Special Issue "The Origin and Early Evolution of Life: Prebiotic Chemistry of Biomolecules"

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Chemistry".

Deadline for manuscript submissions: 31 May 2019

Special Issue Editor

Guest Editor
Dr. Michele Fiore

Institute of Molecular and Supramolecular Chemistry and Biochemistry, University of Lyon, Claude Bernard Lyon 1, Villeurbanne Cedex, France
Website | E-Mail
Interests: systems chemistry; system biology; prebiotic chemistry of biomolecules; origin of life; prebiotic synthesis of amphiphiles; total synthesis of phospholipids; sythesis of fluorescent clickable probles; glycolipids; radical reactons; evolvable molecular systems

Special Issue Information

Dear Colleagues,

What is life? How, where, and when did life arise? These questions have remained most-fascinating over the last hundred years. It is a common opinion, in accord with the words of David Deamer, that “life can emerge where physics and chemistry intersect”. However, this sentence do not exclude biology, astrophysics, geochemistry, geophysics, planetology, earth science, bioinformatics, complexity theory, mathematics and philosophy from the equation. From an evolutionary chemical point of view, is possible to presume that life emerged from a mixture of inanimate matter: Organic and inorganic compounds. Such compounds reacted under favorable conditions, forming molecules that are commonly called “biotic” and that, thanks to a kind of self-organization, gave rise to the first biopolymers and to proto-metabolisms.

This Special Issue has the ultimate aim to summarize the latest discoveries regarding the chemical origins of biotic molecules. Although astrochemical evolution has only been able to give rise to very simple chemical compounds, only the pioneering experiment of Miller (and related experiments) has proven that it is possible to form some of the most relevant biotic bricks fromsimple inorganic compounds In recent years, dozens of excellent reviews and articles appeared in the literature and some breakthroughs have already been achieved. However, a great dealof work remains to be done. I am deeply convinced that, beyond the borders of the traditional domains of scientific activity, the multidisciplinary character of the present Special Issue leaves space for anyone to creatively contribute to any aspect of these and related relevant topics. We hope that the presented works will be stimulating for a new generation of scientists that are taking their first steps in this fascinating field. Submission of original reserach, scientific perspectives and literature reviews on this topic are deeply encouraged.

Dr. Michele Fiore
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 650 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Prebiotic chemistry
  • Origin of life
  • Prebiotic molecules
  • Amphiphiles
  • Dynamic chemical complexity
  • Evolvable molecular systems
  • Protocells
  • Proto-metabolims
  • Energy storage
  • Chemical evolution

Published Papers (12 papers)

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Research

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Open AccessArticle Production of Carbamic Acid Dimer from Ammonia-Carbon Dioxide Ices: Matching Observed and Computed IR Spectra
Received: 20 February 2019 / Revised: 19 April 2019 / Accepted: 19 April 2019 / Published: 23 April 2019
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Abstract
The production of complex molecules in ammonia–carbon dioxide ices is presumed to pass through species of formula H3N:CO2 with further addition of ammonia and carbon dioxide. One possible landmark, carbamic acid, H2NCOOH, has been implicated among the products [...] Read more.
The production of complex molecules in ammonia–carbon dioxide ices is presumed to pass through species of formula H3N:CO2 with further addition of ammonia and carbon dioxide. One possible landmark, carbamic acid, H2NCOOH, has been implicated among the products of warming and irradiation of such ices. Experimental study of the IR spectra of residues has suggested the presence of related species, including weakly bound 1:1 and 2:1 complexes of ammonia with carbon dioxide, zwitterionic carbamic acid, ammonium carbamate, and the dimer of carbamic acid. We computed the energetics and vibrational spectra of these species as well as the complex between ammonia and carbamic acid for gas and condensed phases. By means of a new spectrum-matching scoring between computed and observed vibrational spectra, we infer species that are most probably present. The leading candidates are ammonium carbamate, the carbamic acid–ammonia complex, and the carbamic acid dimer. Full article
Open AccessArticle Plausible Emergence of Autocatalytic Cycles under Prebiotic Conditions
Received: 7 January 2019 / Revised: 22 March 2019 / Accepted: 2 April 2019 / Published: 4 April 2019
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Abstract
The emergence of life in a prebiotic world is an enormous scientific question of paramount philosophical importance. Even when life (in any sense we can define it) can be observed and replicated in the laboratory, it is only an indication of one possible [...] Read more.
The emergence of life in a prebiotic world is an enormous scientific question of paramount philosophical importance. Even when life (in any sense we can define it) can be observed and replicated in the laboratory, it is only an indication of one possible pathway for life emergence, and is by no means be a demonstration of how life really emerged. The best we can hope for is to indicate plausible chemical–physical conditions and mechanisms that might lead to self-organizing and autopoietic systems. Here we present a stochastic simulation, based on chemical reactions already observed in prebiotic environments, that might help in the design of new experiments. We will show how the definition of simple rules for the synthesis of random peptides may lead to the appearance of networks of autocatalytic cycles and the emergence of memory. Full article
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Open AccessArticle The Origin of Prebiotic Information System in the Peptide/RNA World: A Simulation Model of the Evolution of Translation and the Genetic Code
Received: 13 December 2018 / Revised: 9 January 2019 / Accepted: 25 February 2019 / Published: 1 March 2019
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Abstract
Information is the currency of life, but the origin of prebiotic information remains a mystery. We propose transitional pathways from the cosmic building blocks of life to the complex prebiotic organic chemistry that led to the origin of information systems. The prebiotic information [...] Read more.
Information is the currency of life, but the origin of prebiotic information remains a mystery. We propose transitional pathways from the cosmic building blocks of life to the complex prebiotic organic chemistry that led to the origin of information systems. The prebiotic information system, specifically the genetic code, is segregated, linear, and digital, and it appeared before the emergence of DNA. In the peptide/RNA world, lipid membranes randomly encapsulated amino acids, RNA, and peptide molecules, which are drawn from the prebiotic soup, to initiate a molecular symbiosis inside the protocells. This endosymbiosis led to the hierarchical emergence of several requisite components of the translation machine: transfer RNAs (tRNAs), aminoacyl-tRNA synthetase (aaRS), messenger RNAs (mRNAs), ribosomes, and various enzymes. When assembled in the right order, the translation machine created proteins, a process that transferred information from mRNAs to assemble amino acids into polypeptide chains. This was the beginning of the prebiotic information age. The origin of the genetic code is enigmatic; herein, we propose an evolutionary explanation: the demand for a wide range of protein enzymes over peptides in the prebiotic reactions was the main selective pressure for the origin of information-directed protein synthesis. The molecular basis of the genetic code manifests itself in the interaction of aaRS and their cognate tRNAs. In the beginning, aminoacylated ribozymes used amino acids as a cofactor with the help of bridge peptides as a process for selection between amino acids and their cognate codons/anticodons. This process selects amino acids and RNA species for the next steps. The ribozymes would give rise to pre-tRNA and the bridge peptides to pre-aaRS. Later, variants would appear and evolution would produce different but specific aaRS-tRNA-amino acid combinations. Pre-tRNA designed and built pre-mRNA for the storage of information regarding its cognate amino acid. Each pre-mRNA strand became the storage device for the genetic information that encoded the amino acid sequences in triplet nucleotides. As information appeared in the digital languages of the codon within pre-mRNA and mRNA, and the genetic code for protein synthesis evolved, the prebiotic chemistry then became more organized and directional with the emergence of the translation and genetic code. The genetic code developed in three stages that are coincident with the refinement of the translation machines: the GNC code that was developed by the pre-tRNA/pre-aaRS /pre-mRNA machine, SNS code by the tRNA/aaRS/mRNA machine, and finally the universal genetic code by the tRNA/aaRS/mRNA/ribosome machine. We suggest the coevolution of translation machines and the genetic code. The emergence of the translation machines was the beginning of the Darwinian evolution, an interplay between information and its supporting structure. Our hypothesis provides the logical and incremental steps for the origin of the programmed protein synthesis. In order to better understand the prebiotic information system, we converted letter codons into numerical codons in the Universal Genetic Code Table. We have developed a software, called CATI (Codon-Amino Acid-Translator-Imitator), to translate randomly chosen numerical codons into corresponding amino acids and vice versa. This conversion has granted us insight into how the genetic code might have evolved in the peptide/RNA world. There is great potential in the application of numerical codons to bioinformatics, such as barcoding, DNA mining, or DNA fingerprinting. We constructed the likely biochemical pathways for the origin of translation and the genetic code using the Model-View-Controller (MVC) software framework, and the translation machinery step-by-step. While using AnyLogic software, we were able to simulate and visualize the entire evolution of the translation machines, amino acids, and the genetic code. Full article
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Open AccessArticle Low-Digit and High-Digit Polymers in the Origin of Life
Received: 4 January 2019 / Revised: 23 January 2019 / Accepted: 26 January 2019 / Published: 2 February 2019
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Abstract
Extant life uses two kinds of linear biopolymers that mutually control their own production, as well as the cellular metabolism and the production and homeostatic maintenance of other biopolymers. Nucleic acids are linear polymers composed of a relatively low structural variety of monomeric [...] Read more.
Extant life uses two kinds of linear biopolymers that mutually control their own production, as well as the cellular metabolism and the production and homeostatic maintenance of other biopolymers. Nucleic acids are linear polymers composed of a relatively low structural variety of monomeric residues, and thus a low diversity per accessed volume. Proteins are more compact linear polymers that dispose of a huge compositional diversity even at the monomeric level, and thus bear a much higher catalytic potential. The fine-grained diversity of proteins makes an unambiguous information transfer from protein templates too error-prone, so they need to be resynthesized in every generation. But proteins can catalyse both their own reproduction as well as the efficient and faithful replication of nucleic acids, which resolves in a most straightforward way an issue termed “Eigen’s paradox”. Here the importance of the existence of both kinds of linear biopolymers is discussed in the context of the emergence of cellular life, be it for the historic orgin of life on Earth, on some other habitable planet, or in the test tube. An immediate consequence of this analysis is the necessity for translation to appear early during the evolution of life. Full article
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Open AccessArticle Microfluidic Reactors for Carbon Fixation under Ambient-Pressure Alkaline-Hydrothermal-Vent Conditions
Received: 20 December 2018 / Revised: 22 January 2019 / Accepted: 25 January 2019 / Published: 1 February 2019
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Abstract
The alkaline-hydrothermal-vent theory for the origin of life predicts the spontaneous reduction of CO2, dissolved in acidic ocean waters, with H2 from the alkaline vent effluent. This reaction would be catalyzed by Fe(Ni)S clusters precipitated at the interface, which effectively [...] Read more.
The alkaline-hydrothermal-vent theory for the origin of life predicts the spontaneous reduction of CO2, dissolved in acidic ocean waters, with H2 from the alkaline vent effluent. This reaction would be catalyzed by Fe(Ni)S clusters precipitated at the interface, which effectively separate the two fluids into an electrochemical cell. Using microfluidic reactors, we set out to test this concept. We produced thin, long Fe(Ni)S precipitates of less than 10 µm thickness. Mixing simplified analogs of the acidic-ocean and alkaline-vent fluids, we then tested for the reduction of CO2. We were unable to detect reduced carbon products under a number of conditions. As all of our reactions were performed at atmospheric pressure, the lack of reduced carbon products may simply be attributable to the low concentration of hydrogen in our system, suggesting that high-pressure reactors may be a necessity. Full article
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Open AccessArticle Unevolved De Novo Proteins Have Innate Tendencies to Bind Transition Metals
Received: 24 September 2018 / Revised: 31 December 2018 / Accepted: 4 January 2019 / Published: 9 January 2019
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Abstract
Life as we know it would not exist without the ability of protein sequences to bind metal ions. Transition metals, in particular, play essential roles in a wide range of structural and catalytic functions. The ubiquitous occurrence of metalloproteins in all organisms leads [...] Read more.
Life as we know it would not exist without the ability of protein sequences to bind metal ions. Transition metals, in particular, play essential roles in a wide range of structural and catalytic functions. The ubiquitous occurrence of metalloproteins in all organisms leads one to ask whether metal binding is an evolved trait that occurred only rarely in ancestral sequences, or alternatively, whether it is an innate property of amino acid sequences, occurring frequently in unevolved sequence space. To address this question, we studied 52 proteins from a combinatorial library of novel sequences designed to fold into 4-helix bundles. Although these sequences were neither designed nor evolved to bind metals, the majority of them have innate tendencies to bind the transition metals copper, cobalt, and zinc with high nanomolar to low-micromolar affinity. Full article
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Open AccessArticle The Reaction of Aminonitriles with Aminothiols: A Way to Thiol-Containing Peptides and Nitrogen Heterocycles in the Primitive Earth Ocean
Received: 28 September 2018 / Revised: 16 October 2018 / Accepted: 18 October 2018 / Published: 19 October 2018
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Abstract
The Strecker reaction of aldehydes with ammonia and hydrogen cyanide first leads to α-aminonitriles, which are then hydrolyzed to α-amino acids. However, before reacting with water, these aminonitriles can be trapped by aminothiols, such as cysteine or homocysteine, to give 5- or 6-membered [...] Read more.
The Strecker reaction of aldehydes with ammonia and hydrogen cyanide first leads to α-aminonitriles, which are then hydrolyzed to α-amino acids. However, before reacting with water, these aminonitriles can be trapped by aminothiols, such as cysteine or homocysteine, to give 5- or 6-membered ring heterocycles, which in turn are hydrolyzed to dipeptides. We propose that this two-step process enabled the formation of thiol-containing dipeptides in the primitive ocean. These small peptides are able to promote the formation of other peptide bonds and of heterocyclic molecules. Theoretical calculations support our experimental results. They predict that α-aminonitriles should be more reactive than other nitriles, and that imidazoles should be formed from transiently formed amidinonitriles. Overall, this set of reactions delineates a possible early stage of the development of organic chemistry, hence of life, on Earth dominated by nitriles and thiol-rich peptides (TRP). Full article
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Review

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Open AccessReview How Prebiotic Chemistry and Early Life Chose Phosphate
Received: 5 February 2019 / Revised: 23 February 2019 / Accepted: 25 February 2019 / Published: 3 March 2019
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Abstract
The very specific thermodynamic instability and kinetic stability of phosphate esters and anhydrides impart them invaluable properties in living organisms in which highly efficient enzyme catalysts compensate for their low intrinsic reactivity. Considering their role in protein biosynthesis, these properties raise a paradox [...] Read more.
The very specific thermodynamic instability and kinetic stability of phosphate esters and anhydrides impart them invaluable properties in living organisms in which highly efficient enzyme catalysts compensate for their low intrinsic reactivity. Considering their role in protein biosynthesis, these properties raise a paradox about early stages: How could these species be selected in the absence of enzymes? This review is aimed at demonstrating that considering mixed anhydrides or other species more reactive than esters and anhydrides can help in solving the paradox. The consequences of this approach for chemical evolution and early stages of life are analysed. Full article
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Open AccessReview The Beginning of Systems Chemistry
Received: 2 January 2019 / Accepted: 17 January 2019 / Published: 24 January 2019
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Abstract
Systems Chemistry has its roots in the research on the autocatalytic self-replication of biological macromolecules, first of all of synthetic deoxyribonucleic acids. A personal tour through the early works of the founder of Systems Chemistry, and of his first followers, recalls what’s most [...] Read more.
Systems Chemistry has its roots in the research on the autocatalytic self-replication of biological macromolecules, first of all of synthetic deoxyribonucleic acids. A personal tour through the early works of the founder of Systems Chemistry, and of his first followers, recalls what’s most important in this new era of chemistry: the growth and evolution of compartmented macromolecular populations, when provided with “food” and “fuel” and disposed of “waste”. Full article
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Open AccessReview Exploring the Emergence of RNA Nucleosides and Nucleotides on the Early Earth
Received: 2 October 2018 / Revised: 31 October 2018 / Accepted: 3 November 2018 / Published: 6 November 2018
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Abstract
Understanding how life began is one of the most fascinating problems to solve. By approaching this enigma from a chemistry perspective, the goal is to define what series of chemical reactions could lead to the synthesis of nucleotides, amino acids, lipids, and other [...] Read more.
Understanding how life began is one of the most fascinating problems to solve. By approaching this enigma from a chemistry perspective, the goal is to define what series of chemical reactions could lead to the synthesis of nucleotides, amino acids, lipids, and other cellular components from simple feedstocks under prebiotically plausible conditions. It is well established that evolution of life involved RNA which plays central roles in both inheritance and catalysis. In this review, we present historically important and recently published articles aimed at understanding the emergence of RNA nucleosides and nucleotides on the early Earth. Full article
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Open AccessReview Chemomimesis and Molecular Darwinism in Action: From Abiotic Generation of Nucleobases to Nucleosides and RNA
Received: 23 May 2018 / Revised: 14 June 2018 / Accepted: 19 June 2018 / Published: 20 June 2018
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Abstract
Molecular Darwinian evolution is an intrinsic property of reacting pools of molecules resulting in the adaptation of the system to changing conditions. It has no a priori aim. From the point of view of the origin of life, Darwinian selection behavior, when spontaneously [...] Read more.
Molecular Darwinian evolution is an intrinsic property of reacting pools of molecules resulting in the adaptation of the system to changing conditions. It has no a priori aim. From the point of view of the origin of life, Darwinian selection behavior, when spontaneously emerging in the ensembles of molecules composing prebiotic pools, initiates subsequent evolution of increasingly complex and innovative chemical information. On the conservation side, it is a posteriori observed that numerous biological processes are based on prebiotically promptly made compounds, as proposed by the concept of Chemomimesis. Molecular Darwinian evolution and Chemomimesis are principles acting in balanced cooperation in the frame of Systems Chemistry. The one-pot synthesis of nucleosides in radical chemistry conditions is possibly a telling example of the operation of these principles. Other indications of similar cases of molecular evolution can be found among biogenic processes. Full article
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Other

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Open AccessHypothesis Making Molecules with Clay: Layered Double Hydroxides, Pentopyranose Nucleic Acids and the Origin of Life
Received: 2 December 2018 / Revised: 4 February 2019 / Accepted: 9 February 2019 / Published: 15 February 2019
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Abstract
A mixture of sugar diphosphates is produced in reactions between small aldehyde phosphates catalysed by layered double hydroxide (LDH) clays under plausibly prebiotic conditions. A subset of these, pentose diphosphates, constitute the backbone subunits of nucleic acids capable of base pairing, which is [...] Read more.
A mixture of sugar diphosphates is produced in reactions between small aldehyde phosphates catalysed by layered double hydroxide (LDH) clays under plausibly prebiotic conditions. A subset of these, pentose diphosphates, constitute the backbone subunits of nucleic acids capable of base pairing, which is not the case for the other products of these LDH-catalysed reactions. Not only that, but to date no other polymer found capable of base pairing—and therefore information transfer—has a backbone for which its monomer subunits have a plausible prebiotic synthesis, including the ribose-5-phosphate backbone subunit of RNA. Pentose diphosphates comprise the backbone monomers of pentopyranose nucleic acids, some of the strongest base pairing systems so far discovered. We have previously proposed that the first base pairing interactions were between purine nucleobase precursors, and that these were weaker and less specific than standard purine-pyrimidine interactions. We now propose that the inherently stronger pairing of pentopyranose nucleic acids would have compensated for these weaker interactions, and produced an informational polymer capable of undergoing nonenzymatic replication. LDH clays might also have catalysed the synthesis of the purine nucleobase precursors, and the polymerization of pentopyranose nucleotide monomers into oligonucleotides, as well as the formation of the first lipid bilayers. Full article
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

"*Tentative title:* Organocatalysis and Microcompartments in Prebiotic Systems. What can we learn from modern synthetic organic reactions?
Tentative authors: Tecla Gasperi and Pasquale Stano (but we intend to involve also our young co-workers)
Abstract: The manuscript will describe the conceptual and practical importance of organocatalytic mechanisms in basic and applied science, with a special reference to those occurring in water or in a lipid matrix. The text will provide firstly a general introduction to organocatalysis, its reasons, origins and development in modern organic chemistry, then it will focus on specific examples of prebiotic importance. The occurrence of organocatalytic reaction in liposome lumen and liposome membrane will be presented/proposed/discussed. "
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