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Takagi YA, Nguyen DH, Wexler TB, Goldman AD. The Coevolution of Cellularity and Metabolism Following the Origin of Life. J Mol Evol 2020; 88:598-617. [PMID: 32809045 PMCID: PMC7445158 DOI: 10.1007/s00239-020-09961-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 07/27/2020] [Indexed: 01/09/2023]
Abstract
The emergence of cellular organisms occurred sometime between the origin of life and the evolution of the last universal common ancestor and represents one of the major transitions in evolutionary history. Here we describe a series of artificial life simulations that reveal a close relationship between the evolution of cellularity, the evolution of metabolism, and the richness of the environment. When environments are rich in processing energy, a resource that the digital organisms require to both process their genomes and replicate, populations evolve toward a state of non-cellularity. But when processing energy is not readily available in the environment and organisms must produce their own processing energy from food puzzles, populations always evolve both a proficient metabolism and a high level of cellular impermeability. Even between these two environmental extremes, the population-averaged values of cellular impermeability and metabolic proficiency exhibit a very strong correlation with one another. Further investigations show that non-cellularity is selectively advantageous when environmental processing energy is abundant because it allows organisms to access the available energy, while cellularity is selectively advantageous when environmental processing energy is scarce because it affords organisms the genetic fidelity required to incrementally evolve efficient metabolisms. The selection pressures favoring either non-cellularity or cellularity can be reversed when the environment transitions from one of abundant processing energy to one of scarce processing energy. These results have important implications for when and why cellular organisms evolved following the origin of life.
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Affiliation(s)
- Yuta A Takagi
- Department of Biology, Oberlin College, Oberlin, OH, 44074, USA
| | - Diep H Nguyen
- Department of Biology, Oberlin College, Oberlin, OH, 44074, USA.,Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Tom B Wexler
- Department of Computer Science, Oberlin College, Oberlin, OH, 44074, USA.,Verily Life Sciences, Cambridge, MA, USA
| | - Aaron D Goldman
- Department of Biology, Oberlin College, Oberlin, OH, 44074, USA. .,Blue Marble Space Institute of Science, Seattle, WA, 98154, USA.
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Yi R, Tran QP, Ali S, Yoda I, Adam ZR, Cleaves HJ, Fahrenbach AC. A continuous reaction network that produces RNA precursors. Proc Natl Acad Sci U S A 2020; 117:13267-13274. [PMID: 32487725 PMCID: PMC7306801 DOI: 10.1073/pnas.1922139117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Continuous reaction networks, which do not rely on purification or timely additions of reagents, serve as models for chemical evolution and have been demonstrated for compounds thought to have played important roles for the origins of life such as amino acids, hydroxy acids, and sugars. Step-by-step chemical protocols for ribonucleotide synthesis are known, but demonstrating their synthesis in the context of continuous reaction networks remains a major challenge. Herein, compounds proposed to be important for prebiotic RNA synthesis, including glycolaldehyde, cyanamide, 2-aminooxazole, and 2-aminoimidazole, are generated from a continuous reaction network, starting from an aqueous mixture of NaCl, NH4Cl, phosphate, and HCN as the only carbon source. No well-timed addition of any other reagents is required. The reaction network is driven by a combination of γ radiolysis and dry-down. γ Radiolysis results in a complex mixture of organics, including the glycolaldehyde-derived glyceronitrile and cyanamide. This mixture is then dried down, generating free glycolaldehyde that then reacts with cyanamide/NH3 to furnish a combination of 2-aminooxazole and 2-aminoimidazole. This continuous reaction network models how precursors for generating RNA and other classes of compounds may arise spontaneously from a complex mixture that originates from simple reagents.
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Affiliation(s)
- Ruiqin Yi
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Quoc Phuong Tran
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Sarfaraz Ali
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Isao Yoda
- Co-60 Radiation Facility, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Zachary R Adam
- Department of Planetary Sciences, University of Arizona, Tucson, AZ 85721
- Blue Marble Space Institute of Science, Seattle, WA 98154
| | - H James Cleaves
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
- Blue Marble Space Institute of Science, Seattle, WA 98154
- Program in Interdisciplinary Studies, Institute for Advanced Study, Princeton, NJ 08540
| | - Albert C Fahrenbach
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia;
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Yi R, Hongo Y, Yoda I, Adam ZR, Fahrenbach AC. Radiolytic Synthesis of Cyanogen Chloride, Cyanamide and Simple Sugar Precursors. ChemistrySelect 2018. [DOI: 10.1002/slct.201802242] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ruiqin Yi
- Earth-Life Science Institute; Tokyo Institute of Technology 2-12-1-IE-1 Ookayama, Meguro-ku; Tokyo 152-8550 Japan
| | - Yayoi Hongo
- Earth-Life Science Institute; Tokyo Institute of Technology 2-12-1-IE-1 Ookayama, Meguro-ku; Tokyo 152-8550 Japan
| | - Isao Yoda
- Co-60 Radiation Facility; Tokyo Institute of Technology 2-12-1-IE-1 Ookayama, Meguro-ku; Tokyo 152-8550 Japan
| | - Zachary R. Adam
- Department of Earth and Planetary Sciences; Harvard University; Cambridge, MA USA
- Blue Marble Space Institute of Science; Seattle, WA USA
| | - Albert C. Fahrenbach
- Earth-Life Science Institute; Tokyo Institute of Technology 2-12-1-IE-1 Ookayama, Meguro-ku; Tokyo 152-8550 Japan
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Rashydov NM, Hajduch M. Chernobyl seed project. Advances in the identification of differentially abundant proteins in a radio-contaminated environment. FRONTIERS IN PLANT SCIENCE 2015. [PMID: 26217350 PMCID: PMC4492160 DOI: 10.3389/fpls.2015.00493] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Plants have the ability to grow and successfully reproduce in radio-contaminated environments, which has been highlighted by nuclear accidents at Chernobyl (1986) and Fukushima (2011). The main aim of this article is to summarize the advances of the Chernobyl seed project which has the purpose to provide proteomic characterization of plants grown in the Chernobyl area. We present a summary of comparative proteomic studies on soybean and flax seeds harvested from radio-contaminated Chernobyl areas during two successive generations. Using experimental design developed for radio-contaminated areas, altered abundances of glycine betaine, seed storage proteins, and proteins associated with carbon assimilation into fatty acids were detected. Similar studies in Fukushima radio-contaminated areas might complement these data. The results from these Chernobyl experiments can be viewed in a user-friendly format at a dedicated web-based database freely available at http://www.chernobylproteomics.sav.sk.
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Affiliation(s)
- Namik M. Rashydov
- Department of Biophysics and Radiobiology, Institute of Cell Biology and Genetic Engineering, National Academy of Sciences of Ukraine, KievUkraine
| | - Martin Hajduch
- Department of Developmental and Reproduction Biology, Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, NitraSlovakia
- *Correspondence: Martin Hajduch, Department of Developmental and Reproduction Biology, Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Akademicka 2, P.O. Box 39A, Nitra, Slovakia,
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Abstract
The celebrated Miller experiments reported on the spontaneous formation of amino acids from a mixture of simple molecules reacting under an electric discharge, giving birth to the research field of prebiotic chemistry. However, the chemical reactions involved in those experiments have never been studied at the atomic level. Here we report on, to our knowledge, the first ab initio computer simulations of Miller-like experiments in the condensed phase. Our study, based on the recent method of treatment of aqueous systems under electric fields and on metadynamics analysis of chemical reactions, shows that glycine spontaneously forms from mixtures of simple molecules once an electric field is switched on and identifies formic acid and formamide as key intermediate products of the early steps of the Miller reactions, and the crucible of formation of complex biological molecules.
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Stüeken EE, Anderson RE, Bowman JS, Brazelton WJ, Colangelo-Lillis J, Goldman AD, Som SM, Baross JA. Did life originate from a global chemical reactor? GEOBIOLOGY 2013; 11:101-126. [PMID: 23331348 DOI: 10.1111/gbi.12025] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Accepted: 12/03/2012] [Indexed: 06/01/2023]
Abstract
Many decades of experimental and theoretical research on the origin of life have yielded important discoveries regarding the chemical and physical conditions under which organic compounds can be synthesized and polymerized. However, such conditions often seem mutually exclusive, because they are rarely encountered in a single environmental setting. As such, no convincing models explain how living cells formed from abiotic constituents. Here, we propose a new approach that considers the origin of life within the global context of the Hadean Earth. We review previous ideas and synthesize them in four central hypotheses: (i) Multiple microenvironments contributed to the building blocks of life, and these niches were not necessarily inhabitable by the first organisms; (ii) Mineral catalysts were the backbone of prebiotic reaction networks that led to modern metabolism; (iii) Multiple local and global transport processes were essential for linking reactions occurring in separate locations; (iv) Global diversity and local selection of reactants and products provided mechanisms for the generation of most of the diverse building blocks necessary for life. We conclude that no single environmental setting can offer enough chemical and physical diversity for life to originate. Instead, any plausible model for the origin of life must acknowledge the geological complexity and diversity of the Hadean Earth. Future research may therefore benefit from identifying further linkages between organic precursors, minerals, and fluids in various environmental contexts.
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Affiliation(s)
- E E Stüeken
- Department of Earth and Space Sciences, University of Washington, Seattle, WA, USA.
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Brasier MD, Matthewman R, McMahon S, Wacey D. Pumice as a remarkable substrate for the origin of life. ASTROBIOLOGY 2011; 11:725-735. [PMID: 21879814 DOI: 10.1089/ast.2010.0546] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The context for the emergence of life on Earth sometime prior to 3.5 billion years ago is almost as big a puzzle as the definition of life itself. Hitherto, the problem has largely been addressed in terms of theoretical and experimental chemistry plus evidence from extremophile habitats like modern hydrothermal vents and meteorite impact structures. Here, we argue that extensive rafts of glassy, porous, and gas-rich pumice could have had a significant role in the origin of life and provided an important habitat for the earliest communities of microorganisms. This is because pumice has four remarkable properties. First, during eruption it develops the highest surface-area-to-volume ratio known for any rock type. Second, it is the only known rock type that floats as rafts at the air-water interface and then becomes beached in the tidal zone for long periods of time. Third, it is exposed to an unusually wide variety of conditions, including dehydration. Finally, from rafting to burial, it has a remarkable ability to adsorb metals, organics, and phosphates as well as to host organic catalysts such as zeolites and titanium oxides. These remarkable properties now deserve to be rigorously explored in the laboratory and the early rock record.
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Abstract
Ionizing radiation is a ubiquitous feature of the Cosmos, from exogenous cosmic rays (CR) to the intrinsic mineral radioactivity of a habitable world, and its influences on the emergence and persistence of life are wide-ranging and profound. Much attention has already been focused on the deleterious effects of ionizing radiation on organisms and the complex molecules of life, but ionizing radiation also performs many crucial functions in the generation of habitable planetary environments and the origins of life. This review surveys the role of CR and mineral radioactivity in star formation, generation of biogenic elements, and the synthesis of organic molecules and driving of prebiotic chemistry. Another major theme is the multiple layers of shielding of planetary surfaces from the flux of cosmic radiation and the various effects on a biosphere of violent but rare astrophysical events such as supernovae and gamma-ray bursts. The influences of CR can also be duplicitous, such as limiting the survival of surface life on Mars while potentially supporting a subsurface biosphere in the ocean of Europa. This review highlights the common thread that ionizing radiation forms between the disparate component disciplines of astrobiology.
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Affiliation(s)
- Lewis R Dartnell
- UCL Institute for Origins, University College London, London, UK.
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Abstract
There are growing indications that life began in a radioactive beach environment. A geologic framework for the origin or support of life in a Hadean heavy mineral placer beach has been developed, based on the unique chemical properties of the lower-electronic actinides, which act as nuclear fissile and fertile fuels, radiolytic energy sources, oligomer catalysts, and coordinating ions (along with mineralogically associated lanthanides) for prototypical prebiotic homonuclear and dinuclear metalloenzymes. A four-factor nuclear reactor model was constructed to estimate how much uranium would have been required to initiate a sustainable fission reaction within a placer beach sand 4.3 billion years ago. It was calculated that about 1-8 weight percent of the sand would have to have been uraninite, depending on the weight percent, uranium enrichment, and quantity of neutron poisons present within the remaining placer minerals. Radiolysis experiments were conducted with various solvents with the use of uraniumand thorium-rich minerals (metatorbernite and monazite, respectively) as proxies for radioactive beach sand in contact with different carbon, hydrogen, oxygen, and nitrogen reactants. Radiation bombardment ranged in duration of exposure from 3 weeks to 6 months. Low levels of acetonitrile (estimated to be on the order of parts per billion in concentration) were conclusively identified in 2 setups and tentatively indicated in a 3(rd) by gas chromatography/mass spectrometry. These low levels have been interpreted within the context of a Hadean placer beach prebiotic framework to demonstrate the promise of investigating natural nuclear reactors as power production sites that might have assisted the origins of life on young rocky planets with a sufficiently differentiated crust/mantle structure. Future investigations are recommended to better quantify the complex relationships between energy release, radioactive grain size, fissionability, reactant phase, phosphorus release, and possible abiotic production of sugars, amino acids, activated phosphorus, prototypical organometallic enzymes, and oligomer catalysts at a single putative beach site.
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Affiliation(s)
- Zachary Adam
- Department of Aeronautics & Astronautics Engineering, and UW Center for Astrobiology, University of Washington, Seattle, Washington 98195-2400, USA.
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Cintas P. Starting from Scratch: The Rise and Fate of Carbon Atoms. Chemphyschem 2005; 6:1233-5. [PMID: 15952223 DOI: 10.1002/cphc.200500179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Pedro Cintas
- Departamento de Química Orgánica, Facultad de Ciencias-UEX, 06071 Badajoz, Spain.
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Brasier M, Green O, Lindsay J, Steele A. Earth's oldest (approximately 3.5 Ga) fossils and the 'Early Eden hypothesis': questioning the evidence. ORIGINS LIFE EVOL B 2004; 34:257-69. [PMID: 14979661 DOI: 10.1023/b:orig.0000009845.62244.d3] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We question the biogenicity of putative bacterial and cyanobacterial 'microfossils' from 3465 Ma Apex cherts of the Warrawoona Group in Western Australia. They are challenged on the basis of integrated multidisciplinary evidence obtained from field and fabric mapping plus new high-resolution research into their context, sedimentology, filament morphology, 'septation' and arrangement. They cannot be distinguished from (and are reinterpreted as) secondary artefacts of amorphous carbon that formed during devitrification of successive generations of carbonaceous hydrothermal dyke vein quartz. Similar structures occur within associated carbonaceous volcanic glass. The null hypothesis of an abiotic or prebiotic origin for such ancient carbonaceous matter is sustained until mutually supporting contextural, morphological and geochemical evidence for a bacterial rather than abiotic origin is forthcoming.
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Affiliation(s)
- Martin Brasier
- Department of Earth Sciences, Parks Road, Oxford, OX1 3PR, UK.
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