relevant in pre-genetic and pre-metabolic processes. Based on an interdisciplinary approach, we propose basic transformations connecting geochemistry to the chemistry of formamide, and we hint at the possible extension of this perspective to other worlds.
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Affiliation(s)
- Bruno Mattia Bizzarri
- Ecological and Biological Sciences Department (DEB), University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (B.M.B.); (I.D.); (E.D.M.)
| | - Raffaele Saladino
- Ecological and Biological Sciences Department (DEB), University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (B.M.B.); (I.D.); (E.D.M.)
- Correspondence: (R.S.); (J.M.G.-R.)
| | - Ines Delfino
- Ecological and Biological Sciences Department (DEB), University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (B.M.B.); (I.D.); (E.D.M.)
| | - Juan Manuel García-Ruiz
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra, Consejo Superior de Investigaciones Científicas–Universidad de Granada, Avenida de las Palmeras 4, Armilla, 18100 Granada, Spain
- Correspondence: (R.S.); (J.M.G.-R.)
| | - Ernesto Di Mauro
- Ecological and Biological Sciences Department (DEB), University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (B.M.B.); (I.D.); (E.D.M.)
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3
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Maltais TR, VanderVelde D, LaRowe DE, Goldman AD, Barge LM. Reactivity of Metabolic Intermediates and Cofactor Stability under Model Early Earth Conditions. ORIGINS LIFE EVOL B 2020; 50:35-55. [PMID: 31981046 DOI: 10.1007/s11084-019-09590-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/30/2019] [Indexed: 01/24/2023]
Abstract
Understanding the emergence of metabolic pathways is key to unraveling the factors that promoted the origin of life. One popular view is that protein cofactors acted as catalysts prior to the evolution of the protein enzymes with which they are now associated. We investigated the stability of acetyl coenzyme A (Acetyl Co-A, the group transfer cofactor in citric acid synthesis in the TCA cycle) under early Earth conditions, as well as whether Acetyl Co-A or its small molecule analogs thioacetate or acetate can catalyze the transfer of an acetyl group onto oxaloacetate in the absence of the citrate synthase enzyme. Several different temperatures, pH ranges, and compositions of aqueous environments were tested to simulate the Earth's early ocean and its possible components; the effect of these variables on oxaloacetate and cofactor chemistry were assessed under ambient and anoxic conditions. The cofactors tested are chemically stable under early Earth conditions, but none of the three compounds (Acetyl Co-A, thioacetate, or acetate) promoted synthesis of citric acid from oxaloacetate under the conditions tested. Oxaloacetate reacted with itself and/or decomposed to form a sequence of other products under ambient conditions, and under anoxic conditions was more stable; under ambient conditions the specific chemical pathways observed depended on the environmental conditions such as pH and presence/absence of bicarbonate or salt ions in early Earth ocean simulants. This work demonstrates the stability of these metabolic intermediates under anoxic conditions. However, even though free cofactors may be stable in a geological environmental setting, an enzyme or other mechanism to promote reaction specificity would likely be necessary for at least this particular reaction to proceed.
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Affiliation(s)
- Thora R Maltais
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA, 91109, USA
| | - David VanderVelde
- Department of Chemistry, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA, 91125, USA
| | - Douglas E LaRowe
- Department of Earth Sciences, University of Southern California, 3651 Trousdale Pkwy, Los Angeles, CA, 90089, USA
| | - Aaron D Goldman
- Department of Biology, Oberlin College, Science Center K123 119 Woodland St., Oberlin, OH, 44074, USA.,Blue Marble Space Institute for Science, Seattle, Washington, 98154, USA
| | - Laura M Barge
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA, 91109, USA.
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4
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Fornaro T, Steele A, Brucato JR. Catalytic/Protective Properties of Martian Minerals and Implications for Possible Origin of Life on Mars. Life (Basel) 2018; 8:life8040056. [PMID: 30400661 PMCID: PMC6315534 DOI: 10.3390/life8040056] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 10/28/2018] [Accepted: 10/30/2018] [Indexed: 11/16/2022] Open
Abstract
Minerals might have played critical roles for the origin and evolution of possible life forms on Mars. The study of the interactions between the "building blocks of life" and minerals relevant to Mars mineralogy under conditions mimicking the harsh Martian environment may provide key insight into possible prebiotic processes. Therefore, this contribution aims at reviewing the most important investigations carried out so far about the catalytic/protective properties of Martian minerals toward molecular biosignatures under Martian-like conditions. Overall, it turns out that the fate of molecular biosignatures on Mars depends on a delicate balance between multiple preservation and degradation mechanisms, often regulated by minerals, which may take place simultaneously. Such a complexity requires more efforts in simulating realistically the Martian environment in order to better inspect plausible prebiotic pathways and shed light on the nature of the organic compounds detected both in meteorites and on the surface of Mars through in situ analysis.
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Affiliation(s)
- Teresa Fornaro
- Geophysical Laboratory of the Carnegie Institution for Science, 5251 Broad Branch Rd. NW, Washington, DC 20015, USA.
| | - Andrew Steele
- Geophysical Laboratory of the Carnegie Institution for Science, 5251 Broad Branch Rd. NW, Washington, DC 20015, USA.
| | - John Robert Brucato
- INAF-Astrophysical Observatory of Arcetri, L.go E. Fermi 5, 50125 Firenze, Italy.
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5
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Lee K, Lee S. The prevention of ‘burning’ during the hard anodization in formamide for ultrafast growth of highly ordered arrays of TiO2 nanotubes. Electrochim Acta 2018. [DOI: 10.1016/j.electacta.2018.09.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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6
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Fornaro T, Brucato JR, Feuillie C, Sverjensky DA, Hazen RM, Brunetto R, D'Amore M, Barone V. Binding of Nucleic Acid Components to the Serpentinite-Hosted Hydrothermal Mineral Brucite. ASTROBIOLOGY 2018; 18:989-1007. [PMID: 30048146 DOI: 10.1089/ast.2017.1784] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The adsorption of nucleic acid components onto the serpentinite-hosted hydrothermal mineral brucite has been investigated experimentally by determining the equilibrium adsorption isotherms in aqueous solution. Thermodynamic characterization of the adsorption data has been performed using the extended triple-layer model (ETLM) to establish a model for the stoichiometry and equilibrium constants of surface complexes. Infrared characterization of the molecule-mineral complexes has helped gain insight into the molecular functional groups directly interacting with the mineral surface. Quantum mechanical calculations have been carried out to identify the possible complexes formed on surfaces by nucleic acid components and their binding configurations on mineral surfaces, both in the presence of water molecules and in water-free conditions. The results indicate that brucite favors adsorption of nucleotides with respect to nucleosides and nucleobases from dilute aqueous environments. The surface of this mineral is able to induce well-defined orientations of the molecules through specific molecule-mineral interactions. This result suggests plausible roles of the mineral brucite in assisting prebiotic molecular self-organization. Furthermore, the detection of the infrared spectroscopic features of such building blocks of life adsorbed on brucite at very low degrees of coverage provides important support to life detection investigations.
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Affiliation(s)
- Teresa Fornaro
- 1 Geophysical Laboratory, Carnegie Institution for Science , Washington, District of Columbia, United States
- 2 INAF-Astrophysical Observatory of Arcetri , Firenze, Italy
- 3 Scuola Normale Superiore , Pisa, Italy
| | - John R Brucato
- 2 INAF-Astrophysical Observatory of Arcetri , Firenze, Italy
| | - Cécile Feuillie
- 4 Louvain Institute of Biomolecular Science and Technology, University Catholique de Louvain , Louvain-la-Neuve, Belgium
| | - Dimitri A Sverjensky
- 5 Department of Earth and Planetary Sciences, Johns Hopkins University , Baltimore, Maryland, United States
| | - Robert M Hazen
- 1 Geophysical Laboratory, Carnegie Institution for Science , Washington, District of Columbia, United States
| | - Rosario Brunetto
- 6 Institut d'Astrophysique Spatiale, UMR8617 CNRS-Univ. Paris-Sud, Université Paris-Saclay , Orsay, France
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7
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Chemomimesis and Molecular Darwinism in Action: From Abiotic Generation of Nucleobases to Nucleosides and RNA. Life (Basel) 2018; 8:life8020024. [PMID: 29925796 PMCID: PMC6027154 DOI: 10.3390/life8020024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 06/14/2018] [Accepted: 06/19/2018] [Indexed: 01/26/2023] Open
Abstract
Molecular Darwinian evolution is an intrinsic property of reacting pools of molecules resulting in the adaptation of the system to changing conditions. It has no a priori aim. From the point of view of the origin of life, Darwinian selection behavior, when spontaneously emerging in the ensembles of molecules composing prebiotic pools, initiates subsequent evolution of increasingly complex and innovative chemical information. On the conservation side, it is a posteriori observed that numerous biological processes are based on prebiotically promptly made compounds, as proposed by the concept of Chemomimesis. Molecular Darwinian evolution and Chemomimesis are principles acting in balanced cooperation in the frame of Systems Chemistry. The one-pot synthesis of nucleosides in radical chemistry conditions is possibly a telling example of the operation of these principles. Other indications of similar cases of molecular evolution can be found among biogenic processes.
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8
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Novoselov AA, Silva D, Schneider J, Abrevaya XC, Chaffin MS, Serrano P, Navarro MS, Conti MJ, Souza Filho CRD. Geochemical constraints on the Hadean environment from mineral fingerprints of prokaryotes. Sci Rep 2017; 7:4008. [PMID: 28638074 PMCID: PMC5479841 DOI: 10.1038/s41598-017-04161-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 05/22/2017] [Indexed: 11/21/2022] Open
Abstract
The environmental conditions on the Earth before 4 billion years ago are highly uncertain, largely because of the lack of a substantial rock record from this period. During this time interval, known as the Hadean, the young planet transformed from an uninhabited world to the one capable of supporting, and inhabited by the first living cells. These cells formed in a fluid environment they could not at first control, with homeostatic mechanisms developing only later. It is therefore possible that present-day organisms retain some record of the primordial fluid in which the first cells formed. Here we present new data on the elemental compositions and mineral fingerprints of both Bacteria and Archaea, using these data to constrain the environment in which life formed. The cradle solution that produced this elemental signature was saturated in barite, sphene, chalcedony, apatite, and clay minerals. The presence of these minerals, as well as other chemical features, suggests that the cradle environment of life may have been a weathering fluid interacting with dry-land silicate rocks. The specific mineral assemblage provides evidence for a moderate Hadean climate with dry and wet seasons and a lower atmospheric abundance of CO2 than is present today.
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Affiliation(s)
- Alexey A Novoselov
- University of Campinas, Institute of Geosciences, Campinas, 13083-970, Brazil.
- University of Concepción, Institute of Applied Economic Geology, Concepción, Casilla 160-C, Chile.
| | - Dailto Silva
- University of Campinas, Institute of Geosciences, Campinas, 13083-970, Brazil
| | - Jerusa Schneider
- University of Campinas, School of Civil Engineering, Architecture and Urban Design, Campinas, 13083-889, Brazil
| | - Ximena Celeste Abrevaya
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires, C1428EHA, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Astronomía y Física del Espacio (IAFE), Buenos Aires, C1428ZAA, Argentina
| | | | - Paloma Serrano
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, 14473, Germany
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Kollath A, Brezhneva N, Skorb EV, Andreeva DV. Microbubbles trigger oscillation of crystal size in solids. Phys Chem Chem Phys 2017; 19:6286-6291. [DOI: 10.1039/c6cp07456a] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An understanding of the nature and conditions of nonlinear processes in open systems is important for modulation of the microstructure of solids at a new level of complexity.
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Affiliation(s)
- Anna Kollath
- Physical Chemistry II
- University of Bayreuth
- 95440 Bayreuth
- Germany
| | | | - Ekaterina V. Skorb
- Max Planck Institute of Colloids and Interfaces
- 14424 Potsdam
- Germany
- Laboratory of Solution Chemistry of Advanced Materials and Technologies
- ITMO University
| | - Daria V. Andreeva
- Center for Soft and Living Matter
- Institute for Basic Science
- Ulsan National Institute of Science and Technology
- 44919 Ulsan
- Republic of Korea
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10
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Šponer JE, Šponer J, Mauro ED. New evolutionary insights into the non-enzymatic origin of RNA oligomers. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27785893 DOI: 10.1002/wrna.1400] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/14/2016] [Accepted: 09/27/2016] [Indexed: 01/04/2023]
Abstract
We outline novel findings on the non-enzymatic polymerization of nucleotides under plausible prebiotic conditions and on the spontaneous onset of informational complexity in the founding molecule, RNA. We argue that the unique ability of 3', 5' cyclic guanosine monophosphate to form stacked architectures and polymerize in a self-sustained manner suggests that this molecule may serve as the 'seed of life' from which all self-replicating oligonucleotides can be derived via a logically complete sequence of simple events. WIREs RNA 2017, 8:e1400. doi: 10.1002/wrna.1400 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Judit E Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Ernesto Di Mauro
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Viterbo, Italy
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11
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Nguyen HT, Jeilani YA, Hung HM, Nguyen MT. Radical Pathways for the Prebiotic Formation of Pyrimidine Bases from Formamide. J Phys Chem A 2015. [DOI: 10.1021/acs.jpca.5b03625] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Yassin A. Jeilani
- Department
Chemistry and Biochemistry, Spelman College, Atlanta, Georgia 30314, United States
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12
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Meteorite-catalyzed syntheses of nucleosides and of other prebiotic compounds from formamide under proton irradiation. Proc Natl Acad Sci U S A 2015; 112:E2746-55. [PMID: 25870268 DOI: 10.1073/pnas.1422225112] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Liquid formamide has been irradiated by high-energy proton beams in the presence of powdered meteorites, and the products of the catalyzed resulting syntheses were analyzed by mass spectrometry. Relative to the controls (no radiation, or no formamide, or no catalyst), an extremely rich, variegate, and prebiotically relevant panel of compounds was observed. The meteorites tested were representative of the four major classes: iron, stony iron, chondrites, and achondrites. The products obtained were amino acids, carboxylic acids, nucleobases, sugars, and, most notably, four nucleosides: cytidine, uridine, adenosine, and thymidine. In accordance with theoretical studies, the detection of HCN oligomers suggests the occurrence of mechanisms based on the generation of radical cyanide species (CN·) for the synthesis of nucleobases. Given that many of the compounds obtained are key components of extant organisms, these observations contribute to outline plausible exogenous high-energy-based prebiotic scenarios and their possible boundary conditions, as discussed.
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13
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Uncertainty of prebiotic scenarios: the case of the non-enzymatic reverse tricarboxylic acid cycle. Sci Rep 2015; 5:8009. [PMID: 25620471 PMCID: PMC4306138 DOI: 10.1038/srep08009] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 12/22/2014] [Indexed: 11/08/2022] Open
Abstract
We consider the hypothesis of the primordial nature of the non-enzymatic reverse tricarboxylic acid (rTCA) cycle and describe a modeling approach to quantify the uncertainty of this hypothesis due to the combinatorial aspect of the constituent chemical transformations. Our results suggest that a) rTCA cycle belongs to a degenerate optimum of auto-catalytic cycles, and b) the set of targets for investigations of the origin of the common metabolic core should be significantly extended.
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14
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Di Mauro E, Saladino R, Trifonov EN. The path to life's origins. Remaining hurdles. J Biomol Struct Dyn 2013; 32:512-22. [PMID: 23582097 DOI: 10.1080/07391102.2013.783509] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Recent progress in abiotic syntheses, especially self-catalytic syntheses, as well as theoretical breakthroughs such as reconstruction of events of early molecular evolution and tracing repeat expansions in contemporary genomes, converge to a rather simple possible scenario of origin of life, notwithstanding the enormity of the problem. The scenario includes self-replicating RNA duplexes, supplemented by monomers and high-energy compounds that, as demonstrated or assumed, can all be synthesized abiotically. The self-replication would proceed with occasional mutational changes, propagated in later cycles. This audacious, as it may seem, walk toward the life origin already involves many laboratories, each exploring its own scenario. The one suggested in this outline seems to the authors well justified to engage in, while bypassing few steps to deal with later.
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Affiliation(s)
- Ernesto Di Mauro
- a Dipartimento di, Biologia e Biotecnologie "Charles Darwin" , Istituto Pasteur "Fondazione Cenci-Bolognetti", "Sapienza" Universita' , di Roma, P.leAldo Moro, 5, Rome , 00185 , Italy
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15
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Jeilani YA, Nguyen HT, Newallo D, Dimandja JMD, Nguyen MT. Free radical routes for prebiotic formation of DNA nucleobases from formamide. Phys Chem Chem Phys 2013; 15:21084-93. [DOI: 10.1039/c3cp53108b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Ferus M, Civiš S, Mládek A, Šponer J, Juha L, Šponer JE. On the Road from Formamide Ices to Nucleobases: IR-Spectroscopic Observation of a Direct Reaction between Cyano Radicals and Formamide in a High-Energy Impact Event. J Am Chem Soc 2012. [DOI: 10.1021/ja310421z] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Martin Ferus
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague 8, Czech Republic
- Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-182 21 Prague 8, Czech Republic
| | - Svatopluk Civiš
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague 8, Czech Republic
| | - Arnošt Mládek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic
- CEITEC-Central European Institute of Technology, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic
- CEITEC-Central European Institute of Technology, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Libor Juha
- Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-182 21 Prague 8, Czech Republic
| | - Judit E. Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic
- CEITEC-Central European Institute of Technology, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
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17
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Saladino R, Botta G, Pino S, Costanzo G, Di Mauro E. Genetics first or metabolism first? The formamide clue. Chem Soc Rev 2012; 41:5526-65. [PMID: 22684046 DOI: 10.1039/c2cs35066a] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Life is made of the intimate interaction of metabolism and genetics, both built around the chemistry of the most common elements of the Universe (hydrogen, oxygen, nitrogen, and carbon). The transmissible interaction of metabolic and genetic cycles results in the hypercycles of organization and de-organization of chemical information, of living and non-living. The origin-of-life quest has long been split into several attitudes exemplified by the aphorisms "genetics-first" or "metabolism-first". Recently, the opposition between these approaches has been solved by more unitary theoretical and experimental frames taking into account energetic, evolutionary, proto-metabolic and environmental aspects. Nevertheless, a unitary and simple chemical frame is still needed that could afford both the precursors of the synthetic pathways eventually leading to RNA and to the key components of the central metabolic cycles, possibly connected with the synthesis of fatty acids. In order to approach the problem of the origin of life it is therefore reasonable to start from the assumption that both metabolism and genetics had a common origin, shared a common chemical frame, and were embedded under physical-chemical conditions favourable for the onset of both. The singleness of such a prebiotically productive chemical process would partake of Darwinian advantages over more complex fragmentary chemical systems. The prebiotic chemistry of formamide affords in a single and simple physical-chemical frame nucleic bases, acyclonucleosides, nucleotides, biogenic carboxylic acids, sugars, amino sugars, amino acids and condensing agents. Thus, we suggest the possibility that formamide could have jointly provided the main components for the onset of both (pre)genetic and (pre)metabolic processes. As a note of caution, we discuss the fact that these observations only indicate possible solutions at the level of organic substrates, not at the systemic chemical level.
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Affiliation(s)
- Raffaele Saladino
- Dipartimento di Agrobiologia ed Agrochimica, Università della Tuscia, Via San Camillo De Lellis, 01100 Viterbo, Italy.
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Mulkidjanian AY, Bychkov AY, Dibrova DV, Galperin MY, Koonin EV. Origin of first cells at terrestrial, anoxic geothermal fields. Proc Natl Acad Sci U S A 2012; 109:E821-30. [PMID: 22331915 PMCID: PMC3325685 DOI: 10.1073/pnas.1117774109] [Citation(s) in RCA: 210] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
All cells contain much more potassium, phosphate, and transition metals than modern (or reconstructed primeval) oceans, lakes, or rivers. Cells maintain ion gradients by using sophisticated, energy-dependent membrane enzymes (membrane pumps) that are embedded in elaborate ion-tight membranes. The first cells could possess neither ion-tight membranes nor membrane pumps, so the concentrations of small inorganic molecules and ions within protocells and in their environment would equilibrate. Hence, the ion composition of modern cells might reflect the inorganic ion composition of the habitats of protocells. We attempted to reconstruct the "hatcheries" of the first cells by combining geochemical analysis with phylogenomic scrutiny of the inorganic ion requirements of universal components of modern cells. These ubiquitous, and by inference primordial, proteins and functional systems show affinity to and functional requirement for K(+), Zn(2+), Mn(2+), and phosphate. Thus, protocells must have evolved in habitats with a high K(+)/Na(+) ratio and relatively high concentrations of Zn, Mn, and phosphorous compounds. Geochemical reconstruction shows that the ionic composition conducive to the origin of cells could not have existed in marine settings but is compatible with emissions of vapor-dominated zones of inland geothermal systems. Under the anoxic, CO(2)-dominated primordial atmosphere, the chemistry of basins at geothermal fields would resemble the internal milieu of modern cells. The precellular stages of evolution might have transpired in shallow ponds of condensed and cooled geothermal vapor that were lined with porous silicate minerals mixed with metal sulfides and enriched in K(+), Zn(2+), and phosphorous compounds.
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Affiliation(s)
- Armen Y. Mulkidjanian
- School of Physics, University of Osnabrück, D-49069 Osnabrück, Germany
- A. N. Belozersky Institute of Physico-Chemical Biology and Schools of
| | | | - Daria V. Dibrova
- School of Physics, University of Osnabrück, D-49069 Osnabrück, Germany
- Bioengineering and Bioinformatics, Moscow State University, Moscow 119992, Russia; and
| | - Michael Y. Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
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