1
|
Gonçalves D. Rethinking life and predicting its origin. Theory Biosci 2024; 143:205-215. [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] [MESH Headings] [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.
Collapse
Affiliation(s)
- Diogo Gonçalves
- Centro de Química Estrutural and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, University of Lisbon, 1049-001, Lisbon, Portugal.
| |
Collapse
|
2
|
Hyde AS, House CH. Prebiotic thiol-catalyzed thioamide bond formation. GEOCHEMICAL TRANSACTIONS 2024; 25:5. [PMID: 39098875 PMCID: PMC11299287 DOI: 10.1186/s12932-024-00088-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 06/20/2024] [Indexed: 08/06/2024]
Abstract
Thioamide bonds are important intermediates in prebiotic chemistry. In cyanosulfidic prebiotic chemistry, they serve as crucial intermediates in the pathways that lead to the formation of many important biomolecules (e.g., amino acids). They can also serve as purine and pyrimidine precursors, the two classes of heterocycle employed in genetic molecules. Despite their importance, the formation of thioamide bonds from nitriles under prebiotic conditions has required large excesses of sulfide or compounds with unknown prebiotic sources. Here, we describe the thiol-catalyzed formation of thioamide bonds from nitriles. We show that the formation of the simplest of these compounds, thioformamide, forms readily in spark-discharge experiments from hydrogen cyanide, sulfide, and a methanethiol catalyst, suggesting potential accumulation on early Earth. Lastly, we demonstrate that thioformamide has a Gibbs energy of hydrolysis ( Δ G r ∘ ) comparable to other energy-currencies on early Earth such as pyrophosphate and thioester bonds. Overall, our findings imply that thioamides might have been abundant on early Earth and served a variety of functions during chemical evolution.
Collapse
Affiliation(s)
- Andrew S Hyde
- Department of Geosciences and Earth and Environmental Systems Institute, The Pennsylvania State University, University Park, 16802, PA, USA.
| | - Christopher H House
- Department of Geosciences and Earth and Environmental Systems Institute, The Pennsylvania State University, University Park, 16802, PA, USA
| |
Collapse
|
3
|
Lingam M, Nichols R, Balbi A. A Bayesian Analysis of the Probability of the Origin of Life Per Site Conducive to Abiogenesis. ASTROBIOLOGY 2024; 24:813-823. [PMID: 39159441 DOI: 10.1089/ast.2024.0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
The emergence of life from nonlife, or abiogenesis, remains a fundamental question in scientific inquiry. In this article, we investigate the probability of the origin of life (per conducive site) by leveraging insights from Earth's environments. If life originated endogenously on Earth, its existence is indeed endowed with informative value, although the interpretation of the attendant significance hinges critically upon prior assumptions. By adopting a Bayesian framework, for an agnostic prior, we establish a direct connection between the number of potential locations for abiogenesis on Earth and the probability of life's emergence per site. Our findings suggest that constraints on the availability of suitable environments for the origin(s) of life on Earth may offer valuable insights into the probability of abiogenesis and the frequency of life in the universe.
Collapse
Affiliation(s)
- Manasvi Lingam
- Department of Aerospace, Physics and Space Sciences, Florida Institute of Technology, Melbourne, Florida, USA
- Department of Physics, The University of Texas at Austin, Austin, Texas, USA
| | - Ruth Nichols
- Department of Aerospace, Physics and Space Sciences, Florida Institute of Technology, Melbourne, Florida, USA
| | - Amedeo Balbi
- Dipartimento di Fisica, Università di Roma "Tor Vergata," Roma, Italy
| |
Collapse
|
4
|
Malaterre C. Is Life Binary or Gradual? Life (Basel) 2024; 14:564. [PMID: 38792586 PMCID: PMC11121977 DOI: 10.3390/life14050564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/15/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
The binary nature of life is deeply ingrained in daily experiences, evident in the stark distinctions between life and death and the living and the inert. While this binary perspective aligns with disciplines like medicine and much of biology, uncertainties emerge in fields such as microbiology, virology, synthetic biology, and systems chemistry, where intermediate entities challenge straightforward classification as living or non-living. This contribution explores the motivations behind both binary and non-binary conceptualizations of life. Despite the perceived necessity to unequivocally define life, especially in the context of origin of life research and astrobiology, mounting evidence indicates a gray area between what is intuitively clearly alive and what is distinctly not alive. This prompts consideration of a gradualist perspective, depicting life as a spectrum with varying degrees of "lifeness". Given the current state of science, the existence or not of a definite threshold remains open. Nevertheless, shifts in epistemic granularity and epistemic perspective influence the framing of the question, and scientific advancements narrow down possible answers: if a threshold exists, it can only be at a finer level than what is intuitively taken as living or non-living. This underscores the need for a more refined distinction between the inanimate and the living.
Collapse
Affiliation(s)
- Christophe Malaterre
- Département de Philosophie, Université du Québec à Montréal, Montreal, QC H3C 3P8, Canada;
- Centre Interuniversitaire de Recherche sur la Science et la Technologie (CIRST), Montreal, QC H3C 3P8, Canada
| |
Collapse
|
5
|
Rimmer PB, Shorttle O. A Surface Hydrothermal Source of Nitriles and Isonitriles. Life (Basel) 2024; 14:498. [PMID: 38672768 PMCID: PMC11051382 DOI: 10.3390/life14040498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/22/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024] Open
Abstract
Giant impacts can generate transient hydrogen-rich atmospheres, reducing atmospheric carbon. The reduced carbon will form hazes that rain out onto the surface and can become incorporated into the crust. Once heated, a large fraction of the carbon is converted into graphite. The result is that local regions of the Hadean crust were plausibly saturated with graphite. We explore the consequences of such a crust for a prebiotic surface hydrothermal vent scenario. We model a surface vent fed by nitrogen-rich volcanic gas from high-temperature magmas passing through graphite-saturated crust. We consider this occurring at pressures of 1-1000bar and temperatures of 1500-1700 ∘C. The equilibrium with graphite purifies the leftover gas, resulting in substantial quantities of nitriles (0.1% HCN and 1ppm HC3N) and isonitriles (0.01% HNC) relevant for prebiotic chemistry. We use these results to predict gas-phase concentrations of methyl isocyanide of ∼1 ppm. Methyl isocyanide can participate in the non-enzymatic activation and ligation of the monomeric building blocks of life, and surface or shallow hydrothermal environments provide its only known equilibrium geochemical source.
Collapse
Affiliation(s)
- Paul B. Rimmer
- Cavendish Laboratory, University of Cambridge, JJ Thomson Ave, Cambridge CB3 0HE, UK
| | - Oliver Shorttle
- Institute of Astronomy, University of Cambridge, Cambridge CB3 0HA, UK
- Department of Earth Sciences, University of Cambridge, Cambridge CB2 3EQ, UK
| |
Collapse
|
6
|
Maguire OR, Smokers IBA, Oosterom BG, Zheliezniak A, Huck WTS. A Prebiotic Precursor to Life's Phosphate Transfer System with an ATP Analog and Histidyl Peptide Organocatalysts. J Am Chem Soc 2024; 146:7839-7849. [PMID: 38448161 PMCID: PMC10958518 DOI: 10.1021/jacs.4c01156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/08/2024]
Abstract
Biochemistry is dependent upon enzyme catalysts accelerating key reactions. At the origin of life, prebiotic chemistry must have incorporated catalytic reactions. While this would have yielded much needed amplification of certain reaction products, it would come at the possible cost of rapidly depleting the high energy molecules that acted as chemical fuels. Biochemistry solves this problem by combining kinetically stable and thermodynamically activated molecules (e.g., ATP) with enzyme catalysts. Here, we demonstrate a prebiotic phosphate transfer system involving an ATP analog (imidazole phosphate) and histidyl peptides, which function as organocatalytic enzyme analogs. We demonstrate that histidyl peptides catalyze phosphorylations via a phosphorylated histidyl intermediate. We integrate these histidyl-catalyzed phosphorylations into a complete prebiotic scenario whereby inorganic phosphate is incorporated into organic compounds though physicochemical wet-dry cycles. Our work demonstrates a plausible system for the catalyzed production of phosphorylated compounds on the early Earth and how organocatalytic peptides, as enzyme precursors, could have played an important role in this.
Collapse
Affiliation(s)
- Oliver R. Maguire
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen AJ 6525, The Netherlands
| | - Iris B. A. Smokers
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen AJ 6525, The Netherlands
| | - Bob G. Oosterom
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen AJ 6525, The Netherlands
| | - Alla Zheliezniak
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen AJ 6525, The Netherlands
| | - Wilhelm T. S. Huck
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen AJ 6525, The Netherlands
| |
Collapse
|
7
|
Brunk CF, Marshall CR. Opinion: The Key Steps in the Origin of Life to the Formation of the Eukaryotic Cell. Life (Basel) 2024; 14:226. [PMID: 38398735 PMCID: PMC10890422 DOI: 10.3390/life14020226] [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: 11/02/2023] [Revised: 01/16/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
The path from life's origin to the emergence of the eukaryotic cell was long and complex, and as such it is rarely treated in one publication. Here, we offer a sketch of this path, recognizing that there are points of disagreement and that many transitions are still shrouded in mystery. We assume life developed within microchambers of an alkaline hydrothermal vent system. Initial simple reactions were built into more sophisticated reflexively autocatalytic food-generated networks (RAFs), laying the foundation for life's anastomosing metabolism, and eventually for the origin of RNA, which functioned as a genetic repository and as a catalyst (ribozymes). Eventually, protein synthesis developed, leading to life's biology becoming dominated by enzymes and not ribozymes. Subsequent enzymatic innovation included ATP synthase, which generates ATP, fueled by the proton gradient between the alkaline vent flux and the acidic sea. This gradient was later internalized via the evolution of the electron transport chain, a preadaptation for the subsequent emergence of the vent creatures from their microchamber cradles. Differences between bacteria and archaea suggests cellularization evolved at least twice. Later, the bacterial development of oxidative phosphorylation and the archaeal development of proteins to stabilize its DNA laid the foundation for the merger that led to the formation of eukaryotic cells.
Collapse
Affiliation(s)
- Clifford F. Brunk
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095-1606, USA
| | - Charles R. Marshall
- Department of Integrative Biology and Museum of Paleontology, University of California, Berkeley, CA 94720-4780, USA
| |
Collapse
|
8
|
Schoenmakers LLJ, Reydon TAC, Kirschning A. Evolution at the Origins of Life? Life (Basel) 2024; 14:175. [PMID: 38398684 PMCID: PMC10890241 DOI: 10.3390/life14020175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
The role of evolutionary theory at the origin of life is an extensively debated topic. The origin and early development of life is usually separated into a prebiotic phase and a protocellular phase, ultimately leading to the Last Universal Common Ancestor. Most likely, the Last Universal Common Ancestor was subject to Darwinian evolution, but the question remains to what extent Darwinian evolution applies to the prebiotic and protocellular phases. In this review, we reflect on the current status of evolutionary theory in origins of life research by bringing together philosophy of science, evolutionary biology, and empirical research in the origins field. We explore the various ways in which evolutionary theory has been extended beyond biology; we look at how these extensions apply to the prebiotic development of (proto)metabolism; and we investigate how the terminology from evolutionary theory is currently being employed in state-of-the-art origins of life research. In doing so, we identify some of the current obstacles to an evolutionary account of the origins of life, as well as open up new avenues of research.
Collapse
Affiliation(s)
- Ludo L. J. Schoenmakers
- Konrad Lorenz Institute for Evolution and Cognition Research (KLI), 3400 Klosterneuburg, Austria
| | - Thomas A. C. Reydon
- Institute of Philosophy, Centre for Ethics and Law in the Life Sciences (CELLS), Leibniz University Hannover, 30159 Hannover, Germany;
| | - Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, 30167 Hannover, Germany;
| |
Collapse
|
9
|
Qiu L, Cooks RG. Oxazolone mediated peptide chain extension and homochirality in aqueous microdroplets. Proc Natl Acad Sci U S A 2024; 121:e2309360120. [PMID: 38165938 PMCID: PMC10786291 DOI: 10.1073/pnas.2309360120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 11/20/2023] [Indexed: 01/04/2024] Open
Abstract
Peptide formation from amino acids is thermodynamically unfavorable but a recent study provided evidence that the reaction occurs at the air/solution interfaces of aqueous microdroplets. Here, we show that i) the suggested amino acid complex in microdroplets undergoes dehydration to form oxazolone; ii) addition of water to oxazolone forms the dipeptide; and iii) reaction of oxazolone with other amino acids forms tripeptides. Furthermore, the chirality of the reacting amino acids is preserved in the oxazolone product, and strong chiral selectivity is observed when converting the oxazolone to tripeptide. This last fact ensures that optically impure amino acids will undergo chain extension to generate pure homochiral peptides. Peptide formation in bulk by wet-dry cycling shares a common pathway with the microdroplet reaction, both involving the oxazolone intermediate.
Collapse
Affiliation(s)
- Lingqi Qiu
- Department of Chemistry, Purdue University, West Lafayette, IN47907
| | - R. Graham Cooks
- Department of Chemistry, Purdue University, West Lafayette, IN47907
| |
Collapse
|
10
|
Vela-Gallego S, Lewandowski B, Möhler J, Puente A, Gil-Cantero D, Wennemers H, de la Escosura A. Modifying the Catalytic Activity of Lipopeptide Assemblies with Nucleobases. Chemistry 2024; 30:e202303395. [PMID: 37877614 DOI: 10.1002/chem.202303395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 10/26/2023]
Abstract
Biohybrid catalysts that operate in aqueous media are intriguing for systems chemistry. In this paper, we investigate whether control over the self-assembly of biohybrid catalysts can tune their properties. As a model, we use the catalytic activity of functional hybrid molecules consisting of a catalytic H-dPro-Pro-Glu tripeptide, derivatized with fatty acid and nucleobase moieties. This combination of simple biological components merged the catalytic properties of the peptide with the self-assembly of the lipid, and the structural ordering of the nucleobases. The biomolecule hybrids self-assemble in aqueous media into fibrillar assemblies and catalyze the reaction between butanal and nitrostyrene. The interactions between the nucleobases enhanced the order of the supramolecular structures and affected their catalytic activity and stereoselectivity. The results point to the significant control and ordering that nucleobases can provide in the self-assembly of biologically inspired supramolecular catalysts.
Collapse
Affiliation(s)
- Sonia Vela-Gallego
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain
| | - Bartosz Lewandowski
- Laboratory of Organic Chemistry, D-CHAB, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Jasper Möhler
- Laboratory of Organic Chemistry, D-CHAB, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Alonso Puente
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain
| | - David Gil-Cantero
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología / CSIC, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Helma Wennemers
- Laboratory of Organic Chemistry, D-CHAB, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Andrés de la Escosura
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain
- Institute for Advanced Research in Chemistry (IAdChem), Campus de Cantoblanco, 28049, Madrid, Spain
| |
Collapse
|
11
|
Lingam M. Information Transmission via Molecular Communication in Astrobiological Environments. ASTROBIOLOGY 2024; 24:84-99. [PMID: 38109216 DOI: 10.1089/ast.2023.0069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
The ubiquity of information transmission via molecular communication between cells is comprehensively documented on Earth; this phenomenon might even have played a vital role in the origin(s) and early evolution of life. Motivated by these considerations, a simple model for molecular communication entailing the diffusion of signaling molecules from transmitter to receiver is elucidated. The channel capacity C (maximal rate of information transmission) and an optimistic heuristic estimate of the actual information transmission rate ℐ are derived for this communication system; the two quantities, especially the latter, are demonstrated to be broadly consistent with laboratory experiments and more sophisticated theoretical models. The channel capacity exhibits a potentially weak dependence on environmental parameters, whereas the actual information transmission rate may scale with the intercellular distance d as ℐ ∝ d-4 and could vary substantially across settings. These two variables are roughly calculated for diverse astrobiological environments, ranging from Earth's upper oceans (C ∼ 3.1 × 103 bits/s; ℐ ∼ 4.7 × 10-2 bits/s) and deep sea hydrothermal vents (C ∼ 4.2 × 103 bits/s; ℐ ∼ 1.2 × 10-1 bits/s) to the hydrocarbon lakes and seas of Titan (C ∼ 3.8 × 103 bits/s; ℐ ∼ 2.6 × 10-1 bits/s).
Collapse
Affiliation(s)
- Manasvi Lingam
- Department of Aerospace, Physics and Space Sciences, Florida Institute of Technology, Melbourne, Florida, USA
- Department of Physics, The University of Texas at Austin, Austin, Texas, USA
| |
Collapse
|
12
|
Chieffo C, Shvetsova A, Skorda F, Lopez A, Fiore M. The Origin and Early Evolution of Life: Homochirality Emergence in Prebiotic Environments. ASTROBIOLOGY 2023; 23:1368-1382. [PMID: 37862227 DOI: 10.1089/ast.2023.0007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
Homochirality is one of the signatures of life. Numerous geological and prebiotic chemistry studies have proved that disordered soups containing small organic molecules, gases, liquids, and minerals (such as those containing phosphorous) yielded racemic mixtures of building blocks for biomolecule assembly. Polymers obtained from these bricks should have been enantiopure with functional properties similar to modern biomolecules or heterochiral with some functions such as catalyzing a chemical transformation unspecifically. Up until now, no clues have been found as to how symmetry breaking occurred. In this review, we highlight the principal achievements regarding the emergence of homochirality during the prebiotic synthesis of building blocks. Furthermore, we tried to focus on approaches based on prebiotic systems chemistry (bottom-up) and laboratory scales to simulate plausible prebiotic messy environments for the emergence of life. We aim with this review to assemble, even partially, the puzzle pieces of the origin of life regarding the relevant phenomenon of homochiral symmetry breaking.
Collapse
Affiliation(s)
- Carolina Chieffo
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (UMR 5246), Villeurbanne, France
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Anastasiia Shvetsova
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (UMR 5246), Villeurbanne, France
- Université de Lyon, Claude Bernard Lyon 1, Laboratoire de Géologie de Lyon: Terre, Planètes, Environnement, Villeurbanne, France
| | - Fryni Skorda
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (UMR 5246), Villeurbanne, France
- Ecole Centrale de Lyon, Ecully, France
| | - Augustin Lopez
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (UMR 5246), Villeurbanne, France
| | - Michele Fiore
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (UMR 5246), Villeurbanne, France
| |
Collapse
|
13
|
Pross A, Pascal R. On the Emergence of Autonomous Chemical Systems through Dissipation Kinetics. Life (Basel) 2023; 13:2171. [PMID: 38004311 PMCID: PMC10672272 DOI: 10.3390/life13112171] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/28/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
This work addresses the kinetic requirements for compensating the entropic cost of self-organization and natural selection, thereby revealing a fundamental principle in biology. Metabolic and evolutionary features of life cannot therefore be separated from an origin of life perspective. Growth, self-organization, evolution and dissipation processes need to be metabolically coupled and fueled by low-entropy energy harvested from the environment. The evolutionary process requires a reproduction cycle involving out-of-equilibrium intermediates and kinetic barriers that prevent the reproductive cycle from proceeding in reverse. Model analysis leads to the unexpectedly simple relationship that the system should be fed energy with a potential exceeding a value related to the ratio of the generation time to the transition state lifetime, thereby enabling a process mimicking natural selection to take place. Reproducing life's main features, in particular its Darwinian behavior, therefore requires satisfying constraints that relate to time and energy. Irreversible reaction cycles made only of unstable entities reproduce some of these essential features, thereby offering a physical/chemical basis for the possible emergence of autonomy. Such Emerging Autonomous Systems (EASs) are found to be capable of maintaining and reproducing their kind through the transmission of a stable kinetic state, thereby offering a physical/chemical basis for what could be deemed an epigenetic process.
Collapse
Affiliation(s)
- Addy Pross
- Department of Chemistry, Ben-Gurion University of the Negev, Be’er-Sheva 8410501, Israel;
| | - Robert Pascal
- PIIM, Institut Origines, Aix-Marseille Université—CNRS, Service 232, Saint Jérôme, Ave Escadrille Normandie Niemen, 13013 Marseille, France
| |
Collapse
|
14
|
Malaterre C, Ten Kate IL, Baqué M, Debaille V, Grenfell JL, Javaux EJ, Khawaja N, Klenner F, Lara YJ, McMahon S, Moore K, Noack L, Patty CHL, Postberg F. Is There Such a Thing as a Biosignature? ASTROBIOLOGY 2023; 23:1213-1227. [PMID: 37962841 DOI: 10.1089/ast.2023.0042] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The concept of a biosignature is widely used in astrobiology to suggest a link between some observation and a biological cause, given some context. The term itself has been defined and used in several ways in different parts of the scientific community involved in the search for past or present life on Earth and beyond. With the ongoing acceleration in the search for life in distant time and/or deep space, there is a need for clarity and accuracy in the formulation and reporting of claims. Here, we critically review the biosignature concept(s) and the associated nomenclature in light of several problems and ambiguities emphasized by recent works. One worry is that these terms and concepts may imply greater certainty than is usually justified by a rational interpretation of the data. A related worry is that terms such as "biosignature" may be inherently misleading, for example, because the divide between life and non-life-and their observable effects-is fuzzy. Another worry is that different parts of the multidisciplinary community may use non-equivalent or conflicting definitions and conceptions, leading to avoidable confusion. This review leads us to identify a number of pitfalls and to suggest how they can be circumvented. In general, we conclude that astrobiologists should exercise particular caution in deciding whether and how to use the concept of biosignature when thinking and communicating about habitability or life. Concepts and terms should be selected carefully and defined explicitly where appropriate. This would improve clarity and accuracy in the formulation of claims and subsequent technical and public communication about some of the most profound and important questions in science and society. With this objective in mind, we provide a checklist of questions that scientists and other interested parties should ask when assessing any reported detection of a "biosignature" to better understand exactly what is being claimed.
Collapse
Affiliation(s)
- Christophe Malaterre
- Département de philosophie, Chaire de recherche du Canada en philosophie des sciences de la vie, Université du Québec à Montréal (UQAM), Montréal, Québec, Canada
- Centre interuniversitaire de recherche sur la science et la technologie (CIRST), Université du Québec à Montréal (UQAM), Montréal, Québec, Canada
| | - Inge Loes Ten Kate
- Department of Earth Sciences, Utrecht University, Utrecht, the Netherlands
| | - Mickael Baqué
- Planetary Laboratories Department, Institute of Planetary Research, German Aerospace Center (DLR), Berlin, Germany
| | - Vinciane Debaille
- Laboratoire G-Time, Université libre de Bruxelles, Brussels, Belgium
| | - John Lee Grenfell
- Department of Extrasolar Planets and Atmospheres, Institute of Planetary Research, German Aerospace Center (DLR), Berlin, Germany
| | - Emmanuelle J Javaux
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium
| | - Nozair Khawaja
- Institute of Geological Sciences, Freie Universität Berlin, Berlin, Germany
| | - Fabian Klenner
- Institute of Geological Sciences, Freie Universität Berlin, Berlin, Germany
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
| | - Yannick J Lara
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium
| | - Sean McMahon
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
- School of GeoSciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Keavin Moore
- Department of Earth & Planetary Sciences, McGill University, Montreal, Québec, Canada
- Trottier Space Institute, McGill University, Montreal, Québec, Canada
| | - Lena Noack
- Institute of Geological Sciences, Freie Universität Berlin, Berlin, Germany
| | - C H Lucas Patty
- Physikalisches Institut, Universität Bern, Bern, Switzerland
- Center for Space and Habitability, Universität Bern, Bern, Switzerland
| | - Frank Postberg
- Institute of Geological Sciences, Freie Universität Berlin, Berlin, Germany
| |
Collapse
|
15
|
Marcinkowski D, Kubicki M, Consiglio G, Hnatejko Z, Majcher-Fitas AM, Podgajny R, Patroniak V, Gorczyński A. Unexpected structural complexity of d-block metallosupramolecular architectures within the benzimidazole-phenoxo ligand scaffold for crystal engineering aspects. Sci Rep 2023; 13:18055. [PMID: 37872235 PMCID: PMC10593740 DOI: 10.1038/s41598-023-45109-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 10/16/2023] [Indexed: 10/25/2023] Open
Abstract
Design of metallosupramolecular materials encompassing more than one kind of supramolecular interaction can become deceptive, but it is necessary to better understand the concept of the controlled formation of supramolecular systems. Herein, we show the structural diversity of the bis-compartmental phenoxo-benzimidazole ligand H3L1 upon self-assembly with variety of d-block metal ions, accounting for factors such as: counterions, pH, solvent and reaction conditions. Solid-state and solution studies show that the parent ligand can accommodate different forms, related to (de)protonation and proton-transfer, resulting in the formation of mono-, bi- or tetrametallic architectures, which was also confirmed with control studies on the new mono-compartmental phenoxo-benzimidazole H2L2 ligand analogue. For the chosen architectures, structural variables such as porous character, magnetic behaviour or luminescence studies were studied to demonstrate how the form of H3L1 ligand affects the final form of the supramolecular architecture and observed properties. Such complex structural variations within the benzimidazole-phenoxo-type ligand have been demonstrated for the first time and this proof-of-concept can be used to integrate these principles in more sophisticated architectures in the future, combining both the benzimidazole and phenoxide subunits. Ultimately, those principles could be utilized for targeted manipulation of properties through molecular tectonics and crystal engineering aspects.
Collapse
Affiliation(s)
- Dawid Marcinkowski
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznań, Poland
| | - Maciej Kubicki
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznań, Poland
| | - Giuseppe Consiglio
- Dipartimento di Scienze Chimiche, Università di Catania, 95125, Catania, Italy
| | - Zbigniew Hnatejko
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznań, Poland
| | - Anna M Majcher-Fitas
- Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Łojasiewicza 11, 30-348, Kraków, Poland
| | - Robert Podgajny
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Violetta Patroniak
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznań, Poland
| | - Adam Gorczyński
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznań, Poland.
| |
Collapse
|
16
|
Harrison SA, Webb WL, Rammu H, Lane N. Prebiotic Synthesis of Aspartate Using Life's Metabolism as a Guide. Life (Basel) 2023; 13:life13051177. [PMID: 37240822 DOI: 10.3390/life13051177] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 04/29/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
A protometabolic approach to the origins of life assumes that the conserved biochemistry of metabolism has direct continuity with prebiotic chemistry. One of the most important amino acids in modern biology is aspartic acid, serving as a nodal metabolite for the synthesis of many other essential biomolecules. Aspartate's prebiotic synthesis is complicated by the instability of its precursor, oxaloacetate. In this paper, we show that the use of the biologically relevant cofactor pyridoxamine, supported by metal ion catalysis, is sufficiently fast to offset oxaloacetate's degradation. Cu2+-catalysed transamination of oxaloacetate by pyridoxamine achieves around a 5% yield within 1 h, and can operate across a broad range of pH, temperature, and pressure. In addition, the synthesis of the downstream product β-alanine may also take place in the same reaction system at very low yields, directly mimicking an archaeal synthesis route. Amino group transfer supported by pyridoxal is shown to take place from aspartate to alanine, but the reverse reaction (alanine to aspartate) shows a poor yield. Overall, our results show that the nodal metabolite aspartate and related amino acids can indeed be synthesised via protometabolic pathways that foreshadow modern metabolism in the presence of the simple cofactor pyridoxamine and metal ions.
Collapse
Affiliation(s)
- Stuart A Harrison
- Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - William L Webb
- Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Hanadi Rammu
- Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Nick Lane
- Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| |
Collapse
|
17
|
Zhao Q, Garimella SS, Savoie BM. Thermally Accessible Prebiotic Pathways for Forming Ribonucleic Acid and Protein Precursors from Aqueous Hydrogen Cyanide. J Am Chem Soc 2023; 145:6135-6143. [PMID: 36883252 DOI: 10.1021/jacs.2c11857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
The search for prebiotic chemical pathways to biologically relevant molecules is a long-standing puzzle that has generated a menagerie of competing hypotheses with limited experimental prospects for falsification. However, the advent of computational network exploration methodologies has created the opportunity to compare the kinetic plausibility of various channels and even propose new pathways. Here, the space of organic molecules that can be formed within four polar or pericyclic reactions from water and hydrogen cyanide (HCN), two established prebiotic candidates for generating biological precursors, was comprehensively explored with a state-of-the-art exploration algorithm. A surprisingly diverse reactivity landscape was revealed within just a few steps of these simple molecules. Reaction pathways to several biologically relevant molecules were discovered involving lower activation energies and fewer reaction steps compared with recently proposed alternatives. Accounting for water-catalyzed reactions qualitatively affects the interpretation of the network kinetics. The case-study also highlights omissions of simpler and lower barrier reaction pathways to certain products by other algorithms that qualitatively affect the interpretation of HCN reactivity.
Collapse
Affiliation(s)
- Qiyuan Zhao
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47906, United States
| | - Sanjay S Garimella
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47906, United States
| | - Brett M Savoie
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47906, United States
| |
Collapse
|
18
|
Towards an RNA/Peptides World by the Direct RNA Template Mechanism: The Emergence of Membrane-Stabilizing Peptides in RNA-Based Protocells. Life (Basel) 2023; 13:life13020523. [PMID: 36836881 PMCID: PMC9966593 DOI: 10.3390/life13020523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/29/2023] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
How functional peptides may have arisen is a significant problem for the scenario of the RNA world. An attractive idea, the direct RNA template (DRT) hypothesis, proposes that RNA molecules can bind amino acids specifically and promote the synthesis of corresponding peptides, thereby starting the RNA/peptides world. To investigate the plausibility of this idea, we modeled the emergence of a "membrane-stabilizing peptide" in RNA-based protocells-such a peptide was suggested to have appeared early in the RNA world based on experimental evidence. The computer simulation demonstrated that the protocells containing the "RNA gene" encoding this peptide may spread in the system owing to the peptide's function. The RNA gene may either originate de novo in protocells or emerge in protocells already containing ribozymes-here we adopt a nucleotide synthetase ribozyme as an example. Furthermore, interestingly, we show that a "nucleotide synthetase peptide" encoded by RNA (also via the DRT mechanism) may substitute the nucleotide synthetase ribozyme in evolution, which may represent how "functional-takeover" in the RNA world could have occurred. Overall, we conclude that the transition from the RNA world towards an RNA/peptides world may well have been mediated by the DRT mechanism. Remarkably, the successful modeling on the emergence of membrane-stabilizing peptide in RNA-based protocells is per se significant, which may imply a "promising" way for peptides to enter the RNA world, especially considering the weak interaction between RNA and the membrane in chemistry.
Collapse
|
19
|
Pastorek A, Clark VHJ, Yurchenko SN, Ferus M, Civiš S. New physical insights: Formamide discharge decomposition and the role of fragments in the formation of large biomolecules. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 278:121322. [PMID: 35537261 DOI: 10.1016/j.saa.2022.121322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 06/14/2023]
Abstract
In this work we present a time-resolved FTIR spectroscopic study on kinetics of atomic and molecular species, specifically CO, CN radical, N2, HCN and CO2 generated in a glow discharge of formamide-nitrogen-water mixture in a helium buffer gas. Radicals such as NH, CH and OH have been proven to be fundamental stones of subsequent chemical reactions having a crucial role in a prebiotic synthesis of large organic molecules. This work contains three main goals. Firstly, we present our time-resolved spectra of formamide decomposition products and discuss the mechanism of collisional excitations between specific species. Secondly, according to our time resolution, we demonstrate and explain the band shape of CO's first overtone and the energy transfer between excited nitrogen and CO, present in our spectra. Lastly, we present theoretical results for the non-LTE modelling of the spectra using bi-temperature approach and a 1D harmonic Franck-Condon approach for the multi-molecule spectra of the formamide decomposition process in the 1800-5600 cm-1 spectral range.
Collapse
Affiliation(s)
- Adam Pastorek
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 2155/3, 18200 Prague 8, Czech Republic; Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 78/7, 11519 Prague 1, Czech Republic
| | - Victoria H J Clark
- Faculty of Mathematics and Physical Sciences, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Sergei N Yurchenko
- Faculty of Mathematics and Physical Sciences, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Martin Ferus
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 2155/3, 18200 Prague 8, Czech Republic
| | - Svatopluk Civiš
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 2155/3, 18200 Prague 8, Czech Republic.
| |
Collapse
|
20
|
Vela-Gallego S, Pardo-Botero Z, Moya C, de la Escosura A. Collective adaptability in a replication network of minimal nucleobase sequences. Chem Sci 2022; 13:10715-10724. [PMID: 36320689 PMCID: PMC9491195 DOI: 10.1039/d2sc02419e] [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: 04/29/2022] [Accepted: 08/05/2022] [Indexed: 12/05/2022] Open
Abstract
A major challenge for understanding the origins of life is to explore how replication networks can engage in an evolutionary process. Herein, we shed light on this problem by implementing a network constituted by two different types of extremely simple biological components: the amino acid cysteine and the canonical nucleobases adenine and thymine, connected through amide bonds to the cysteine amino group and oxidation of its thiol into three possible disulfides. Supramolecular and kinetic analyses revealed that both self- and mutual interactions between such dinucleobase compounds drive their assembly and replication pathways. Those pathways involving sequence complementarity led to enhanced replication rates, suggesting a potential bias for selection. The interplay of synergistic dynamics and competition between replicators was then simulated, under conditions that are not easily accessible with experiments, in an open reactor parametrized and constrained with the unprecedentedly complete experimental kinetic data obtained for our replicative network. Interestingly, the simulations show bistability, as a selective amplification of different species depending on the initial mixture composition. Overall, this network configuration can favor a collective adaptability to changes in the availability of feedstock molecules, with disulfide exchange reactions serving as 'wires' that connect the different individual auto- and cross-catalytic pathways.
Collapse
Affiliation(s)
- Sonia Vela-Gallego
- Department of Organic Chemistry, Universidad Autónoma de Madrid Campus de Cantoblanco 28049 Madrid Spain
| | | | - Cristian Moya
- Department of Organic Chemistry, Universidad Autónoma de Madrid Campus de Cantoblanco 28049 Madrid Spain
| | - Andrés de la Escosura
- Department of Organic Chemistry, Universidad Autónoma de Madrid Campus de Cantoblanco 28049 Madrid Spain
- Institute for Advanced Research in Chemistry (IAdChem) Cantoblanco 28049 Madrid Spain
| |
Collapse
|
21
|
Kumar Bandela A, Sadihov‐Hanoch H, Cohen‐Luria R, Gordon C, Blake A, Poppitz G, Lynn DG, Ashkenasy G. The Systems Chemistry of Nucleic‐acid‐Peptide Networks. Isr J Chem 2022. [DOI: 10.1002/ijch.202200030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anil Kumar Bandela
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Hava Sadihov‐Hanoch
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Rivka Cohen‐Luria
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Christella Gordon
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Alexis Blake
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - George Poppitz
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - David G. Lynn
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Gonen Ashkenasy
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| |
Collapse
|
22
|
Ekesan Ş, York DM. Who stole the proton? Suspect general base guanine found with a smoking gun in the pistol ribozyme. Org Biomol Chem 2022; 20:6219-6230. [PMID: 35452066 PMCID: PMC9378597 DOI: 10.1039/d2ob00234e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The pistol ribozyme (Psr) is one among the most recently discovered classes of small nucleolytic ribozymes that catalyze site-specific RNA self-cleavage through 2'-O-transphosphorylation. The Psr contains a conserved guanine (G40) that in crystal structures is in a position suggesting it plays the role of the general base to abstract a proton from the nucleophile to activate the reaction. Although some functional data is consistent with this mechanistic role, a notable exception is 2-aminopurine (2AP) substitution which has no effect on the rate, unlike similar substitutions across other so-called "G + M" and "G + A" ribozyme classes. Herein we postulate that an alternate conserved guanine, G42, is the primary general base, and provide evidence from molecular simulations that the active site of Psr can undergo local refolding into a structure that is consistent with the common "L-platform/L-scaffold" architecture identified in G + M and G + A ribozyme classes with Psr currently the notable exception. We summarize the key currently available experimental data and present new classical and combined quantum mechanical/molecular mechanical simulation results that collectively suggest a new hypothesis. We hypothesize that there are two available catalytic pathways supported by different conformational states connected by a local refolding of the active site: (1) a primary pathway with an active site architecture aligned with the L-platform/L-scaffold framework where G42 acts as a general base, and (2) a secondary pathway with the crystallographic active site architecture where G40 acts as a general base. We go on to make several experimentally testable predictions, and suggest specific experiments that would ultimately bring closure to the mystery as to "who stole the proton in the pistol ribozyme?".
Collapse
Affiliation(s)
- Şölen Ekesan
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
| |
Collapse
|
23
|
McClain CR, Bryant SR, Hanks G, Bowles MW. Extremophiles in Earth's Deep Seas: A View Toward Life in Exo-Oceans. ASTROBIOLOGY 2022; 22:1009-1028. [PMID: 35549348 DOI: 10.1089/ast.2021.0120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Humanity's search for extraterrestrial life is a modern manifestation of the exploratory and curious nature that has led us through millennia of scientific discoveries. With the ongoing exploration of extraterrestrial bodies, the potential for discovery of extraterrestrial life has expanded. We may better inform this search through an understanding of how life persists and flourishes on Earth in a myriad of environmental extremes. A significant proportion of our knowledge of extremophiles on Earth comes from studies on deep ocean life. Here, we review and synthesize the range of environmental extremes observed in the deep sea, the life that persists in these extreme conditions, and the biological adaptations utilized by these remarkable life-forms. We also review confirmed and predicted extraterrestrial oceans in our solar system and propose deep-sea sites that may serve as planetary field analog environments. We show that the clever ingenuity of evolution under deep-sea conditions suggests that the plausibility of extraterrestrial life is much greater than previously thought.
Collapse
Affiliation(s)
- Craig R McClain
- Louisiana Universities Marine Consortium, Chauvin, Louisiana, USA
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
| | - S River Bryant
- Louisiana Universities Marine Consortium, Chauvin, Louisiana, USA
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
| | - Granger Hanks
- Louisiana Universities Marine Consortium, Chauvin, Louisiana, USA
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
| | | |
Collapse
|
24
|
Kouznetsov VV, Hernández JG. Nanostructured silicate catalysts for environmentally benign Strecker-type reactions: status quo and quo vadis. RSC Adv 2022; 12:20807-20828. [PMID: 35919186 PMCID: PMC9299969 DOI: 10.1039/d2ra03102g] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/30/2022] [Indexed: 01/26/2023] Open
Abstract
Chemical processes are usually catalytic transformations. The use of catalytic reagents can reduce the reaction temperature, decrease reagent-based waste, and enhance the selectivity of a reaction potentially avoiding unwanted side reactions leading to green technology. Chemical processes are also frequently based on multicomponent reactions (MCRs) that possess evident improvements over multistep processes. Both MCRs and catalysis tools are the most valuable principles of green chemistry. Among diverse MCRs, the three-component Strecker reaction (S-3-CR) is a particular transformation conducive to the formation of valuable bifunctional building blocks (α-amino nitriles) in organic synthesis, medicinal chemistry, drug research, and organic materials science. To be a practical synthetic tool, the S-3-CR must be achieved using alternative energy input systems, safe reaction media, and effective catalysts. These latter reagents are now deeply associated with nanoscience and nanocatalysis. Continuously developed, nanostructured silicate catalysts symbolize green pathways in our quest to attain sustainability. Studying and developing nanocatalyzed S-3-CR condensations as an important model will be suitable for achieving the current green mission. This critical review aims to highlight the advances in the development of nanostructured catalysts for technologically important Strecker-type reactions and to analyze this progress from the viewpoint of green and sustainable chemistry.
Collapse
Affiliation(s)
- Vladimir V Kouznetsov
- Laboratorio de Química Orgánica y Biomolecular, CMN, Universidad Industrial de Santander, Parque Tecnológico Guatiguará Km 2 Vía Refugio, Piedecuesta 681011 Colombia +57 7 634 4000 ext. 3593
| | - José G Hernández
- Grupo Ciencia de los Materiales, Instituto de Química, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia Calle 70 No. 52-21 Medellín Colombia
| |
Collapse
|
25
|
Malaterre C, Jeancolas C, Nghe P. The Origin of Life: What Is the Question? ASTROBIOLOGY 2022; 22:851-862. [PMID: 35594335 PMCID: PMC9298494 DOI: 10.1089/ast.2021.0162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 03/12/2022] [Indexed: 06/15/2023]
Abstract
The question of the origin of life is a tenacious question that challenges many branches of science but is also extremely multifaceted. While prebiotic chemistry and micropaleontology reformulate the question as that of explaining the appearance of life on Earth in the deep past, systems chemistry and synthetic biology typically understand the question as that of demonstrating the synthesis of novel living matter from nonliving matter independently of historical constraints. The objective of this contribution is to disentangle the different readings of the origin-of-life question found in science. We identify three main dimensions along which the question can be differently constrained depending on context: historical adequacy, natural spontaneity, and similarity to life-as-we-know-it. We argue that the epistemic status of what needs to be explained-the explanandum-varies from approximately true when the origin-of-life question is the most constrained to entirely speculative when the constraints are the most relaxed. This difference in epistemic status triggers a shift in the nature of the origin-of-life question from an explanation-seeking question in the most constrained case to a fact-establishing question in the lesser-constrained ones. We furthermore explore how answers to some interpretations of the origin-of-life questions matter for other interpretations.
Collapse
Affiliation(s)
- Christophe Malaterre
- Département de philosophie, Université du Québec à Montréal (UQAM), Montréal, Canada
- Centre interuniversitaire de recherche sur la science et la technologie (CIRST), Université du Québec à Montréal (UQAM), Montréal, Canada
| | - Cyrille Jeancolas
- Laboratoire Biophysique et Évolution, UMR Chimie Biologie Innovation 8231, ESPCI Paris, Université PSL, CNRS, Paris, France
- Laboratoire d'Anthropologie Sociale, Collège de France, Paris, France
| | - Philippe Nghe
- Laboratoire Biophysique et Évolution, UMR Chimie Biologie Innovation 8231, ESPCI Paris, Université PSL, CNRS, Paris, France
| |
Collapse
|
26
|
Liu C, Ji J, Wu W, Arhin SG, Papadakis VG, Goula MA, Zhang S, Zhang Y, Wang W. Heterogeneous Catalyst–Microbiome Hybrids for Efficient CO-Driven C6 Carboxylic Acid Synthesis via Metabolic Pathway Manipulation. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Chao Liu
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jiacheng Ji
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wanling Wu
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology, Beijing 100029, China
| | - Samuel Gyebi Arhin
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology, Beijing 100029, China
| | - Vagelis G. Papadakis
- Department of Environmental Engineering, University of Patras, Agrinio 30100, Greece
| | - Maria A. Goula
- Laboratory of Alternative Fuels and Environmental Catalysis, Department of Chemical Engineering, University of Western Macedonia, Kozani 50100, Greece
| | - Sanpeng Zhang
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yi Zhang
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wen Wang
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology, Beijing 100029, China
| |
Collapse
|
27
|
Nejdl L, Petera L, Šponer J, Zemánková K, Pavelicová K, Knížek A, Adam V, Vaculovičová M, Ivanek O, Ferus M. Quantum Dots in Peroxidase-like Chemistry and Formamide-Based Hot Spring Synthesis of Nucleobases. ASTROBIOLOGY 2022; 22:541-551. [PMID: 35333585 DOI: 10.1089/ast.2021.0099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Quantum dots (QDs) are usually seen as artificial semiconductor particles exhibiting optical and electronic properties interesting for nanotechnological applications. However, they may also play a role in prebiotic chemistry. Starting from zinc acetate, cadmium acetate, and mercaptosuccinic acid, we demonstrate the formation of ZnCd QDs upon UV irradiation in prebiotic liquid formamide. We show that ZnCd QDs are able to increase the yield of RNA nucleobase synthesis from formamide up to 300 times, suggesting they might have served as universal catalysts in a primordial milieu. Based on the experimentally observed peroxidase-like activity of ZnCd QDs upon irradiation with visible light, we propose that QDs could be relevant to a broad variety of processes relating to the emergence of terrestrial life.
Collapse
Affiliation(s)
- Lukáš Nejdl
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Lukáš Petera
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic
- Charles University in Prague, Faculty of Science, Prague, Czech Republic
| | - Judit Šponer
- Charles University in Prague, Faculty of Science, Prague, Czech Republic
| | - Kristýna Zemánková
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Kristýna Pavelicová
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Antonín Knížek
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic
- Charles University in Prague, Faculty of Science, Prague, Czech Republic
| | - Vojtěch Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Markéta Vaculovičová
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Ondřej Ivanek
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Martin Ferus
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| |
Collapse
|
28
|
Groß M. Moleküle aus dem Weltraum. CHEM UNSERER ZEIT 2022. [DOI: 10.1002/ciuz.202100007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
29
|
Nitschke W, Schoepp‐Cothenet B, Duval S, Zuchan K, Farr O, Baymann F, Panico F, Minguzzi A, Branscomb E, Russell MJ. Aqueous electrochemistry: The toolbox for life's emergence from redox disequilibria. ELECTROCHEMICAL SCIENCE ADVANCES 2022. [DOI: 10.1002/elsa.202100192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
| | | | - Simon Duval
- CNRS, BIP (UMR 7281), Aix Marseille Univ Marseille France
| | - Kilian Zuchan
- CNRS, BIP (UMR 7281), Aix Marseille Univ Marseille France
| | - Orion Farr
- CNRS, BIP (UMR 7281), Aix Marseille Univ Marseille France
- Aix Marseille Univ CINaM (UMR 7325) Luminy France
| | - Frauke Baymann
- CNRS, BIP (UMR 7281), Aix Marseille Univ Marseille France
| | - Francesco Panico
- Dipartimento di Chimica Università degli Studi di Milano Milan Italy
| | | | - Elbert Branscomb
- Department of Physics Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana Illinois USA
| | | |
Collapse
|
30
|
Hatai J, Altay Y, Sood A, Kiani A, Eleveld MJ, Motiei L, Margulies D, Otto S. An Optical Probe for Real-Time Monitoring of Self-Replicator Emergence and Distinguishing between Replicators. J Am Chem Soc 2022; 144:3074-3082. [PMID: 35139307 PMCID: PMC8874894 DOI: 10.1021/jacs.1c11594] [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: 11/02/2021] [Indexed: 11/30/2022]
Abstract
Self-replicating systems play an important role in research on the synthesis and origin of life. Monitoring of these systems has mostly relied on techniques such as NMR or chromatography, which are limited in throughput and demanding when monitoring replication in real time. To circumvent these problems, we now developed a pattern-generating fluorescent molecular probe (an ID-probe) capable of discriminating replicators of different chemical composition and monitoring the process of replicator formation in real time, giving distinct signatures for starting materials, intermediates, and final products. Optical monitoring of replicators dramatically reduces the analysis time and sample quantities compared to most currently used methods and opens the door for future high-throughput experimentation in protocell environments.
Collapse
Affiliation(s)
- Joydev Hatai
- Centre
for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Yigit Altay
- Centre
for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ankush Sood
- Centre
for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Armin Kiani
- Centre
for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marcel J. Eleveld
- Centre
for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Leila Motiei
- Department
of Chemical and Structural Biology, Weizmann
Institute of Science, Rehovot 7610001, Israel
| | - David Margulies
- Department
of Chemical and Structural Biology, Weizmann
Institute of Science, Rehovot 7610001, Israel
| | - Sijbren Otto
- Centre
for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| |
Collapse
|
31
|
Charlat S, Ariew A, Bourrat P, Ferreira Ruiz M, Heams T, Huneman P, Krishna S, Lachmann M, Lartillot N, Le Sergeant d’Hendecourt L, Malaterre C, Nghe P, Rajon E, Rivoire O, Smerlak M, Zeravcic Z. Natural Selection beyond Life? A Workshop Report. Life (Basel) 2021; 11:life11101051. [PMID: 34685422 PMCID: PMC8538383 DOI: 10.3390/life11101051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/24/2021] [Accepted: 09/29/2021] [Indexed: 11/16/2022] Open
Abstract
Natural selection is commonly seen not just as an explanation for adaptive evolution, but as the inevitable consequence of “heritable variation in fitness among individuals”. Although it remains embedded in biological concepts, such a formalisation makes it tempting to explore whether this precondition may be met not only in life as we know it, but also in other physical systems. This would imply that these systems are subject to natural selection and may perhaps be investigated in a biological framework, where properties are typically examined in light of their putative functions. Here we relate the major questions that were debated during a three-day workshop devoted to discussing whether natural selection may take place in non-living physical systems. We start this report with a brief overview of research fields dealing with “life-like” or “proto-biotic” systems, where mimicking evolution by natural selection in test tubes stands as a major objective. We contend the challenge may be as much conceptual as technical. Taking the problem from a physical angle, we then discuss the framework of dissipative structures. Although life is viewed in this context as a particular case within a larger ensemble of physical phenomena, this approach does not provide general principles from which natural selection can be derived. Turning back to evolutionary biology, we ask to what extent the most general formulations of the necessary conditions or signatures of natural selection may be applicable beyond biology. In our view, such a cross-disciplinary jump is impeded by reliance on individuality as a central yet implicit and loosely defined concept. Overall, these discussions thus lead us to conjecture that understanding, in physico-chemical terms, how individuality emerges and how it can be recognised, will be essential in the search for instances of evolution by natural selection outside of living systems.
Collapse
Affiliation(s)
- Sylvain Charlat
- Laboratoire de Biométrie et Biologie Évolutive, Université de Lyon, Université Lyon 1, CNRS, UMR 5558, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne, France; (N.L.); (E.R.)
- Correspondence:
| | - André Ariew
- Department of Philosophy, University of Missouri, 438 Strickland Hall, Columbia, MO 65211, USA;
| | - Pierrick Bourrat
- Department of Philosophy, Macquarie University, Balaclava Road, North Ryde, NSW 2109, Australia;
- Charles Perkins Centre, Department of Philosophy, The University of Sydney, Camperdown, NSW 2006, Australia
| | - María Ferreira Ruiz
- Department of Philosophy, University of Bielefeld, 33615 Bielefeld, Germany;
| | - Thomas Heams
- INRAE, Domaine de Vilvert Bâtiment 211, 78352 Jouy-en-Josas, France;
| | - Philippe Huneman
- Institut d’Histoire et de Philosophie des Sciences et des Techniques, CNRS (Centre National de la Recherche Scientifique), Université Paris I Sorbonne, 13 Rue du Four, 75006 Paris, France;
| | - Sandeep Krishna
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India;
| | | | - Nicolas Lartillot
- Laboratoire de Biométrie et Biologie Évolutive, Université de Lyon, Université Lyon 1, CNRS, UMR 5558, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne, France; (N.L.); (E.R.)
| | - Louis Le Sergeant d’Hendecourt
- Centre de St-Jérôme, Laboratoire de Physique des Interactions Ioniques et Moléculaires, Aix-Marseille Université, CNRS, UMR 7345, 13013 Marseille, France;
| | - Christophe Malaterre
- Centre de Recherche Interuniversitaire sur la Science et la Technologie (CIRST), Département de Philosophie, Université du Québec à Montréal (UQAM), 455 Boulevard René-Lévesque Est, Montréal, QC H3C 3P8, Canada;
| | - Philippe Nghe
- Laboratoire Biophysique et Evolution, CNRS UMR Chimie Biologie Innovation 8231, ESPCI Paris, Université PSL, 10 Rue Vauquelin, 75005 Paris, France;
| | - Etienne Rajon
- Laboratoire de Biométrie et Biologie Évolutive, Université de Lyon, Université Lyon 1, CNRS, UMR 5558, 43 Boulevard du 11 Novembre 1918, 69622 Villeurbanne, France; (N.L.); (E.R.)
| | - Olivier Rivoire
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, 75005 Paris, France;
| | - Matteo Smerlak
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, 04103 Leipzig, Germany;
| | - Zorana Zeravcic
- Gulliver Lab, CNRS UMR 7083, ESPCI Paris, PSL University, 75005 Paris, France;
| |
Collapse
|
32
|
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.
Collapse
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.
| |
Collapse
|
33
|
Miao X, Paikar A, Lerner B, Diskin‐Posner Y, Shmul G, Semenov SN. Kinetic Selection in the Out‐of‐Equilibrium Autocatalytic Reaction Networks that Produce Macrocyclic Peptides. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xiaoming Miao
- Department of Molecular Chemistry and Materials Science Weizmann Institute of Science Rehovot 7610001 Israel
| | - Arpita Paikar
- Department of Molecular Chemistry and Materials Science Weizmann Institute of Science Rehovot 7610001 Israel
| | - Benjamin Lerner
- Department of Molecular Chemistry and Materials Science Weizmann Institute of Science Rehovot 7610001 Israel
| | - Yael Diskin‐Posner
- Department of Chemical Research Support Weizmann Institute of Science Rehovot 7610001 Israel
| | - Guy Shmul
- Department of Chemical Research Support Weizmann Institute of Science Rehovot 7610001 Israel
| | - Sergey N. Semenov
- Department of Molecular Chemistry and Materials Science Weizmann Institute of Science Rehovot 7610001 Israel
| |
Collapse
|
34
|
Rimmer PB, Thompson SJ, Xu J, Russell DA, Green NJ, Ritson DJ, Sutherland JD, Queloz DP. Timescales for Prebiotic Photochemistry Under Realistic Surface Ultraviolet Conditions. ASTROBIOLOGY 2021; 21:1099-1120. [PMID: 34152196 PMCID: PMC8570677 DOI: 10.1089/ast.2020.2335] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Ultraviolet (UV) light has long been invoked as a source of energy for prebiotic chemical synthesis, but experimental support does not involve sources of UV light that look like the young Sun. Here we experimentally investigate whether the UV flux available on the surface of early Earth, given a favorable atmosphere, can facilitate a variety of prebiotic chemical syntheses. We construct a solar simulator for the UV light of the faint young Sun on the surface of early Earth, called StarLab. We then attempt a series of reactions testing different aspects of a prebiotic chemical scenario involving hydrogen cyanide (HCN), sulfites, and sulfides under the UV light of StarLab, including hypophosphite oxidation by UV light and hydrogen sulfide, photoreduction of HCN with bisulfite, the photoanomerization of α-thiocytidine, the production of a chemical precursor of a potentially prebiotic activating agent (nitroprusside), the photoreduction of thioanhydrouridine and thioanhydroadenosine, and the oxidation of ethanol (EtOH) by photochemically generated hydroxyl radicals. We compare the output of StarLab to the light of the faint young Sun to constrain the timescales over which these reactions would occur on the surface of early Earth. We predict that hypophosphite oxidation, HCN reduction, and photoproduction of nitroprusside would all operate on the surface of early Earth in a matter of days to weeks. The photoanomerization of α-thiocytidine would take months to complete, and the production of oxidation products from hydroxyl radicals would take years. The photoreduction of thioanhydrouridine with hydrogen sulfide did not succeed even after a long period of irradiation, providing a lower limit on the timescale of several years. The photoreduction of thioanhydroadenosine with bisulfite produced 2'-deoxyriboadenosine (dA) on the timescale of days. This suggests the plausibility of the photoproduction of purine deoxyribonucleotides, such as the photoproduction of simple sugars, proceeds more efficiently in the presence of bisulfite.
Collapse
Affiliation(s)
- Paul B. Rimmer
- Department of Earth Sciences, University of Cambridge, Cambridge, United Kingdom
- Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Address correspondence to: Paul B. Rimmer, Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EQ, United Kingdom
| | | | - Jianfeng Xu
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | | | | | | | - Didier P. Queloz
- Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
35
|
Lauber N, Flamm C, Ruiz-Mirazo K. "Minimal metabolism": A key concept to investigate the origins and nature of biological systems. Bioessays 2021; 43:e2100103. [PMID: 34426986 DOI: 10.1002/bies.202100103] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/18/2021] [Accepted: 07/20/2021] [Indexed: 11/07/2022]
Abstract
The systems view on life and its emergence from complex chemistry has remarkably increased the scientific attention on metabolism in the last two decades. However, during this time there has not been much theoretical discussion on what constitutes a metabolism and what role it actually played in biogenesis. A critical and updated review on the topic is here offered, including some references to classical models from last century, but focusing more on current and future research. Metabolism is considered as intrinsically related to the living but not necessarily equivalent to it. More precisely, the idea of "minimal metabolism", in contrast to previous, top-down conceptions, is formulated as a heuristic construct, halfway between chemistry and biology. Thus, rather than providing a complete or final characterization of metabolism, our aim is to encourage further investigations on it, particularly in the context of life's origin, for which some concrete methodological suggestions are provided. Also see the video abstract here: https://youtu.be/DP7VMKk2qpA.
Collapse
Affiliation(s)
- Nino Lauber
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain.,Department of Philosophy, University of the Basque Country, Leioa, Spain
| | - Christoph Flamm
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Kepa Ruiz-Mirazo
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain.,Department of Philosophy, University of the Basque Country, Leioa, Spain
| |
Collapse
|
36
|
Adams D, Luo Y, Wong ML, Dunn P, Christensen M, Dong C, Hu R, Yung Y. Nitrogen Fixation at Early Mars. ASTROBIOLOGY 2021; 21:968-980. [PMID: 34339294 DOI: 10.1089/ast.2020.2273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The Mars Science Laboratory (MSL) recently discovered nitrates in Gale Crater (e.g., Stern et al., 2015; Sutter et al., 2017). One possible mechanism for ancient nitrate deposition on Mars is through HNOx formation and rain out in the atmosphere, for which lightning-induced NO is likely the fundamental source. This study investigates nitrogen (N2) fixation in early Mars' atmosphere, with implications for early Mars' habitability. We consider a 1 bar atmosphere of background CO2, with abundance of N2, hydrogen, and methane varied from 1% to 10% to explore a swath of potential early Mars climates. We derive lightning-induced thermochemical equilibrium fluxes of NO and HCN by coupling the lightning-rate parametrization from the study of Romps et al. (2014) with chemical equilibrium with applications, and we use a Geant4 simulation platform to estimate the effect of solar energetic particle events. These fluxes are used as input into KINETICS, the Caltech/JPL coupled photochemistry and transport code, which models the chemistry of 50 species linked by 495 reactions to derive rain-out fluxes of HNOx and HCN. We compute equilibrium concentrations of cyanide and nitrate in a putative northern ocean at early Mars, assuming hydrothermal vent circulation and photoreduction act as the dominant loss mechanisms. We find average oceanic concentrations of ∼0.1-2 nM nitrate and ∼0.01-2 mM cyanide. HCN is critical for protein synthesis at concentrations >0.01 M (e.g., Holm and Neubeck, 2009), and our result is astrobiologically significant if secondary local concentration mechanisms occurred. Nitrates may act as high-potential electron acceptors for early metabolisms, although the minimum concentration required is unknown. Our study derives concentrations that will be useful for future laboratory studies to investigate the habitability at early Mars. The aqueous nitrate concentrations correspond to surface nitrate precipitates of ∼1-8 × 10-4 wt % that may have formed after the evaporation of surface waters, and these values roughly agree with recent MSL measurements.
Collapse
Affiliation(s)
- Danica Adams
- Department of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Yangcheng Luo
- Department of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
| | - Michael L Wong
- Department of Astronomy and Astrobiology Program, University of Washington, Seattle, Washington, USA
- Virtual Planet Laboratory, University of Washington, Seattle, Washington, USA
| | - Patrick Dunn
- Space Sciences Laboratory, University of California, Berkeley, Berkeley, California, USA
| | - Madeline Christensen
- Department of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
- Bellarmine Preparatory, Tacoma, Washington, USA
| | - Chuanfei Dong
- Department of Astrophysical Sciences, Princeton University, Princeton, California, USA
| | - Renyu Hu
- Department of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Yuk Yung
- Department of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| |
Collapse
|
37
|
Miao X, Paikar A, Lerner B, Diskin-Posner Y, Shmul G, Semenov SN. Kinetic Selection in the Out-of-Equilibrium Autocatalytic Reaction Networks that Produce Macrocyclic Peptides. Angew Chem Int Ed Engl 2021; 60:20366-20375. [PMID: 34144635 DOI: 10.1002/anie.202105790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/03/2021] [Indexed: 02/05/2023]
Abstract
Autocatalytic reaction networks are instrumental for validating scenarios for the emergence of life on Earth and for synthesizing life de novo. Here, we demonstrate that dimeric thioesters of tripeptides with the general structure (Cys-Xxx-Gly-SEt)2 form strongly interconnected autocatalytic reaction networks that predominantly generate macrocyclic peptides up to 69 amino acids long. Some macrocycles of 6-12 amino acids were isolated from the product pool and were characterized by NMR spectroscopy and single-crystal X-ray analysis. We studied the autocatalytic formation of macrocycles in a flow reactor in the presence of acrylamide, whose conjugate addition to thiols served as a model "removal" reaction. These results indicate that even not template-assisted autocatalytic production combined with competing removal of molecular species in an open compartment could be a feasible route for selecting functional molecules during the pre-Darwinian stages of molecular evolution.
Collapse
Affiliation(s)
- Xiaoming Miao
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Arpita Paikar
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Benjamin Lerner
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Yael Diskin-Posner
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Guy Shmul
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Sergey N Semenov
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| |
Collapse
|
38
|
'Whole Organism', Systems Biology, and Top-Down Criteria for Evaluating Scenarios for the Origin of Life. Life (Basel) 2021; 11:life11070690. [PMID: 34357062 PMCID: PMC8306273 DOI: 10.3390/life11070690] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 12/22/2022] Open
Abstract
While most advances in the study of the origin of life on Earth (OoLoE) are piecemeal, tested against the laws of chemistry and physics, ultimately the goal is to develop an overall scenario for life's origin(s). However, the dimensionality of non-equilibrium chemical systems, from the range of possible boundary conditions and chemical interactions, renders the application of chemical and physical laws difficult. Here we outline a set of simple criteria for evaluating OoLoE scenarios. These include the need for containment, steady energy and material flows, and structured spatial heterogeneity from the outset. The Principle of Continuity, the fact that all life today was derived from first life, suggests favoring scenarios with fewer non-analog (not seen in life today) to analog (seen in life today) transitions in the inferred first biochemical pathways. Top-down data also indicate that a complex metabolism predated ribozymes and enzymes, and that full cellular autonomy and motility occurred post-LUCA. Using these criteria, we find the alkaline hydrothermal vent microchamber complex scenario with a late evolving exploitation of the natural occurring pH (or Na+ gradient) by ATP synthase the most compelling. However, there are as yet so many unknowns, we also advocate for the continued development of as many plausible scenarios as possible.
Collapse
|
39
|
Lingam M. Theoretical Constraints Imposed by Gradient Detection and Dispersal on Microbial Size in Astrobiological Environments. ASTROBIOLOGY 2021; 21:813-830. [PMID: 33902321 DOI: 10.1089/ast.2020.2392] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The capacity to sense gradients efficiently and acquire information about the ambient environment confers many advantages such as facilitating movement toward nutrient sources or away from toxic chemicals. The amplified dispersal evinced by organisms endowed with motility is possibly beneficial in related contexts. Hence, the connections between information acquisition, motility, and microbial size are explored from an explicitly astrobiological standpoint. By using prior theoretical models, the constraints on organism size imposed by gradient detection and motility are elucidated in the form of simple heuristic scaling relations. It is argued that environments such as alkaline hydrothermal vents, which are distinguished by the presence of steep gradients, might be conducive to the existence of "small" microbes (with radii of ≳0.1 μm) in principle, when only the above two factors are considered; other biological functions (e.g., metabolism and genetic exchange) could, however, regulate the lower bound on microbial size and elevate it. The derived expressions are potentially applicable to a diverse array of settings, including those entailing solvents other than water; for example, the lakes and seas of Titan. The article concludes with a brief exposition of how this formalism may be of practical and theoretical value to astrobiology.
Collapse
Affiliation(s)
- Manasvi Lingam
- Department of Aerospace, Physics and Space Science, Florida Institute of Technology, Melbourne, Florida, USA
- Institute for Theory and Computation, Harvard University, Cambridge, Massachusetts, USA
| |
Collapse
|
40
|
Toparlak Ö, Wang A, Mansy SS. Population-Level Membrane Diversity Triggers Growth and Division of Protocells. JACS AU 2021; 1:560-568. [PMID: 34467319 PMCID: PMC8395648 DOI: 10.1021/jacsau.0c00079] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Indexed: 06/01/2023]
Abstract
To date, multiple mechanisms have been described for the growth and division of model protocells, all of which exploit the lipid dynamics of fatty acids. In some examples, the more heterogeneous aggregate consisting of fatty acid and diacyl phospholipid or fatty acid and peptide grows at the expense of the more homogeneous aggregate containing a restricted set of lipids with similar dynamics. Imbalances between surface area and volume during growth can generate filamentous vesicles, which are typically divided by shear forces. Here, we describe another pathway for growth and division that depends simply on differences in the compositions of fatty acid membranes without additional components. Growth is driven by the thermodynamically favorable mixing of lipids between two populations, i.e., the system as a whole proceeds toward equilibrium. Division is the result of growth-induced curvature. Importantly, growth and division do not require a specific composition of lipids. For example, vesicles made from one type of lipid, e.g., short-chain fatty acids, grow and divide when fed with vesicles consisting of another type of lipid, e.g., long-chain fatty acids, and vice versa. After equilibration, additional rounds of growth and division could potentially proceed by the introduction of compositionally distinct aggregates. Since prebiotic synthesis likely gave rise to mixtures of lipids, the data are consistent with the presence of growing and dividing protocells on the prebiotic Earth.
Collapse
Affiliation(s)
- Ö.
Duhan Toparlak
- Department
of Cellular, Computational and Integrative Biology (D-CIBIO), University of Trento, Via Sommarive 9, 38123 Povo, TN, Italy
| | - Anna Wang
- School
of Chemistry and Australian Centre for Astrobiology, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Sheref S. Mansy
- Department
of Cellular, Computational and Integrative Biology (D-CIBIO), University of Trento, Via Sommarive 9, 38123 Povo, TN, Italy
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB T6G
2G2, Canada
| |
Collapse
|
41
|
Green NJ, Xu J, Sutherland JD. Illuminating Life's Origins: UV Photochemistry in Abiotic Synthesis of Biomolecules. J Am Chem Soc 2021; 143:7219-7236. [PMID: 33880920 PMCID: PMC8240947 DOI: 10.1021/jacs.1c01839] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Indexed: 01/15/2023]
Abstract
Solar radiation is the principal source of energy available to Earth and has unmatched potential for the synthesis of organic material from primordial molecular building blocks. As well as providing the energy for photochemical synthesis of (proto)biomolecules of interest in origins of life-related research, light has also been found to often provide remarkable selectivity in these processes, for molecules that function in extant biology and against those that do not. As such, light is heavily implicated as an environmental input on the nascent Earth that was important for the emergence of complex yet selective chemical systems underpinning life. Reactivity and selectivity in photochemical prebiotic synthesis are discussed, as are their implications for origins of life scenarios and their plausibility, and the future directions of this research.
Collapse
Affiliation(s)
- Nicholas J. Green
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge
Biomedical Campus, Cambridge CB2 0QH, U.K.
| | - Jianfeng Xu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge
Biomedical Campus, Cambridge CB2 0QH, U.K.
| | - John D. Sutherland
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge
Biomedical Campus, Cambridge CB2 0QH, U.K.
| |
Collapse
|
42
|
Dašková V, Buter J, Schoonen AK, Lutz M, de Vries F, Feringa BL. Chiral Amplification of Phosphoramidates of Amines and Amino Acids in Water. Angew Chem Int Ed Engl 2021; 60:11120-11126. [PMID: 33605523 PMCID: PMC8252365 DOI: 10.1002/anie.202014955] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/04/2021] [Indexed: 01/22/2023]
Abstract
The origin of biomolecular homochirality continues to be one of the most fascinating aspects of prebiotic chemistry. Various amplification strategies for chiral compounds to enhance a small chiral preference have been reported, but none of these involves phosphorylation, one of nature's essential chemical reactions. Here we present a simple and robust concept of phosphorylation-based chiral amplification of amines and amino acids in water. By exploiting the difference in solubility of a racemic phosphoramidate and its enantiopure form, we achieved enantioenrichment in solution. Starting with near racemic, phenylethylamine-based phosphoramidates, ee's of up to 95 % are reached in a single amplification step. Particularly noteworthy is the enantioenrichment of phosphorylated amino acids and their derivatives, which might point to a potential role of phosphorus en-route to prebiotic homochirality.
Collapse
Affiliation(s)
- Vanda Dašková
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Jeffrey Buter
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Anne K. Schoonen
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Martin Lutz
- Crystal and Structural ChemistryBijvoet Centre for Biomolecular ResearchUtrecht UniversityPadualaan 83584CHUtrechtThe Netherlands
| | - Folkert de Vries
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Ben L. Feringa
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| |
Collapse
|
43
|
Russell MJ. The "Water Problem"( sic), the Illusory Pond and Life's Submarine Emergence-A Review. Life (Basel) 2021; 11:429. [PMID: 34068713 PMCID: PMC8151828 DOI: 10.3390/life11050429] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 04/30/2021] [Accepted: 05/01/2021] [Indexed: 01/10/2023] Open
Abstract
The assumption that there was a "water problem" at the emergence of life-that the Hadean Ocean was simply too wet and salty for life to have emerged in it-is here subjected to geological and experimental reality checks. The "warm little pond" that would take the place of the submarine alkaline vent theory (AVT), as recently extolled in the journal Nature, flies in the face of decades of geological, microbiological and evolutionary research and reasoning. To the present author, the evidence refuting the warm little pond scheme is overwhelming given the facts that (i) the early Earth was a water world, (ii) its all-enveloping ocean was never less than 4 km deep, (iii) there were no figurative "Icelands" or "Hawaiis", nor even an "Ontong Java" then because (iv) the solidifying magma ocean beneath was still too mushy to support such salient loadings on the oceanic crust. In place of the supposed warm little pond, we offer a well-protected mineral mound precipitated at a submarine alkaline vent as life's womb: in place of lipid membranes, we suggest peptides; we replace poisonous cyanide with ammonium and hydrazine; instead of deleterious radiation we have the appropriate life-giving redox and pH disequilibria; and in place of messy chemistry we offer the potential for life's emergence from the simplest of geochemically available molecules and ions focused at a submarine alkaline vent in the Hadean-specifically within the nano-confined flexible and redox active interlayer walls of the mixed-valent double layer oxyhydroxide mineral, fougerite/green rust comprising much of that mound.
Collapse
Affiliation(s)
- Michael J Russell
- Dipartimento di Chimica, Università degli Studi di Torino, via P. Giuria 7, 10125 Turin, Italy
| |
Collapse
|
44
|
Dašková V, Buter J, Schoonen AK, Lutz M, Vries F, Feringa BL. Chiral Amplification of Phosphoramidates of Amines and Amino Acids in Water. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Vanda Dašková
- Stratingh Institute for Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Jeffrey Buter
- Stratingh Institute for Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Anne K. Schoonen
- Stratingh Institute for Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Martin Lutz
- Crystal and Structural Chemistry Bijvoet Centre for Biomolecular Research Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Folkert Vries
- Stratingh Institute for Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Ben L. Feringa
- Stratingh Institute for Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| |
Collapse
|
45
|
Can coacervation unify disparate hypotheses in the origin of cellular life? Curr Opin Colloid Interface Sci 2021. [DOI: 10.1016/j.cocis.2020.101415] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
46
|
Ching WY, Adhikari P, Jawad B, Podgornik R. Ultra-large-scale ab initio quantum chemical computation of bio-molecular systems: The case of spike protein of SARS-CoV-2 virus. Comput Struct Biotechnol J 2021; 19:1288-1301. [PMID: 33623641 PMCID: PMC7893244 DOI: 10.1016/j.csbj.2021.02.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/20/2021] [Accepted: 02/06/2021] [Indexed: 02/07/2023] Open
Abstract
The COVID-19 pandemic poses a severe threat to human health with an unprecedented social and economic disruption. Spike (S) glycoprotein of the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the first contact with the ACE2 receptor in the human cell. We report results of ab initio computation of the spike protein, the largest ab initio quantum chemical computation to date on any bio-molecular system, using a divide and conquer strategy by focusing on individual structural domains. In this approach we divided the S-protein into seven structural domains: N-terminal domain (NTD), receptor binding domain (RBD), subdomain 1 (SD1), subdomain 2 (SD2), fusion peptide (FP), heptad repeat 1 with central helix (HR1-CH) and connector domain (CD). The entire Chain A has 14,488 atoms including the hydrogen atoms but excluding the amino acids with missing coordinates based on the PDB data (ID: 6VSB). The results include structural refinement, ab initio calculation of intra-molecular bonding mechanism, 3- dimensional non-local inter-amino acid interaction with implications for the inter-domain interaction. Details of the electronic structure, interatomic bonding, partial charge distribution and the role played by hydrogen bond network are discussed. In the interaction among structural domains, we present new insights for crucial hinge-like movement and fusion process. Extension of such calculation to the interface between the S-protein binding domain and ACE2 receptor can provide a pathway for computational understanding of mutations and the design of therapeutic drugs to combat the COVID-19 pandemic.
Collapse
Affiliation(s)
- Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Puja Adhikari
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Bahaa Jawad
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Rudolf Podgornik
- School of Physical Sciences and Kavli Institute of Theoretical Science, University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100090, China
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| |
Collapse
|
47
|
The Dissipative Photochemical Origin of Life: UVC Abiogenesis of Adenine. ENTROPY 2021; 23:e23020217. [PMID: 33579010 PMCID: PMC7916814 DOI: 10.3390/e23020217] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/22/2021] [Accepted: 02/03/2021] [Indexed: 11/21/2022]
Abstract
The non-equilibrium thermodynamics and the photochemical reaction mechanisms are described which may have been involved in the dissipative structuring, proliferation and complexation of the fundamental molecules of life from simpler and more common precursors under the UVC photon flux prevalent at the Earth’s surface at the origin of life. Dissipative structuring of the fundamental molecules is evidenced by their strong and broad wavelength absorption bands in the UVC and rapid radiationless deexcitation. Proliferation arises from the auto- and cross-catalytic nature of the intermediate products. Inherent non-linearity gives rise to numerous stationary states permitting the system to evolve, on amplification of a fluctuation, towards concentration profiles providing generally greater photon dissipation through a thermodynamic selection of dissipative efficacy. An example is given of photochemical dissipative abiogenesis of adenine from the precursor HCN in water solvent within a fatty acid vesicle floating on a hot ocean surface and driven far from equilibrium by the incident UVC light. The kinetic equations for the photochemical reactions with diffusion are resolved under different environmental conditions and the results analyzed within the framework of non-linear Classical Irreversible Thermodynamic theory.
Collapse
|
48
|
Jankowska J, Góra RW. Ultrafast nonradiative deactivation of photoexcited 8-oxo-hypoxanthine: a nonadiabatic molecular dynamics study. Phys Chem Chem Phys 2021; 23:1234-1241. [PMID: 33355573 DOI: 10.1039/d0cp05271j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In the scientific endeavor to understand the chemical origins of life, the photochemistry of the smallest life building blocks, nucleobases, has been a constant object of focus and intense research. Here, we report the results of the first theoretical study on the photo-properties of an 8-oxo-hypoxanthine molecule, the chromophore of 8-oxo-inosine, which is relevant to the recently proposed, prebiotically plausible synthetic routes to the formation of purine- and pyrimidine-nucleotides. With ab initio and semi-empirical OM2/MRCI quantum-chemistry calculations, we predict a strong photostability of the 8-oxo-hypoxanthine system and see the origin of this effect in ultrafast nonradiative relaxation through puckering of the 6-membered heterocyclic ring.
Collapse
Affiliation(s)
- Joanna Jankowska
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland.
| | - Robert W Góra
- Department of Physical and Quantum Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland.
| |
Collapse
|
49
|
|
50
|
Abstract
Thresholds are widespread in origin of life scenarios, from the emergence of chirality, to the appearance of vesicles, of autocatalysis, all the way up to Darwinian evolution. Here, we analyze the “error threshold,” which poses a condition for sustaining polymer replication, and generalize the threshold approach to other properties of prebiotic systems. Thresholds provide theoretical predictions, prescribe experimental tests, and integrate interdisciplinary knowledge. The coupling between systems and their environment determines how thresholds can be crossed, leading to different categories of prebiotic transitions. Articulating multiple thresholds reveals evolutionary properties in prebiotic scenarios. Overall, thresholds indicate how to assess, revise, and compare origin of life scenarios.
Collapse
Affiliation(s)
- Cyrille Jeancolas
- Laboratoire de Biochimie, UMR CNRS-ESPCI 8231 Chimie Biologie Innovation, PSL University, ESPCI Paris, 10 rue Vauquelin, 75005 Paris, France.,Laboratoire d'Anthropologie Sociale, Collège de France, 52 rue du Cardinal Lemoine, 75005 Paris, France
| | - Christophe Malaterre
- Département de Philosophie and Centre de Recherche Interuniversitaire sur la Science et la Technologie (CIRST), Université du Québec à Montréal (UQAM), 455 boulevard René-Lévesque Est, Montréal, QC H3C 3P8, Canada
| | - Philippe Nghe
- Laboratoire de Biochimie, UMR CNRS-ESPCI 8231 Chimie Biologie Innovation, PSL University, ESPCI Paris, 10 rue Vauquelin, 75005 Paris, France
| |
Collapse
|