1
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Gonçalves D. Rethinking life and predicting its origin. Theory Biosci 2024:10.1007/s12064-024-00420-9. [PMID: 38922566 DOI: 10.1007/s12064-024-00420-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 06/24/2024] [Indexed: 06/27/2024]
Abstract
The definition, origin and recreation of life remain elusive. As others have suggested, only once we put life into reductionist physical terms will we be able to solve those questions. To that end, this work proposes the phenomenon of life to be the product of two dissipative mechanisms. From them, one characterises extant biological life and deduces a testable scenario for its origin. The proposed theory of life allows its replication, reinterprets ecological evolution and creates new constraints on the search for life.
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Affiliation(s)
- Diogo Gonçalves
- Centro de Química Estrutural and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001, Lisbon, Portugal.
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2
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Nicholls JWF, Chin JP, Williams TA, Lenton TM, O’Flaherty V, McGrath JW. On the potential roles of phosphorus in the early evolution of energy metabolism. Front Microbiol 2023; 14:1239189. [PMID: 37601379 PMCID: PMC10433651 DOI: 10.3389/fmicb.2023.1239189] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/20/2023] [Indexed: 08/22/2023] Open
Abstract
Energy metabolism in extant life is centered around phosphate and the energy-dense phosphoanhydride bonds of adenosine triphosphate (ATP), a deeply conserved and ancient bioenergetic system. Yet, ATP synthesis relies on numerous complex enzymes and has an autocatalytic requirement for ATP itself. This implies the existence of evolutionarily simpler bioenergetic pathways and potentially primordial alternatives to ATP. The centrality of phosphate in modern bioenergetics, coupled with the energetic properties of phosphorylated compounds, may suggest that primordial precursors to ATP also utilized phosphate in compounds such as pyrophosphate, acetyl phosphate and polyphosphate. However, bioavailable phosphate may have been notably scarce on the early Earth, raising doubts about the roles that phosphorylated molecules might have played in the early evolution of life. A largely overlooked phosphorus redox cycle on the ancient Earth might have provided phosphorus and energy, with reduced phosphorus compounds potentially playing a key role in the early evolution of energy metabolism. Here, we speculate on the biological phosphorus compounds that may have acted as primordial energy currencies, sources of environmental energy, or sources of phosphorus for the synthesis of phosphorylated energy currencies. This review encompasses discussions on the evolutionary history of modern bioenergetics, and specifically those pathways with primordial relevance, and the geochemistry of bioavailable phosphorus on the ancient Earth. We highlight the importance of phosphorus, not only in the form of phosphate, to early biology and suggest future directions of study that may improve our understanding of the early evolution of bioenergetics.
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Affiliation(s)
- Jack W. F. Nicholls
- School of Biological Sciences, Queen’s University of Belfast, Belfast, United Kingdom
| | - Jason P. Chin
- School of Biological Sciences, Queen’s University of Belfast, Belfast, United Kingdom
| | - Tom A. Williams
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Timothy M. Lenton
- Global Systems Institute, University of Exeter, Exeter, United Kingdom
| | | | - John W. McGrath
- School of Biological Sciences, Queen’s University of Belfast, Belfast, United Kingdom
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3
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Prebiotic Synthesis of ATP: A Terrestrial Volcanism-Dependent Pathway. Life (Basel) 2023; 13:life13030731. [PMID: 36983886 PMCID: PMC10053121 DOI: 10.3390/life13030731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
Adenosine triphosphate (ATP) is a multifunctional small molecule, necessary for all modern Earth life, which must be a component of the last universal common ancestor (LUCA). However, the relatively complex structure of ATP causes doubts about its accessibility on prebiotic Earth. In this paper, based on previous studies on the synthesis of ATP components, a plausible prebiotic pathway yielding this key molecule is constructed, which relies on terrestrial volcanism to provide the required materials and suitable conditions.
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4
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Organophosphorus Compound Formation Through the Oxidation of Reduced Oxidation State Phosphorus Compounds on the Hadean Earth. J Mol Evol 2023; 91:60-75. [PMID: 36576533 DOI: 10.1007/s00239-022-10086-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/16/2022] [Indexed: 12/29/2022]
Abstract
Reduced oxidation state phosphorus compounds may have been brought to the early Earth via meteorites or could have formed through geologic processes. These compounds could have played a role in the origin of biological phosphorus (P, hereafter) compounds. Reduced oxidation state P compounds are generally more soluble in water and are more reactive than orthophosphate and its associated minerals. However, to date no facile routes to generate C-O-P type compounds using reduced oxidation state P compounds have been reported under prebiotic conditions. In this study, we investigate the reactions between reduced oxidation state P compounds-and their oxidized products generated via Fenton reactions-with the nucleosides uridine and adenosine. The inorganic P compounds generated via Fenton chemistry readily react with nucleosides to produce organophosphites and organophosphates, including phosphate diesters via one-pot syntheses. The reactions were facilitated by NH4+ ions and urea as a condensation agent. We also present the results of the plausible stability of the organic compounds such as adenosine in an environment containing an abundance of H2O2. Such results have direct implications on finding organic compounds in Martian environments and other rocky planets (including early Earth) that were richer in H2O2 than O2. Finally, we also suggest a route for the sink of these inorganic P compounds, as a part of a plausible natural P cycle and show the possible formation of secondary phosphate minerals such as struvite and brushite on the early Earth.
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5
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Brady MP, Tostevin R, Tosca NJ. Marine phosphate availability and the chemical origins of life on Earth. Nat Commun 2022; 13:5162. [PMID: 36056017 PMCID: PMC9440033 DOI: 10.1038/s41467-022-32815-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 08/17/2022] [Indexed: 11/21/2022] Open
Abstract
Prebiotic systems chemistry suggests that high phosphate concentrations were necessary to synthesise molecular building blocks and sustain primitive cellular systems. However, current understanding of mineral solubility predicts negligible phosphate concentrations for most natural waters, yet the role of Fe2+, ubiquitous on early Earth, is poorly quantified. Here we determine the solubility of Fe(II)-phosphate in synthetic seawater as a function of pH and ionic strength, integrate these observations into a thermodynamic model that predicts phosphate concentrations across a range of aquatic conditions, and validate these predictions against modern anoxic sediment pore waters. Experiments and models show that Fe2+ significantly increases the solubility of all phosphate minerals in anoxic systems, suggesting that Hadean and Archean seawater featured phosphate concentrations ~103–104 times higher than currently estimated. This suggests that seawater readily met the phosphorus requirements of emergent cellular systems and early microbial life, perhaps fueling primary production during the advent of oxygenic photosynthesis. Phosphate is critical for all life on Earth but its origins have remained enigmatic. Experiments indicate that phosphate may have been abundant in ancient Fe-rich seawater, providing a crucial ingredient for the origins of life on Earth.
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Affiliation(s)
- Matthew P Brady
- Department of Earth Sciences, University of Cambridge, Cambridge, CB2 3EQ, UK
| | - Rosalie Tostevin
- Department of Geological Sciences, University of Cape Town, Cape Town, 7700, South Africa
| | - Nicholas J Tosca
- Department of Earth Sciences, University of Cambridge, Cambridge, CB2 3EQ, UK.
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6
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Prosdocimi F, de Farias ST, José MV. Prebiotic chemical refugia: multifaceted scenario for the formation of biomolecules in primitive Earth. Theory Biosci 2022; 141:339-347. [PMID: 36042123 DOI: 10.1007/s12064-022-00377-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/17/2022] [Indexed: 11/25/2022]
Abstract
The origin of life was a cosmic event happened on primitive Earth. A critical problem to better understand the origins of life in Earth is the search for chemical scenarios on which the basic building blocks of biological molecules could be produced. Classic works in pre-biotic chemistry frequently considered early Earth as an homogeneous atmosphere constituted by chemical elements such as methane (CH4), ammonia (NH3), water (H2O), hydrogen (H2) and hydrogen sulfide (H2S). Under that scenario, Stanley Miller was capable to produce amino acids and solved the question about the abiotic origin of proteins. Conversely, the origin of nucleic acids has tricked scientists for decades once nucleotides are complex, though necessary molecules to allow the existence of life. Here we review possible chemical scenarios that allowed not only the formation of nucleotides but also other significant biomolecules. We aim to provide a theoretical solution for the origin of biomolecules at specific sites named "Prebiotic Chemical Refugia." Prebiotic chemical refugium should therefore be understood as a geographic site in prebiotic Earth on which certain chemical elements were accumulated in higher proportion than expected, facilitating the production of basic building blocks for biomolecules. This higher proportion should not be understood as static, but dynamic; once the physicochemical conditions of our planet changed periodically. These different concentration of elements, together with geochemical and astronomical changes along days, synodic months and years provided somewhat periodic changes in temperature, pressure, electromagnetic fields, and conditions of humidity, among other features. Recent and classic works suggesting most likely prebiotic refugia on which the main building blocks for biological molecules might be accumulated are reviewed and discussed.
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Affiliation(s)
- Francisco Prosdocimi
- Laboratório de Biologia Teórica E de Sistemas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal Do Rio de Janeiro, 21.941-902, Rio de Janeiro, Brazil. .,Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, CDMX, Mexico.
| | - Sávio Torres de Farias
- Laboratório de Genética Evolutiva Paulo Leminsk, Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | - Marco V José
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, CDMX, Mexico.
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7
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Gan D, Ying J, Zhao Y. Prebiotic Chemistry: The Role of Trimetaphosphate in Prebiotic Chemical Evolution. Front Chem 2022; 10:941228. [PMID: 35910738 PMCID: PMC9326000 DOI: 10.3389/fchem.2022.941228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/23/2022] [Indexed: 11/22/2022] Open
Abstract
Life’s origins have always been a scientific puzzle. Understanding the production of biomolecules is crucial for understanding the evolution of life on Earth. Numerous studies on trimetaphosphate have been conducted in the field of prebiotic chemistry. However, its role in prebiotic chemistry has been documented infrequently in the review literature. The goal of this thesis is to review the role of trimetaphosphate in the early Earth’s biomolecule synthesis and phosphorylation. Additionally, various trimetaphosphate-mediated reaction pathways are discussed, as well as the role of trimetaphosphate in prebiotic chemistry. Finally, in our opinion, interactions between biomolecules should be considered in prebiotic synthesis scenarios since this may result in some advances in subsequent research on this subject. The research establishes an essential and opportune foundation for an in-depth examination of the “mystery of life".
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Affiliation(s)
- Dingwei Gan
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
| | - Jianxi Ying
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
- *Correspondence: Jianxi Ying,
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
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8
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Sithamparam M, Satthiyasilan N, Chen C, Jia TZ, Chandru K. A material-based panspermia hypothesis: The potential of polymer gels and membraneless droplets. Biopolymers 2022; 113:e23486. [PMID: 35148427 DOI: 10.1002/bip.23486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 01/08/2023]
Abstract
The Panspermia hypothesis posits that either life's building blocks (molecular Panspermia) or life itself (organism-based Panspermia) may have been interplanetarily transferred to facilitate the origins of life (OoL) on a given planet, complementing several current OoL frameworks. Although many spaceflight experiments were performed in the past to test for potential terrestrial organisms as Panspermia seeds, it is uncertain whether such organisms will likely "seed" a new planet even if they are able to survive spaceflight. Therefore, rather than using organisms, using abiotic chemicals as seeds has been proposed as part of the molecular Panspermia hypothesis. Here, as an extension of this hypothesis, we introduce and review the plausibility of a polymeric material-based Panspermia seed (M-BPS) as a theoretical concept, where the type of polymeric material that can function as a M-BPS must be able to: (1) survive spaceflight and (2) "function", i.e., contingently drive chemical evolution toward some form of abiogenesis once arriving on a foreign planet. We use polymeric gels as a model example of a potential M-BPS. Polymeric gels that can be prebiotically synthesized on one planet (such as polyester gels) could be transferred to another planet via meteoritic transfer, where upon landing on a liquid bearing planet, can assemble into structures containing cellular-like characteristics and functionalities. Such features presupposed that these gels can assemble into compartments through phase separation to accomplish relevant functions such as encapsulation of primitive metabolic, genetic and catalytic materials, exchange of these materials, motion, coalescence, and evolution. All of these functions can result in the gels' capability to alter local geochemical niches on other planets, thereby allowing chemical evolution to lead to OoL events.
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Affiliation(s)
- Mahendran Sithamparam
- Space Science Center (ANGKASA), Institute of Climate Change, National University of Malaysia (UKM), Bangi, Selangor, Malaysia
| | - Nirmell Satthiyasilan
- Space Science Center (ANGKASA), Institute of Climate Change, National University of Malaysia (UKM), Bangi, Selangor, Malaysia
| | - Chen Chen
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Tony Z Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Blue Marble Space Institute of Science, Seattle, Washington, USA
| | - Kuhan Chandru
- Space Science Center (ANGKASA), Institute of Climate Change, National University of Malaysia (UKM), Bangi, Selangor, Malaysia
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9
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Maguire OR, Smokers IBA, Huck WTS. A physicochemical orthophosphate cycle via a kinetically stable thermodynamically activated intermediate enables mild prebiotic phosphorylations. Nat Commun 2021; 12:5517. [PMID: 34535651 PMCID: PMC8448844 DOI: 10.1038/s41467-021-25555-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/18/2021] [Indexed: 12/02/2022] Open
Abstract
The incorporation of orthophosphate from scarce geochemical sources into the organic compounds essential for life under mild conditions is a fundamental challenge for prebiotic chemistry. Here we report a prebiotic system capable of overcoming this challenge by taking inspiration from extant life's recycling of orthophosphate via its conversion into kinetically stable thermodynamically activated (KSTA) nucleotide triphosphates (e.g. ATP). We separate the activation of orthophosphate from its transfer to organic compounds by, crucially, first accumulating a KSTA phosphoramidate. We use cyanate to activate orthophosphate in aqueous solution under mild conditions and then react it with imidazole to accumulate the KSTA imidazole phosphate. In a paste, imidazole phosphate phosphorylates all the essential building blocks of life. Integration of this chemistry into a wet/dry cycle enables the continuous recycling of orthophosphate and the accretion of phosphorylated compounds. This system functions even at low reagent concentrations due to solutes concentrating during evaporation. Our system demonstrates a general strategy for how to maximise the usage of scarce resources based upon cycles which accumulate and then release activated intermediates.
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Affiliation(s)
- Oliver R Maguire
- Institute for Molecules and Materials, Radboud University Nijmegen, 6525, AJ, Nijmegen, The Netherlands
| | - Iris B A Smokers
- Institute for Molecules and Materials, Radboud University Nijmegen, 6525, AJ, Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University Nijmegen, 6525, AJ, Nijmegen, The Netherlands.
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10
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Fialho DM, Karunakaran SC, Greeson KW, Martínez I, Schuster GB, Krishnamurthy R, Hud NV. Depsipeptide Nucleic Acids: Prebiotic Formation, Oligomerization, and Self-Assembly of a New Proto-Nucleic Acid Candidate. J Am Chem Soc 2021; 143:13525-13537. [PMID: 34398608 DOI: 10.1021/jacs.1c02287] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The mechanism by which informational polymers first formed on the early earth is currently unknown. The RNA world hypothesis implies that RNA oligomers were produced prebiotically, before the emergence of enzymes, but the demonstration of such a process remains challenging. Alternatively, RNA may have been preceded by an earlier ancestral polymer, or proto-RNA, that had a greater propensity for self-assembly than RNA, with the eventual transition to functionally superior RNA being the result of chemical or biological evolution. We report a new class of nucleic acid analog, depsipeptide nucleic acid (DepsiPNA), which displays several properties that are attractive as a candidate for proto-RNA. The monomers of depsipeptide nucleic acids can form under plausibly prebiotic conditions. These monomers oligomerize spontaneously when dried from aqueous solutions to form nucleobase-functionalized depsipeptides. Once formed, these DepsiPNA oligomers are capable of complementary self-assembly and are resistant to hydrolysis in the assembled state. These results suggest that the initial formation of primitive, self-assembling, informational polymers on the early earth may have been relatively facile if the constraints of an RNA-first scenario are relaxed.
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Affiliation(s)
- David M Fialho
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Suneesh C Karunakaran
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Katherine W Greeson
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Isaac Martínez
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Gary B Schuster
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ramanarayanan Krishnamurthy
- NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Nicholas V Hud
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
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11
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12
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Gaylor MO, Miro P, Vlaisavljevich B, Kondage AAS, Barge LM, Omran A, Videau P, Swenson VA, Leinen LJ, Fitch NW, Cole KL, Stone C, Drummond SM, Rageth K, Dewitt LR, González Henao S, Karanauskus V. Plausible Emergence and Self Assembly of a Primitive Phospholipid from Reduced Phosphorus on the Primordial Earth. ORIGINS LIFE EVOL B 2021; 51:185-213. [PMID: 34279769 DOI: 10.1007/s11084-021-09613-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 06/19/2021] [Indexed: 11/28/2022]
Abstract
How life arose on the primitive Earth is one of the biggest questions in science. Biomolecular emergence scenarios have proliferated in the literature but accounting for the ubiquity of oxidized (+ 5) phosphate (PO43-) in extant biochemistries has been challenging due to the dearth of phosphate and molecular oxygen on the primordial Earth. A compelling body of work suggests that exogenous schreibersite ((Fe,Ni)3P) was delivered to Earth via meteorite impacts during the Heavy Bombardment (ca. 4.1-3.8 Gya) and there converted to reduced P oxyanions (e.g., phosphite (HPO32-) and hypophosphite (H2PO2-)) and phosphonates. Inspired by this idea, we review the relevant literature to deduce a plausible reduced phospholipid analog of modern phosphatidylcholines that could have emerged in a primordial hydrothermal setting. A shallow alkaline lacustrine basin underlain by active hydrothermal fissures and meteoritic schreibersite-, clay-, and metal-enriched sediments is envisioned. The water column is laden with known and putative primordial hydrothermal reagents. Small system dimensions and thermal- and UV-driven evaporation further concentrate chemical precursors. We hypothesize that a reduced phospholipid arises from Fischer-Tropsch-type (FTT) production of a C8 alkanoic acid, which condenses with an organophosphinate (derived from schreibersite corrosion to hypophosphite with subsequent methylation/oxidation), to yield a reduced protophospholipid. This then condenses with an α-amino nitrile (derived from Strecker-type reactions) to form the polar head. Preliminary modeling results indicate that reduced phospholipids do not aggregate rapidly; however, single layer micelles are stable up to aggregates with approximately 100 molecules.
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Affiliation(s)
- Michael O Gaylor
- Department of Chemistry, Dakota State University, Madison, SD, 57042, USA.
| | - Pere Miro
- Department of Chemistry, University of South Dakota, Vermillion, SD, 57069, USA
| | - Bess Vlaisavljevich
- Department of Chemistry, University of South Dakota, Vermillion, SD, 57069, USA
| | | | - Laura M Barge
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, 91109, USA
| | - Arthur Omran
- School of Geosciences, University of South Florida, Tampa, FL, 33620, USA.,Department of Chemistry, University of North Florida, Jacksonville, FL, 32224, USA
| | - Patrick Videau
- Department of Biology, Southern Oregon University, Ashland, OR, 97520, USA.,Bayer Crop Science, Chesterfield, MO, 63017, USA
| | - Vaille A Swenson
- Department of Chemistry, Dakota State University, Madison, SD, 57042, USA.,Department of Molecular Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Lucas J Leinen
- Department of Chemistry, Dakota State University, Madison, SD, 57042, USA
| | - Nathaniel W Fitch
- Department of Chemistry, Dakota State University, Madison, SD, 57042, USA
| | - Krista L Cole
- Department of Chemistry, Dakota State University, Madison, SD, 57042, USA
| | - Chris Stone
- Department of Biology, Southern Oregon University, Ashland, OR, 97520, USA
| | - Samuel M Drummond
- Department of Chemistry, Dakota State University, Madison, SD, 57042, USA
| | - Kayli Rageth
- Department of Chemistry, Dakota State University, Madison, SD, 57042, USA
| | - Lillian R Dewitt
- Department of Chemistry, Dakota State University, Madison, SD, 57042, USA
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13
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Smith HH, Hyde AS, Simkus DN, Libby E, Maurer SE, Graham HV, Kempes CP, Sherwood Lollar B, Chou L, Ellington AD, Fricke GM, Girguis PR, Grefenstette NM, Pozarycki CI, House CH, Johnson SS. The Grayness of the Origin of Life. Life (Basel) 2021; 11:498. [PMID: 34072344 PMCID: PMC8226951 DOI: 10.3390/life11060498] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/22/2021] [Accepted: 05/26/2021] [Indexed: 12/05/2022] Open
Abstract
In the search for life beyond Earth, distinguishing the living from the non-living is paramount. However, this distinction is often elusive, as the origin of life is likely a stepwise evolutionary process, not a singular event. Regardless of the favored origin of life model, an inherent "grayness" blurs the theorized threshold defining life. Here, we explore the ambiguities between the biotic and the abiotic at the origin of life. The role of grayness extends into later transitions as well. By recognizing the limitations posed by grayness, life detection researchers will be better able to develop methods sensitive to prebiotic chemical systems and life with alternative biochemistries.
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Affiliation(s)
- Hillary H. Smith
- Department of Geosciences, The Pennsylvania State University, University Park, PA 16802, USA;
- Earth and Environmental Systems Institute, The Pennsylvania State University, University Park, PA 16802, USA
| | - Andrew S. Hyde
- Department of Geosciences, The Pennsylvania State University, University Park, PA 16802, USA;
- Earth and Environmental Systems Institute, The Pennsylvania State University, University Park, PA 16802, USA
| | - Danielle N. Simkus
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA; (D.N.S.); (H.V.G.); (L.C.); (C.I.P.)
- NASA Postdoctoral Program, USRA, Columbia, MD 20146, USA
- Department of Physics, Catholic University of America, Washington, DC 20064, USA
| | - Eric Libby
- Santa Fe Institute, Santa Fe, NM 87501, USA; (E.L.); (C.P.K.); (N.M.G.)
- Department of Mathematics and Mathematical Statistics, Umeå University, 90187 Umeå, Sweden
- Icelab, Umeå University, 90187 Umeå, Sweden
| | - Sarah E. Maurer
- Department of Chemistry and Biochemistry, Central Connecticut State University, New Britain, CT 06050, USA;
| | - Heather V. Graham
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA; (D.N.S.); (H.V.G.); (L.C.); (C.I.P.)
- Department of Physics, Catholic University of America, Washington, DC 20064, USA
| | | | | | - Luoth Chou
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA; (D.N.S.); (H.V.G.); (L.C.); (C.I.P.)
- NASA Postdoctoral Program, USRA, Columbia, MD 20146, USA
- Department of Biology, Georgetown University, Washington, DC 20057, USA
| | - Andrew D. Ellington
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA;
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - G. Matthew Fricke
- Department of Computer Science, University of New Mexico, Albuquerque, NM 87108, USA;
| | - Peter R. Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA;
| | - Natalie M. Grefenstette
- Santa Fe Institute, Santa Fe, NM 87501, USA; (E.L.); (C.P.K.); (N.M.G.)
- Blue Marble Space Institute of Science, Seattle, WA 98104, USA
| | - Chad I. Pozarycki
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA; (D.N.S.); (H.V.G.); (L.C.); (C.I.P.)
- Department of Biology, Georgetown University, Washington, DC 20057, USA
| | - Christopher H. House
- Department of Geosciences, The Pennsylvania State University, University Park, PA 16802, USA;
- Earth and Environmental Systems Institute, The Pennsylvania State University, University Park, PA 16802, USA
| | - Sarah Stewart Johnson
- Department of Biology, Georgetown University, Washington, DC 20057, USA
- Science, Technology and International Affairs Program, Georgetown University, Washington, DC 20057, USA
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14
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Jia TZ, Wang PH, Niwa T, Mamajanov I. Connecting primitive phase separation to biotechnology, synthetic biology, and engineering. J Biosci 2021; 46:79. [PMID: 34373367 PMCID: PMC8342986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
One aspect of the study of the origins of life focuses on how primitive chemistries assembled into the first cells on Earth and how these primitive cells evolved into modern cells. Membraneless droplets generated from liquid-liquid phase separation (LLPS) are one potential primitive cell-like compartment; current research in origins of life includes study of the structure, function, and evolution of such systems. However, the goal of primitive LLPS research is not simply curiosity or striving to understand one of life's biggest unanswered questions, but also the possibility to discover functions or structures useful for application in the modern day. Many applicational fields, including biotechnology, synthetic biology, and engineering, utilize similar phaseseparated structures to accomplish specific functions afforded by LLPS. Here, we briefly review LLPS applied to primitive compartment research and then present some examples of LLPS applied to biomolecule purification, drug delivery, artificial cell construction, waste and pollution management, and flavor encapsulation. Due to a significant focus on similar functions and structures, there appears to be much for origins of life researchers to learn from those working on LLPS in applicational fields, and vice versa, and we hope that such researchers can start meaningful cross-disciplinary collaborations in the future.
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Affiliation(s)
- Tony Z Jia
- grid.32197.3e0000 0001 2179 2105Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550 Japan ,grid.482804.2Blue Marble Space Institute of Science, 1001 4th Ave., Suite 3201, Seattle, Washington 98154 USA
| | - Po-Hsiang Wang
- grid.32197.3e0000 0001 2179 2105Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550 Japan ,grid.37589.300000 0004 0532 3167Graduate Institute of Environmental Engineering, National Central University, Zhongli Dist, 300 Zhongda Rd, Taoyuan City, 32001 Taiwan
| | - Tatsuya Niwa
- grid.32197.3e0000 0001 2179 2105Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, 226-8503 Japan
| | - Irena Mamajanov
- grid.32197.3e0000 0001 2179 2105Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550 Japan
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15
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Gull M, Omran A, Feng T, Pasek MA. Silicate-, Magnesium Ion-, and Urea-Induced Prebiotic Phosphorylation of Uridine via Pyrophosphate; Revisiting the Hot Drying Water Pool Scenario. Life (Basel) 2020; 10:life10080122. [PMID: 32722517 PMCID: PMC7459484 DOI: 10.3390/life10080122] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/24/2020] [Accepted: 07/24/2020] [Indexed: 12/15/2022] Open
Abstract
The availability of nucleotides on the early Earth is of great significance for the origin of a self-replicating system capable of undergoing evolution. We hereby report the successful phosphorylation reactions of the nucleoside uridine under heating in the "drying pool" prebiotic model at temperatures ranging from 60-75 °C, and by using pyrophosphate as a phosphorylation agent. Uridine monophosphates (UMP) such as uridine-5'-monophosphate (5'-UMP), 2'-UMP, and 3'-UMP, as well as cyclic 2'-3'-UMP, were identified by 31P-NMR. In addition to the above-mentioned products, a dimer of uridine-phosphate-uridine (U-P-U) was also observed. The reactions were promoted by white quartz sand, Mg2+, and by using urea as a condensation agent. The reactions also proceeded without this mixture; however, the yields increased remarkably with the presence of the above-mentioned materials. The results suggest that a hot/evaporating-drying pool of water containing organics, salts, and reactive phosphorus could be sufficient to form significant phosphate esters.
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16
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The Prebiotic Provenance of Semi-Aqueous Solvents. ORIGINS LIFE EVOL B 2020; 50:1-14. [PMID: 32388697 DOI: 10.1007/s11084-020-09595-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 03/20/2020] [Indexed: 10/24/2022]
Abstract
The numerous and varied roles of phosphorylated organic molecules in biochemistry suggest they may have been important to the origin of life. The prominence of phosphorylated molecules presents a conundrum given that phosphorylation is a thermodynamically unfavorable, endergonic process in water, and most natural sources of phosphate are poorly soluble. We recently demonstrated that a semi-aqueous solvent consisting of urea, ammonium formate, and water (UAFW) supports the dissolution of phosphate and the phosphorylation of nucleosides. However, the prebiotic feasibility and robustness of the UAFW system are unclear. Here, we study the UAFW system as a medium in which phosphate minerals are potentially solubilized. Specifically, we conduct a series of chemical experiments alongside thermodynamic models that simulate the formation of ammonium formate from the hydrolysis of hydrogen cyanide, and demonstrate the stability of formamide in such solvents (as an aqueous mixture). The dissolution of hydroxylapatite requires a liquid medium, and we investigate whether a UAFW system is solid or liquid over varied conditions, finding that this characteristic is controlled by the molar ratios of the three components. For liquid UAFW mixtures, we also find the solubility of phosphate is higher when the quantity of ammonium formate is greater than urea. We suggest the urea within the system can lower the activity of water, help create a stable and persistent solution, and may act as a condensing agent/catalyst to improve nucleoside phosphorylation yields.
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17
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Bartlett S, Wong ML. Defining Lyfe in the Universe: From Three Privileged Functions to Four Pillars. Life (Basel) 2020; 10:E42. [PMID: 32316364 PMCID: PMC7235751 DOI: 10.3390/life10040042] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 01/08/2023] Open
Abstract
Motivated by the need to paint a more general picture of what life is-and could be-with respect to the rest of the phenomena of the universe, we propose a new vocabulary for astrobiological research. Lyfe is defined as any system that fulfills all four processes of the living state, namely: dissipation, autocatalysis, homeostasis, and learning. Life is defined as the instance of lyfe that we are familiar with on Earth, one that uses a specific organometallic molecular toolbox to record information about its environment and achieve dynamical order by dissipating certain planetary disequilibria. This new classification system allows the astrobiological community to more clearly define the questions that propel their research-e.g., whether they are developing a historical narrative to explain the origin of life (on Earth), or a universal narrative for the emergence of lyfe, or whether they are seeking signs of life specifically, or lyfe at large across the universe. While the concept of "life as we don't know it" is not new, the four pillars of lyfe offer a novel perspective on the living state that is indifferent to the particular components that might produce it.
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Affiliation(s)
- Stuart Bartlett
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Michael L. Wong
- Department of Astronomy and Astrobiology Program, University of Washington, Seattle, WA 98195, USA;
- NASA Nexus for Exoplanet System Science’s Virtual Planetary Laboratory, University of Washington, Seattle, WA 98195, USA
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18
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Franco A, Ascenso JR, Ilharco L, Silva JALD. Synthesis of ribonucleotides from the corresponding ribonucleosides under plausible prebiotic conditions within self-assembled supramolecular structures. NEW J CHEM 2020. [DOI: 10.1039/c9nj05601g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abiotic synthesis of ribonucleotides, mainly at the 5′ position, from the corresponding ribonucleosides within guanosine:borate hydrogels in the temperature range of 70–90 °C, using urea and a phosphate source (K2HPO4 or hydroxyapatite).
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Affiliation(s)
- A. Franco
- Centro de Química Estrutural
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisboa
- Portugal
| | - J. R. Ascenso
- Centro de Química Estrutural
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisboa
- Portugal
| | - L. Ilharco
- IBB
- Instituto de Bioengenharia e Biociências
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisboa
| | - J. A. L. da Silva
- Centro de Química Estrutural
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049-001 Lisboa
- Portugal
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19
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Goldford JE, Hartman H, Marsland R, Segrè D. Environmental boundary conditions for the origin of life converge to an organo-sulfur metabolism. Nat Ecol Evol 2019; 3:1715-1724. [PMID: 31712697 PMCID: PMC6881557 DOI: 10.1038/s41559-019-1018-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 09/27/2019] [Indexed: 11/30/2022]
Abstract
It has been suggested that a deep memory of early life is hidden in the architecture of metabolic networks, whose reactions could have been catalyzed by small molecules or minerals before genetically encoded enzymes. A major challenge in unravelling these early steps is assessing the plausibility of a connected, thermodynamically consistent proto-metabolism under different geochemical conditions, which are still surrounded by high uncertainty. Here we combine network-based algorithms with physico-chemical constraints on chemical reaction networks to systematically show how different combinations of parameters (temperature, pH, redox potential and availability of molecular precursors) could have affected the evolution of a proto-metabolism. Our analysis of possible trajectories indicates that a subset of boundary conditions converges to an organo-sulfur-based proto-metabolic network fuelled by a thioester- and redox-driven variant of the reductive tricarboxylic acid cycle that is capable of producing lipids and keto acids. Surprisingly, environmental sources of fixed nitrogen and low-potential electron donors are not necessary for the earliest phases of biochemical evolution. We use one of these networks to build a steady-state dynamical metabolic model of a protocell, and find that different combinations of carbon sources and electron donors can support the continuous production of a minimal ancient 'biomass' composed of putative early biopolymers and fatty acids.
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Affiliation(s)
- Joshua E Goldford
- Bioinformatics Program, Boston University, Boston, MA, USA.
- Department of Chemistry, Boston University, Boston, MA, USA.
- Biological Design Center, Boston University, Boston, MA, USA.
| | - Hyman Hartman
- Earth, Atmosphere and Planetary Science Department, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Daniel Segrè
- Bioinformatics Program, Boston University, Boston, MA, USA.
- Biological Design Center, Boston University, Boston, MA, USA.
- Department of Physics, Boston University, Boston, MA, USA.
- Department of Biomedical Engineering, Department of Biology, Boston University, Boston, MA, USA.
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20
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Affiliation(s)
- Matthew A. Pasek
- School of Geosciences, University of South Florida, 4202 E. Fowler Avenue NES 204, Tampa, Florida 33620, United States
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21
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How Prebiotic Chemistry and Early Life Chose Phosphate. Life (Basel) 2019; 9:life9010026. [PMID: 30832398 PMCID: PMC6462974 DOI: 10.3390/life9010026] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 02/23/2019] [Accepted: 02/25/2019] [Indexed: 12/18/2022] Open
Abstract
The very specific thermodynamic instability and kinetic stability of phosphate esters and anhydrides impart them invaluable properties in living organisms in which highly efficient enzyme catalysts compensate for their low intrinsic reactivity. Considering their role in protein biosynthesis, these properties raise a paradox about early stages: How could these species be selected in the absence of enzymes? This review is aimed at demonstrating that considering mixed anhydrides or other species more reactive than esters and anhydrides can help in solving the paradox. The consequences of this approach for chemical evolution and early stages of life are analysed.
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22
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Pasek M. A role for phosphorus redox in emerging and modern biochemistry. Curr Opin Chem Biol 2018; 49:53-58. [PMID: 30316126 DOI: 10.1016/j.cbpa.2018.09.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/12/2018] [Accepted: 09/21/2018] [Indexed: 11/28/2022]
Abstract
Phosphorus is a major biogeochemical element controlling growth in many ecosystems. It has presumably been an important element since the onset of life. In most chemical and biochemical considerations, phosphorus is synonymous with phosphates, a pentavalent oxidation state that includes the phosphate backbone of DNA and RNA, as well as major metabolites such as ATP. However, redox processing of phosphates to phosphites and phosphonates, and to even lower oxidation states provides a work-around to many of the problems of prebiotic chemistry, including phosphorus's low solubility and poor reactivity. In addition, modern phosphorus cycling has increasingly identified reduced P compounds as playing a role, sometimes significant, in biogeochemical processes. This suggests that phosphorus is not redox-insensitive and reduced P compounds should be considered as part of the phosphorus biogeochemical cycle.
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Affiliation(s)
- Matthew Pasek
- University of South Florida, School of Geosciences, 4202 E Fowler Ave, NES 204, Tampa, FL, 3360, USA.
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23
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Turner AM, Bergantini A, Abplanalp MJ, Zhu C, Góbi S, Sun BJ, Chao KH, Chang AHH, Meinert C, Kaiser RI. An interstellar synthesis of phosphorus oxoacids. Nat Commun 2018; 9:3851. [PMID: 30242164 PMCID: PMC6155066 DOI: 10.1038/s41467-018-06415-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 08/29/2018] [Indexed: 11/09/2022] Open
Abstract
Phosphorus signifies an essential element in molecular biology, yet given the limited solubility of phosphates on early Earth, alternative sources like meteoritic phosphides have been proposed to incorporate phosphorus into biomolecules under prebiotic terrestrial conditions. Here, we report on a previously overlooked source of prebiotic phosphorus from interstellar phosphine (PH3) that produces key phosphorus oxoacids-phosphoric acid (H3PO4), phosphonic acid (H3PO3), and pyrophosphoric acid (H4P2O7)-in interstellar analog ices exposed to ionizing radiation at temperatures as low as 5 K. Since the processed material of molecular clouds eventually enters circumstellar disks and is partially incorporated into planetesimals like proto Earth, an understanding of the facile synthesis of oxoacids is essential to untangle the origin of water-soluble prebiotic phosphorus compounds and how they might have been incorporated into organisms not only on Earth, but potentially in our universe as well.
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Affiliation(s)
- Andrew M Turner
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
- W.M. Keck Laboratory in Astrochemistry, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Alexandre Bergantini
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
- W.M. Keck Laboratory in Astrochemistry, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Matthew J Abplanalp
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
- W.M. Keck Laboratory in Astrochemistry, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Cheng Zhu
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
- W.M. Keck Laboratory in Astrochemistry, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Sándor Góbi
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
- W.M. Keck Laboratory in Astrochemistry, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Bing-Jian Sun
- Department of Chemistry, National Dong Hwa University, Shoufeng, 974, Hualien, Taiwan
| | - Kang-Heng Chao
- Department of Chemistry, National Dong Hwa University, Shoufeng, 974, Hualien, Taiwan
| | - Agnes H H Chang
- Department of Chemistry, National Dong Hwa University, Shoufeng, 974, Hualien, Taiwan
| | - Cornelia Meinert
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, Nice, France
| | - Ralf I Kaiser
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI, 96822, USA.
- W.M. Keck Laboratory in Astrochemistry, University of Hawaii at Manoa, Honolulu, HI, 96822, USA.
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24
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Shi D, Caldovic L, Tuchman M. Sources and Fates of Carbamyl Phosphate: A Labile Energy-Rich Molecule with Multiple Facets. BIOLOGY 2018; 7:biology7020034. [PMID: 29895729 PMCID: PMC6022934 DOI: 10.3390/biology7020034] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/25/2018] [Accepted: 06/07/2018] [Indexed: 11/16/2022]
Abstract
Carbamyl phosphate (CP) is well-known as an essential intermediate of pyrimidine and arginine/urea biosynthesis. Chemically, CP can be easily synthesized from dihydrogen phosphate and cyanate. Enzymatically, CP can be synthesized using three different classes of enzymes: (1) ATP-grasp fold protein based carbamyl phosphate synthetase (CPS); (2) Amino-acid kinase fold carbamate kinase (CK)-like CPS (anabolic CK or aCK); and (3) Catabolic transcarbamylase. The first class of CPS can be further divided into three different types of CPS as CPS I, CPS II, and CPS III depending on the usage of ammonium or glutamine as its nitrogen source, and whether N-acetyl-glutamate is its essential co-factor. CP can donate its carbamyl group to the amino nitrogen of many important molecules including the most well-known ornithine and aspartate in the arginine/urea and pyrimidine biosynthetic pathways. CP can also donate its carbamyl group to the hydroxyl oxygen of a variety of molecules, particularly in many antibiotic biosynthetic pathways. Transfer of the carbamyl group to the nitrogen group is catalyzed by the anabolic transcarbamylase using a direct attack mechanism, while transfer of the carbamyl group to the oxygen group is catalyzed by a different class of enzymes, CmcH/NodU CTase, using a different mechanism involving a three-step reaction, decomposition of CP to carbamate and phosphate, transfer of the carbamyl group from carbamate to ATP to form carbamyladenylate and pyrophosphate, and transfer of the carbamyl group from carbamyladenylate to the oxygen group of the substrate. CP is also involved in transferring its phosphate group to ADP to generate ATP in the fermentation of many microorganisms. The reaction is catalyzed by carbamate kinase, which may be termed as catabolic CK (cCK) in order to distinguish it from CP generating CK. CP is a thermally labile molecule, easily decomposed into phosphate and cyanate, or phosphate and carbamate depending on the pH of the solution, or the presence of enzyme. Biological systems have developed several mechanisms including channeling between enzymes, increased affinity of CP to enzymes, and keeping CP in a specific conformation to protect CP from decomposition. CP is highly important for our health as both a lack of, or decreased, CP production and CP accumulation results in many disease conditions.
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Affiliation(s)
- Dashuang Shi
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA.
- Department of Genomics and Precision Medicine, The George Washington University, Washington, DC 20010, USA.
| | - Ljubica Caldovic
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA.
- Department of Genomics and Precision Medicine, The George Washington University, Washington, DC 20010, USA.
| | - Mendel Tuchman
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC 20010, USA.
- Department of Genomics and Precision Medicine, The George Washington University, Washington, DC 20010, USA.
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25
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Wang L, Yan J, Wise MJ, Liu Q, Asenso J, Huang Y, Dai S, Liu Z, Du Y, Tang D. Distribution Patterns of Polyphosphate Metabolism Pathway and Its Relationships With Bacterial Durability and Virulence. Front Microbiol 2018; 9:782. [PMID: 29755430 PMCID: PMC5932413 DOI: 10.3389/fmicb.2018.00782] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 04/06/2018] [Indexed: 12/15/2022] Open
Abstract
Inorganic polyphosphate (polyP) is a linear polymer of orthophosphate residues. It is reported to be present in all life forms. Experimental studies showed that polyP plays important roles in bacterial durability and virulence. Here we investigated the relationships of polyP with bacterial durability and virulence theoretically. Bacterial lifestyle, environmental persistence, virulence factors (VFs), and species evolution are all included in the analysis. The presence of seven genes involved in polyP metabolism (ppk1, ppk2, pap, surE, gppA, ppnK, and ppgK) and 2595 core VFs were verified in 944 bacterial reference proteomes for distribution patterns via HMMER. Proteome size and VFs were compared in terms of gain and loss of polyP pathway. Literature mining and phylogenetic analysis were recruited to support the study. Our analyzes revealed that the presence of polyP metabolism is positively correlated with bacterial proteome size and the number of virulence genes. A potential relationship of polyP in bacterial lifestyle and environmental durability is suggested. Evolutionary analysis shows that polyP genes are randomly lost along the phylogenetic tree. In sum, based on our theoretical analysis, we confirmed that bacteria with polyP metabolism are associated with high environmental durability and more VFs.
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Affiliation(s)
- Liang Wang
- Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, China
| | - Jiawei Yan
- Xuzhou Infectious Diseases Hospital, Xuzhou, China
| | - Michael J Wise
- School of Computer Science and Software Engineering, University of Western Australia, Perth, WA, Australia.,The Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Perth, WA, Australia
| | - Qinghua Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - James Asenso
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Yue Huang
- Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, China
| | - Shiyun Dai
- School of Anesthesiology, Xuzhou Medical University, Xuzhou, China
| | | | - Yan Du
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Daoquan Tang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China.,Center for Experimental Animals, Xuzhou Medical University, Xuzhou, China
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26
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Potential Role of Inorganic Confined Environments in Prebiotic Phosphorylation. Life (Basel) 2018; 8:life8010007. [PMID: 29510574 PMCID: PMC5871939 DOI: 10.3390/life8010007] [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: 11/06/2017] [Revised: 01/25/2018] [Accepted: 02/28/2018] [Indexed: 01/19/2023] Open
Abstract
A concise outlook on the potential role of confinement in phosphorylation and phosphate condensation pertaining to prebiotic chemistry is presented. Inorganic confinement is a relatively uncharted domain in studies concerning prebiotic chemistry, and even more so in terms of experimentation. However, molecular crowding within confined dimensions is central to the functioning of contemporary biology. There are numerous advantages to confined environments and an attempt to highlight this fact, within this article, has been undertaken, keeping in context the limitations of aqueous phase chemistry in phosphorylation and, to a certain extent, traditional approaches in prebiotic chemistry.
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27
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Karki M, Gibard C, Bhowmik S, Krishnamurthy R. Nitrogenous Derivatives of Phosphorus and the Origins of Life: Plausible Prebiotic Phosphorylating Agents in Water. Life (Basel) 2017; 7:E32. [PMID: 28758921 PMCID: PMC5617957 DOI: 10.3390/life7030032] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 07/27/2017] [Accepted: 07/27/2017] [Indexed: 12/02/2022] Open
Abstract
Phosphorylation under plausible prebiotic conditions continues to be one of the defining issues for the role of phosphorus in the origins of life processes. In this review, we cover the reactions of alternative forms of phosphate, specifically the nitrogenous versions of phosphate (and other forms of reduced phosphorus species) from a prebiotic, synthetic organic and biochemistry perspective. The ease with which such amidophosphates or phosphoramidate derivatives phosphorylate a wide variety of substrates suggests that alternative forms of phosphate could have played a role in overcoming the "phosphorylation in water problem". We submit that serious consideration should be given to the search for primordial sources of nitrogenous versions of phosphate and other versions of phosphorus.
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Affiliation(s)
- Megha Karki
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 USA.
| | - Clémentine Gibard
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 USA.
| | - Subhendu Bhowmik
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 USA.
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 USA.
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28
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Fernández-García C, Coggins AJ, Powner MW. A Chemist's Perspective on the Role of Phosphorus at the Origins of Life. Life (Basel) 2017; 7:E31. [PMID: 28703763 PMCID: PMC5617956 DOI: 10.3390/life7030031] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 07/06/2017] [Accepted: 07/11/2017] [Indexed: 11/17/2022] Open
Abstract
The central role that phosphates play in biological systems, suggests they also played an important role in the emergence of life on Earth. In recent years, numerous important advances have been made towards understanding the influence that phosphates may have had on prebiotic chemistry, and here, we highlight two important aspects of prebiotic phosphate chemistry. Firstly, we discuss prebiotic phosphorylation reactions; we specifically contrast aqueous electrophilic phosphorylation, and aqueous nucleophilic phosphorylation strategies, with dry-state phosphorylations that are mediated by dissociative phosphoryl-transfer. Secondly, we discuss the non-structural roles that phosphates can play in prebiotic chemistry. Here, we focus on the mechanisms by which phosphate has guided prebiotic reactivity through catalysis or buffering effects, to facilitating selective transformations in neutral water. Several prebiotic routes towards the synthesis of nucleotides, amino acids, and core metabolites, that have been facilitated or controlled by phosphate acting as a general acid-base catalyst, pH buffer, or a chemical buffer, are outlined. These facile and subtle mechanisms for incorporation and exploitation of phosphates to orchestrate selective, robust prebiotic chemistry, coupled with the central and universally conserved roles of phosphates in biochemistry, provide an increasingly clear message that understanding phosphate chemistry will be a key element in elucidating the origins of life on Earth.
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29
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Has Inositol Played Any Role in the Origin of Life? Life (Basel) 2017; 7:life7020024. [PMID: 28587245 PMCID: PMC5492146 DOI: 10.3390/life7020024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 05/26/2017] [Accepted: 06/02/2017] [Indexed: 12/11/2022] Open
Abstract
Phosphorus, as phosphate, plays a paramount role in biology. Since phosphate transfer reactions are an integral part of contemporary life, phosphate may have been incorporated into the initial molecules at the very beginning. To facilitate the studies into early phosphate utilization, we should look retrospectively to phosphate-rich molecules present in today’s cells. Overlooked by origin of life studies until now, inositol and the inositol phosphates, of which some species possess more phosphate groups that carbon atoms, represent ideal molecules to consider in this context. The current sophisticated association of inositol with phosphate, and the roles that some inositol phosphates play in regulating cellular phosphate homeostasis, intriguingly suggest that inositol might have played some role in the prebiotic process of phosphate exploitation. Inositol can be synthesized abiotically and, unlike glucose or ribose, is chemically stable. This stability makes inositol the ideal candidate for the earliest organophosphate molecules, as primitive inositol phosphates. I also present arguments suggesting roles for some inositol phosphates in early chemical evolution events. Finally, the possible prebiotic synthesis of inositol pyrophosphates could have generated high-energy molecules to be utilized in primitive trans-phosphorylating processes.
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30
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Zambrano J, Marchand P, Swenson NG. Local neighbourhood and regional climatic contexts interact to explain tree performance. Proc Biol Sci 2017; 284:20170523. [PMID: 28566487 PMCID: PMC5454270 DOI: 10.1098/rspb.2017.0523] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/03/2017] [Indexed: 11/12/2022] Open
Abstract
Tree neighbourhood modelling has significantly contributed to our understanding of the mechanisms structuring communities. Investigations into the impact of neighbouring crowding on tree performance have generally been conducted at local scales, missing important regional-scale context such as the suitability of the climate for each species. Favourable climates may enhance tree performance, but this may come at the cost of increased neighbourhood crowding and competition negatively impacting survival and growth. Through the synthesis of continental-scale forest inventory and trait datasets from the northeast USA and Puerto Rico we present an analytical approach that elucidates the important interactions between local competitive and regional climatic contexts. Our results show strong asymmetries in competitive interactions and significant niche differences that are dependent on habitat suitability. The strong interaction between local neighbourhood and regional climate highlights the need for models that consider the interaction between these two processes that have been previously ignored.
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Affiliation(s)
- Jenny Zambrano
- National Socio-Environmental Synthesis Center (SESYNC), Annapolis, MD 21401, USA
| | - Philippe Marchand
- National Socio-Environmental Synthesis Center (SESYNC), Annapolis, MD 21401, USA
| | - Nathan G Swenson
- Department of Biology, University of Maryland, College Park, MD 20742, USA
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31
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Wang W, Huang F, Sun C, Liu J, Sheng X, Chen D. A theoretical insight into the formation mechanisms of C/N-ribonucleosides with pyrimidine and ribose. Phys Chem Chem Phys 2017; 19:10413-10426. [PMID: 28379245 DOI: 10.1039/c6cp08068e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The detailed formation mechanisms of C-ribonucleoside and N-ribonucleoside via the reaction of 2,4,6-triaminopyrimidine (TAP) with (d)-ribose in aqueous solution were explored using density functional theory (DFT). The calculations indicate that five isomers (α,β-furanose, α,β-pyranose and open-chain aldehyde) of (d)-ribose can exist in equilibrium in aqueous solution. In contrast to cyclic isomers, an open-chain aldehyde is most feasible to react with TAP. In general, the formation pathways of C-nucleoside and N-nucleoside proceed in three steps including nucleophilic addition, dehydration and cyclization. The calculated apparent activation energies are 28.8 kcal mol-1 and 29.2 kcal mol-1, respectively. It suggests that both C- and N-nucleoside can be formed in aqueous solution, which is in good agreement with the experimental results. The water molecule plays an important "H-bridge" role by the hydrogen atom relay. Finally, a model structure of nucleobase, which will be beneficial for the C-C glycosidic bond formation, is proposed.
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Affiliation(s)
- Wenjuan Wang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China.
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32
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Remnants of an Ancient Metabolism without Phosphate. Cell 2017; 168:1126-1134.e9. [PMID: 28262353 DOI: 10.1016/j.cell.2017.02.001] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 12/16/2016] [Accepted: 01/31/2017] [Indexed: 11/23/2022]
Abstract
Phosphate is essential for all living systems, serving as a building block of genetic and metabolic machinery. However, it is unclear how phosphate could have assumed these central roles on primordial Earth, given its poor geochemical accessibility. We used systems biology approaches to explore the alternative hypothesis that a protometabolism could have emerged prior to the incorporation of phosphate. Surprisingly, we identified a cryptic phosphate-independent core metabolism producible from simple prebiotic compounds. This network is predicted to support the biosynthesis of a broad category of key biomolecules. Its enrichment for enzymes utilizing iron-sulfur clusters, and the fact that thermodynamic bottlenecks are more readily overcome by thioester rather than phosphate couplings, suggest that this network may constitute a "metabolic fossil" of an early phosphate-free nonenzymatic biochemistry. Our results corroborate and expand previous proposals that a putative thioester-based metabolism could have predated the incorporation of phosphate and an RNA-based genetic system. PAPERCLIP.
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33
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Coggins AJ, Powner MW. Prebiotic synthesis of phosphoenol pyruvate by α-phosphorylation-controlled triose glycolysis. Nat Chem 2016; 9:310-317. [PMID: 28338685 DOI: 10.1038/nchem.2624] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Accepted: 08/23/2016] [Indexed: 01/28/2023]
Abstract
Phosphoenol pyruvate is the highest-energy phosphate found in living organisms and is one of the most versatile molecules in metabolism. Consequently, it is an essential intermediate in a wide variety of biochemical pathways, including carbon fixation, the shikimate pathway, substrate-level phosphorylation, gluconeogenesis and glycolysis. Triose glycolysis (generation of ATP from glyceraldehyde 3-phosphate via phosphoenol pyruvate) is among the most central and highly conserved pathways in metabolism. Here, we demonstrate the efficient and robust synthesis of phosphoenol pyruvate from prebiotic nucleotide precursors, glycolaldehyde and glyceraldehyde. Furthermore, phosphoenol pyruvate is derived within an α-phosphorylation controlled reaction network that gives access to glyceric acid 2-phosphate, glyceric acid 3-phosphate, phosphoserine and pyruvate. Our results demonstrate that the key components of a core metabolic pathway central to energy transduction and amino acid, sugar, nucleotide and lipid biosyntheses can be reconstituted in high yield under mild, prebiotically plausible conditions.
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Affiliation(s)
- Adam J Coggins
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - Matthew W Powner
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
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34
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Dass AV, Hickman-Lewis K, Brack A, Kee TP, Westall F. Stochastic Prebiotic Chemistry within Realistic Geological Systems. ChemistrySelect 2016. [DOI: 10.1002/slct.201600829] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
| | | | - André Brack
- CNRS Centre de Biophysique Moléculaire; Rue Charles Sadron 45071 Orléans France
| | - Terence P. Kee
- School of Chemistry; University of Leeds; Leeds LS2 9JT UK
| | - Frances Westall
- CNRS Centre de Biophysique Moléculaire; Rue Charles Sadron 45071 Orléans France
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35
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Smith KE, House CH, Dworkin JP, Callahan MP. Spontaneous Oligomerization of Nucleotide Alternatives in Aqueous Solutions. ORIGINS LIFE EVOL B 2016; 47:3-11. [PMID: 27029792 DOI: 10.1007/s11084-016-9484-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 02/23/2016] [Indexed: 11/25/2022]
Abstract
On early Earth, a primitive polymer that could spontaneously form from likely available precursors may have preceded both RNA and DNA as the first genetic material. Here, we report that heated aqueous solutions containing 5-hydroxymethyluracil (HMU) result in oligomers of uracil, heated solutions containing 5-hydroxymethylcytosine (HMC) result in oligomers of cytosine, and heated solutions containing both HMU and HMC result in mixed oligomers of uracil and cytosine. Oligomerization of hydroxymethylated pyrimidines, which may have been abundant on the primitive Earth, might have been important in the development of simple informational polymers.
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Affiliation(s)
- Karen E Smith
- Department of Geosciences and Penn State Astrobiology Research Center, Pennsylvania State University, University Park, PA, 16802, USA
| | - Christopher H House
- Department of Geosciences and Penn State Astrobiology Research Center, Pennsylvania State University, University Park, PA, 16802, USA
| | - Jason P Dworkin
- Solar System Exploration Division and Goddard Center for Astrobiology, National Aeronautics and Space Administration Goddard Space Flight Center, Greenbelt, MD, 20771, USA
| | - Michael P Callahan
- Solar System Exploration Division and Goddard Center for Astrobiology, National Aeronautics and Space Administration Goddard Space Flight Center, Greenbelt, MD, 20771, USA.
- Department of Chemistry and Biochemistry, Boise State University, Boise, ID, 83725, USA.
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36
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Sproul G. Abiogenic Syntheses of Lipoamino Acids and Lipopeptides and their Prebiotic Significance. ORIGINS LIFE EVOL B 2015; 45:427-37. [PMID: 26248658 DOI: 10.1007/s11084-015-9451-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 03/05/2015] [Indexed: 11/30/2022]
Abstract
Researchers have formed peptide bonds under a variety of presumed prebiotic conditions. Here it is proposed that these same conditions would have also formed amide bonds between fatty acids and amino acids, producing phosphate-free amphipathic lipoamino acids and lipopeptides. These compounds are known to form vesicles and are ubiquitous in living organisms. They could represent molecules that provided protection by membranes as well as possibilities for proto-life metabolism . It is here demonstrated that when a fatty acid is heated with various amino acids, optimally in the presence of suitable salts or minerals, lipoamino acids are formed. Magnesium and potassium carbonates as well as iron (II) sulfide are found to be particularly useful in these reactions. In this manner N-lauroylglycine, N-lauroylalanine, N-stearoylalanine and several other lipoamino acids have been synthesized. Similarly, when glycylglycine was heated with lauric acid in the presence of magnesium carbonate, the lipopeptide N-lauroylglycylglycine was formed. Such compounds are proposed to have been critical precursors to the development of life.
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Affiliation(s)
- Gordon Sproul
- University of South Carolina Beaufort, 801 Carteret St, Beaufort, SC, 29902, USA,
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37
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Nucleoside phosphorylation by the mineral schreibersite. Sci Rep 2015; 5:17198. [PMID: 26606901 PMCID: PMC4660433 DOI: 10.1038/srep17198] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 10/27/2015] [Indexed: 11/08/2022] Open
Abstract
Phosphorylation of the nucleosides adenosine and uridine by the simple mixing and
mild heating of aqueous solutions of the organic compounds with synthetic analogs of
the meteoritic mineral schreibersite, (Fe,Ni)3P under slightly basic
conditions (pH ~9) is reported. These results suggest a potential role
for meteoritic phosphorus in the origin and development of early life.
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38
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Pasek M, Herschy B, Kee TP. Phosphorus: a case for mineral-organic reactions in prebiotic chemistry. ORIGINS LIFE EVOL B 2015; 45:207-18. [PMID: 25773584 DOI: 10.1007/s11084-015-9420-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/11/2015] [Indexed: 11/25/2022]
Abstract
The ubiquity of phosphorus (P) in modern biochemistry suggests that P may have participated in prebiotic chemistry prior to the emergence of life. Of the major biogenic elements, phosphorus alone lacks a substantial volatile phase and its ultimate source therefore had to have been a mineral. However, as most native P minerals are chemically un-reactive within the temperature-pressure-pH regimes of contemporary life, it begs the question as to whether the most primitive early living systems on earth had access to a more chemically reactive P-mineral inventory. The meteoritic mineral schreibersite has been proposed as an important source of reactive P on the early earth. The chemistry of schreibersite as a P source is summarized and reviewed here. Recent work has also shown that reduced oxidation state P compounds were present on the early earth; these compounds lend credence to the relevance of schreibersite as a prebiotic mineral. Ultimately, schreibersite will oxidize to phosphate, but several high-energy P intermediates may have provided the reactive material necessary for incorporating P into prebiotic molecules.
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Affiliation(s)
- Matthew Pasek
- School of Geosciences, University of South Florida, 4202 E Fowler Ave, Tampa, FL, 33620, USA,
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39
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Ni F, Fu C, Gao X, Liu Y, Xu P, Liu L, Lv Y, Fu S, Sun Y, Han D, Li Y, Zhao Y. N-phosphoryl amino acid models for P-N bonds in prebiotic chemical evolution. Sci China Chem 2015. [DOI: 10.1007/s11426-015-5321-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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40
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Srivastava P, Abou El Asrar R, Knies C, Abramov M, Froeyen M, Rozenski J, Rosemeyer H, Herdewijn P. Achiral, acyclic nucleic acids: synthesis and biophysical studies of a possible prebiotic polymer. Org Biomol Chem 2015; 13:9249-60. [DOI: 10.1039/c5ob00898k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The search for prebiotic, nucleic acid precursors is, at its best, a speculative undertaking.
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Affiliation(s)
| | | | - C. Knies
- Organic Materials Chemistry and Bioorganic Chemistry
- Institute or Chemistry
- University of Osnabrück
- 49069 Osnabrück
- Germany
| | - M. Abramov
- Medicinal Chemistry
- KU Leuven
- B-3000 Leuven
- Belgium
| | - M. Froeyen
- Medicinal Chemistry
- KU Leuven
- B-3000 Leuven
- Belgium
| | - J. Rozenski
- Medicinal Chemistry
- KU Leuven
- B-3000 Leuven
- Belgium
| | - H. Rosemeyer
- Organic Materials Chemistry and Bioorganic Chemistry
- Institute or Chemistry
- University of Osnabrück
- 49069 Osnabrück
- Germany
| | - P. Herdewijn
- Medicinal Chemistry
- KU Leuven
- B-3000 Leuven
- Belgium
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41
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Cafferty BJ, Hud NV. Abiotic synthesis of RNA in water: a common goal of prebiotic chemistry and bottom-up synthetic biology. Curr Opin Chem Biol 2014; 22:146-57. [PMID: 25438801 DOI: 10.1016/j.cbpa.2014.09.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 09/13/2014] [Indexed: 01/01/2023]
Abstract
For more than half a century chemists have searched for a plausible prebiotic synthesis of RNA. The initial advances of the 1960s and 1970s were followed by decades of measured progress and a growing pessimism about overcoming remaining challenges. Fortunately, the past few years have provided a number of important advances, including new abiotic routes for the synthesis of nucleobases, nucleosides, and nucleotides. Recent discoveries also provide additional support for the hypothesis that RNA is the product of evolution, being preceded by ancestral genetic polymers, or pre-RNAs, that are synthesized more easily than RNA. In some cases, parallel searches for plausible prebiotic routes to RNA and pre-RNAs have provided more than one experimentally verified synthesis of RNA substructures and possible predecessors. Just as the synthesis of a contemporary biological molecule cannot be understood without knowledge of cellular metabolism, it is likely that an integrated approach that takes into account both plausible prebiotic reactions and plausible prebiotic environments will ultimately provide the most satisfactory and unifying chemical scenarios for the origin of nucleic acids. In this context, recent advances towards the abiotic synthesis of RNA and candidates for pre-RNAs are beginning to suggest that some molecules (e.g., urea) were multi-faceted contributors to the origin of nucleic acids, and the origin of life.
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Affiliation(s)
- Brian J Cafferty
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Nicholas V Hud
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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42
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Holm NG. Glasses as sources of condensed phosphates on the early earth. GEOCHEMICAL TRANSACTIONS 2014; 15:8. [PMID: 24959099 PMCID: PMC4057523 DOI: 10.1186/1467-4866-15-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 06/03/2014] [Indexed: 05/30/2023]
Abstract
Procedures for the analysis of phosphorus in geological material normally aims for the determination of the total amount of P expressed as orthophosphate [Formula: see text] or the differentiation between inorganic and organic P. This is probably due to analytical difficulties but also to the prevalent opinion that the chemistry of phosphorus in geological environments is almost entirely restricted to the mineral apatite. Because of the low solubility of apatite it is, therefore, commonly argued that little P was around for prebiotic chemistry and that pre-biological processes would essentially have had to do without this indispensable element unless it was provided by alternative sources or mechanisms (such as reduction and activation by lightning or delivery to Earth by celestial bodies). It is a paradox that the potential existence of reactive phosphorus compounds, such as the mineral schreibersite - iron phosphide, in geological material on Earth is seldom considered although we are aware of the existence of such compounds in meteorite material. The content of Al2O3 in rocks appears to be important for the speciation of phosphorus and for how strongly it binds to silicates. In general, low alumina seems to promote the existence of isolated charge-balanced phosphorus complexes.
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Affiliation(s)
- Nils G Holm
- Department of Geological Sciences, Stockholm University, Stockholm, Sweden
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43
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Hud NV, Cafferty BJ, Krishnamurthy R, Williams LD. The origin of RNA and "my grandfather's axe". ACTA ACUST UNITED AC 2013; 20:466-74. [PMID: 23601635 DOI: 10.1016/j.chembiol.2013.03.012] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 03/20/2013] [Accepted: 03/22/2013] [Indexed: 12/27/2022]
Abstract
The origin of RNA is one of the most formidable problems facing prebiotic chemists. We consider RNA as a product of evolution, as opposed to the more conventional view of RNA as originally being the product of abiotic processes. We have come to accept that life's informational polymers have changed in chemical structure since their emergence, which presents a quandary similar to the paradox of "My Grandfather's Axe". Here, we discuss reasons why all contemporary components of RNA--the nucleobases, ribose, and phosphate--are not likely the original components of the first informational polymer(s) of life. We also evaluate three distinct models put forth as pathways for how the earliest informational polymers might have assembled. We see the quest to uncover the ancestors of RNA as an exciting scientific journey, one that is already providing additional chemical constraints on the origin of life and one that has the potential to produce self-assembling materials, novel catalysis, and bioactive compounds.
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Affiliation(s)
- Nicholas V Hud
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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44
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Toxvaerd S. The role of carbohydrates at the origin of homochirality in biosystems. ORIGINS LIFE EVOL B 2013; 43:391-409. [PMID: 23996458 DOI: 10.1007/s11084-013-9342-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 07/12/2013] [Indexed: 01/18/2023]
Abstract
Pasteur has demonstrated that the chiral components in a racemic mixture can separate in homochiral crystals. But with a strong chiral discrimination the chiral components in a concentrated mixture can also phase separate into homochiral fluid domains, and the isomerization kinetics can then perform a symmetry breaking into one thermodynamical stable homochiral system. Glyceraldehyde has a sufficient chiral discrimination to perform such a symmetry breaking. The requirement of a high concentration of the chiral reactant(s) in an aqueous solution in order to perform and maintain homochirality; the appearance of phosphorylation of almost all carbohydrates in the central machinery of life; the basic ideas that the biochemistry and the glycolysis and gluconeogenesis contain the trace of the biochemical evolution, all point in the direction of that homochirality was obtained just after- or at a phosphorylation of the very first products of the formose reaction, at high concentrations of the reactants in phosphate rich compartments in submarine hydrothermal vents. A racemic solution of D,L-glyceraldehyde-3-phosphate could be the template for obtaining homochiral D-glyceraldehyde-3-phosphate(aq) as well as L-amino acids.
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Affiliation(s)
- Søren Toxvaerd
- DNRF centre "Glass and Time", IMFUFA, Department of Sciences, Roskilde University, Postbox 260, 4000, Roskilde, Denmark,
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45
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Kee TP, Bryant DE, Herschy B, Marriott KER, Cosgrove NE, Pasek MA, Atlas ZD, Cousins CR. Phosphate Activation via Reduced Oxidation State Phosphorus (P). Mild Routes to Condensed-P Energy Currency Molecules. Life (Basel) 2013; 3:386-402. [PMID: 25369812 PMCID: PMC4187178 DOI: 10.3390/life3030386] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 06/08/2013] [Accepted: 06/13/2013] [Indexed: 12/29/2022] Open
Abstract
The emergence of mechanisms for phosphorylating organic and inorganic molecules is a key step en route to the earliest living systems. At the heart of all contemporary biochemical systems reside reactive phosphorus (P) molecules (such as adenosine triphosphate, ATP) as energy currency molecules to drive endergonic metabolic processes and it has been proposed that a predecessor of such molecules could have been pyrophosphate [P2O74−; PPi(V)]. Arguably the most geologically plausible route to PPi(V) is dehydration of orthophosphate, Pi(V), normally a highly endergonic process in the absence of mechanisms for activating Pi(V). One possible solution to this problem recognizes the presence of reactive-P containing mineral phases, such as schreibersite [(Fe,Ni)3P] within meteorites whose abundance on the early Earth would likely have been significant during a putative Hadean-Archean heavy bombardment. Here, we propose that the reduced oxidation state P-oxyacid, H-phosphite [HPO32−; Pi(III)] could have activated Pi(V) towards condensation via the intermediacy of the condensed oxyacid pyrophosphite [H2P2O52−; PPi(III)]. We provide geologically plausible provenance for PPi(III) along with evidence of its ability to activate Pi(V) towards PPi(V) formation under mild conditions (80 °C) in water.
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Affiliation(s)
- Terence P Kee
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
| | - David E Bryant
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
| | - Barry Herschy
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
| | - Katie E R Marriott
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
| | - Nichola E Cosgrove
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
| | - Matthew A Pasek
- Department of Geology, University of South Florida, 4202 East Fowler Ave., SCA 528, Tampa, FL 33620, USA.
| | - Zachary D Atlas
- Department of Geology, University of South Florida, 4202 East Fowler Ave., SCA 528, Tampa, FL 33620, USA.
| | - Claire R Cousins
- Department of Earth and Planetary Science, Birkbeck College, University of London, Gower Street, London, WC1E 6BT, UK.
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46
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Evidence for reactive reduced phosphorus species in the early Archean ocean. Proc Natl Acad Sci U S A 2013; 110:10089-94. [PMID: 23733935 DOI: 10.1073/pnas.1303904110] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It has been hypothesized that before the emergence of modern DNA-RNA-protein life, biology evolved from an "RNA world." However, synthesizing RNA and other organophosphates under plausible early Earth conditions has proved difficult, with the incorporation of phosphorus (P) causing a particular problem because phosphate, where most environmental P resides, is relatively insoluble and unreactive. Recently, it has been proposed that during the Hadean-Archean heavy bombardment by extraterrestrial impactors, meteorites would have provided reactive P in the form of the iron-nickel phosphide mineral schreibersite. This reacts in water, releasing soluble and reactive reduced P species, such as phosphite, that could then be readily incorporated into prebiotic molecules. Here, we report the occurrence of phosphite in early Archean marine carbonates at levels indicating that this was an abundant dissolved species in the ocean before 3.5 Ga. Additionally, we show that schreibersite readily reacts with an aqueous solution of glycerol to generate phosphite and the membrane biomolecule glycerol-phosphate under mild thermal conditions, with this synthesis using a mineral source of P. Phosphite derived from schreibersite was, hence, a plausible reagent in the prebiotic synthesis of phosphorylated biomolecules and was also present on the early Earth in quantities large enough to have affected the redox state of P in the ocean. Phosphorylated biomolecules like RNA may, thus, have first formed from the reaction of reduced P species with the prebiotic organic milieu on the early Earth.
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47
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Dick CF, Dos-Santos ALA, Majerowicz D, Paes LS, Giarola NL, Gondim KC, Vieyra A, Meyer-Fernandes JR. Inorganic phosphate uptake in Trypanosoma cruzi is coupled to K(+) cycling and to active Na(+) extrusion. Biochim Biophys Acta Gen Subj 2013; 1830:4265-73. [PMID: 23643965 DOI: 10.1016/j.bbagen.2013.04.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 03/30/2013] [Accepted: 04/26/2013] [Indexed: 02/07/2023]
Abstract
BACKGROUND Orthophosphate (Pi) is a central compound in the metabolism of all organisms, including parasites. There are no reports regarding the mechanisms of Pi acquisition by Trypanosoma cruzi. METHODS (32)Pi influx was measured in T. cruzi epimastigotes. The expression of Pi transporter genes and the coupling of the uptake to Na(+), H(+) and K(+) fluxes were also investigated. The transport capacities of different evolutive forms were compared. RESULTS Epimastigotes grew significantly more slowly in 2mM than in 50mM Pi. Influx of Pi into parasites grown under low Pi conditions took place in the absence and presence of Na(+). We found that the parasites express TcPho84, a H(+):Pi-symporter, and TcPho89, a Na(+):Pi-symporter. Both Pi influx mechanisms showed Michaelis-Menten kinetics, with a one-order of magnitude higher affinity for the Na(+)-dependent system. Collapsing the membrane potential with carbonylcyanide-p-trifluoromethoxyphenylhydrazone strongly impaired the influx of Pi. Valinomycin (K(+) ionophore) or SCH28028 (inhibitor of (H(+)+K(+))ATPase) significantly inhibited Pi uptake, indicating that an inwardly-directed H(+) gradient energizes uphill Pi entry and that K(+) recycling plays a key role in Pi influx. Furosemide, an inhibitor of the ouabain-insensitive Na(+)-ATPase, decreased only the Na(+)-dependent Pi uptake, indicating that this Na(+) pump generates the Na(+) gradient utilized by the symporter. Trypomastigote forms take up Pi inefficiently. CONCLUSIONS Pi starvation stimulates membrane potential-sensitive Pi uptake through different pathways coupled to Na(+) or H(+)/K(+) fluxes. GENERAL SIGNIFICANCE This study unravels the mechanisms of Pi acquisition by T. cruzi, a key process in epimastigote development and differentiation to trypomastigote forms.
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Affiliation(s)
- C F Dick
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Cleaves HJ, Michalkova Scott A, Hill FC, Leszczynski J, Sahai N, Hazen R. Mineral-organic interfacial processes: potential roles in the origins of life. Chem Soc Rev 2012; 41:5502-25. [PMID: 22743683 DOI: 10.1039/c2cs35112a] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Life is believed to have originated on Earth ∼4.4-3.5 Ga ago, via processes in which organic compounds supplied by the environment self-organized, in some geochemical environmental niches, into systems capable of replication with hereditary mutation. This process is generally supposed to have occurred in an aqueous environment and, likely, in the presence of minerals. Mineral surfaces present rich opportunities for heterogeneous catalysis and concentration which may have significantly altered and directed the process of prebiotic organic complexification leading to life. We review here general concepts in prebiotic mineral-organic interfacial processes, as well as recent advances in the study of mineral surface-organic interactions of potential relevance to understanding the origin of life.
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Affiliation(s)
- H James Cleaves
- Blue Marble Space Institute of Science, Washington, DC 20016, USA
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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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New insight into the transcarbamylase family: the structure of putrescine transcarbamylase, a key catalyst for fermentative utilization of agmatine. PLoS One 2012; 7:e31528. [PMID: 22363663 PMCID: PMC3282769 DOI: 10.1371/journal.pone.0031528] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 01/09/2012] [Indexed: 02/05/2023] Open
Abstract
Transcarbamylases reversibly transfer a carbamyl group from carbamylphosphate (CP) to an amine. Although aspartate transcarbamylase and ornithine transcarbamylase (OTC) are well characterized, little was known about putrescine transcarbamylase (PTC), the enzyme that generates CP for ATP production in the fermentative catabolism of agmatine. We demonstrate that PTC (from Enterococcus faecalis), in addition to using putrescine, can utilize L-ornithine as a poor substrate. Crystal structures at 2.5 Å and 2.0 Å resolutions of PTC bound to its respective bisubstrate analog inhibitors for putrescine and ornithine use, N-(phosphonoacetyl)-putrescine and δ-N-(phosphonoacetyl)-L-ornithine, shed light on PTC preference for putrescine. Except for a highly prominent C-terminal helix that projects away and embraces an adjacent subunit, PTC closely resembles OTCs, suggesting recent divergence of the two enzymes. Since differences between the respective 230 and SMG loops of PTC and OTC appeared to account for the differential preference of these enzymes for putrescine and ornithine, we engineered the 230-loop of PTC to make it to resemble the SMG loop of OTCs, increasing the activity with ornithine and greatly decreasing the activity with putrescine. We also examined the role of the C-terminal helix that appears a constant and exclusive PTC trait. The enzyme lacking this helix remained active but the PTC trimer stability appeared decreased, since some of the enzyme eluted as monomers from a gel filtration column. In addition, truncated PTC tended to aggregate to hexamers, as shown both chromatographically and by X-ray crystallography. Therefore, the extra C-terminal helix plays a dual role: it stabilizes the PTC trimer and, by shielding helix 1 of an adjacent subunit, it prevents the supratrimeric oligomerizations of obscure significance observed with some OTCs. Guided by the structural data we identify signature traits that permit easy and unambiguous annotation of PTC sequences.
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