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The Origin and Early Evolution of Life: Prebiotic Systems Chemistry...
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The Origin and Early Evolution of Life: Prebiotic Systems Chemistry Perspective

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

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 70757

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editors

Dr. Michele Fiore

E-Mail Website
Guest Editor
Institute of Molecular and Supramolecular Chemistry and Biochemistry, University of Lyon, Claude Bernard Lyon 1, UMR 5246, CEDEX, 69100 Villeurbanne, France
Interests: systems chemistry; systems biology; prebiotic chemistry and prebiotic systems chemistry; origin of life; prebiotic synthesis of amphiphiles; total synthesis of racemic and enantiopure phospholipids; evolvable molecular systems synthesis of fluorescent clickable probes; synthesis and application of glycolipids; radical reactions
Special Issues, Collections and Topics in MDPI journals
Dr. Emiliano Altamura

E-Mail Website
Guest Editor
Department of Chemistry, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari BA, Italy
Interests: artificial photosynthetic cell; synthetic biology; systems chemistry; origin of life; giant lipid vesicles; ATP production in compartmentalized systems; natural and artificial organelles; liposomes; confined enzymatic reactions; protein chemistry; membrane proteins; confocal microscopy; flow cytometry

Special Issue Information

What is life? How, where, and when did life arise? These questions have remained most-fascinating over the last hundred years. Aristoteles 2400 years ago postulated that “nature does not do anything endless” and many years later the German biologist Carl Richard Woese (1928 -2012) emphasized the urgency of conducting in-depth studies in search of what we call Life with the following words: “Biology today is no more fully understood in principle than physics was a century or so ago. In both cases the guiding vision has (or had) reached its end, and in both, a new, deeper, more invigorating representation of reality is (or was) called for”. (Woese, A New Biology for a New Century. Microbiol Mol Biol Rev 68:173–186. https://0-doi-org.brum.beds.ac.uk/10.1128/MMBR.68.2.173-186.2004) Systems chemistry (Ashkenasy G, Hermans TM, Otto S, Taylor AF (2017) Systems chemistry. Chem Soc Rev 46:2543–2554. https://0-doi-org.brum.beds.ac.uk/10.1039/C7CS00117G) is the way to go to better understan the problem and to try replying the unsolved question about the origin of Life. Self-organization, thanks to the role of lipid boundaries made possible the rising of protocells. The role of this boundaries is to spatially distinct, separate and co-locate micro-environments; to protect and keep them at defined concentrations; to enable a multitude of often competing and interfering biochemical reactions to occur simultaneously.

The aim of this Special Issue is to summarize the latest discoveries in prebiotic chemistry of biomolecules field, self-organization, protocells and origin of life. In recent years, thousands of excellent reviews and articles appeared in the literature and some breakthroughs have already been achieved. However, a great deal of 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, essentially based on systems chemistry (and biology, physics, geology, mineralogy and astronomy) 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 research, scientific perspectives and literature reviews on this topic are deeply encouraged.

For hypothesis and perspective article, they should not simply be novel ways of thinking about life, they should also be testable, either by future observations or by experiment.

Published Papers (22 papers)

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Editorial

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3 pages, 185 KiB  
Editorial
The Origin and Early Evolution of Life: (Prebiotic) Systems Chemistry Perspective
by Emiliano Altamura and Michele Fiore
Life 2022, 12(5), 710; https://0-doi-org.brum.beds.ac.uk/10.3390/life12050710 - 10 May 2022
Viewed by 1575
Abstract
Aristotle considered that “nature does not do anything endless” [...] Full article
(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Systems Chemistry Perspective)

Research

Jump to: Editorial, Review, Other

26 pages, 17439 KiB  
Article
The Formation of RNA Pre-Polymers in the Presence of Different Prebiotic Mineral Surfaces Studied by Molecular Dynamics Simulations
by Alix Dujardin, Sebastian Himbert, Ralph Pudritz and Maikel C. Rheinstädter
Life 2023, 13(1), 112; https://0-doi-org.brum.beds.ac.uk/10.3390/life13010112 - 30 Dec 2022
Viewed by 2697
Abstract
We used all-atom Molecular Dynamics (MD) computer simulations to study the formation of pre-polymers between the four nucleotides in RNA (AMP, UMP, CMP, GMP) in the presence of different substrates that could have been present in a prebiotic environment. Pre-polymers are [...] Read more.
We used all-atom Molecular Dynamics (MD) computer simulations to study the formation of pre-polymers between the four nucleotides in RNA (AMP, UMP, CMP, GMP) in the presence of different substrates that could have been present in a prebiotic environment. Pre-polymers are C3′–C5′ hydrogen-bonded nucleotides that have been suggested to be the precursors of phosphodiester-bonded RNA polymers. We simulated wet–dry cycles by successively removing water molecules from the simulations, from ~60 to 3 water molecules per nucleotide. The nine substrates in this study include three clay minerals, one mica, one phosphate mineral, one silica, and two metal oxides. The substrates differ in their surface charge and ability to form hydrogen bonds with the nucleotides. From the MD simulations, we quantify the interactions between different nucleotides, and between nucleotides and substrates. For comparison, we included graphite as an inert substrate, which is not charged and cannot form hydrogen bonds. We also simulated the dehydration of a nucleotide-only system, which mimics the drying of small droplets. The number of hydrogen bonds between nucleotides and nucleotides and substrates was found to increase significantly when water molecules were removed from the systems. The largest number of C3′–C5′ hydrogen bonds between nucleotides occurred in the graphite and nucleotide-only systems. While the surface of the substrates led to an organization and periodic arrangement of the nucleotides, none of the substrates was found to be a catalyst for pre-polymer formation, neither at full hydration, nor when dehydrated. While confinement and dehydration seem to be the main drivers for hydrogen bond formation, substrate interactions reduced the interactions between nucleotides in all cases. Our findings suggest that small supersaturated water droplets that could have been produced by geysers or springs on the primitive Earth may play an important role in non-enzymatic RNA polymerization. Full article
(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Systems Chemistry Perspective)
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16 pages, 2982 KiB  
Article
Life on Minerals: Binding Behaviors of Oligonucleotides on Zirconium Silicate and Its Inhibitory Activity for the Self-Cleavage of Hammerhead Ribozyme
by Kunio Kawamura, Jean-François Lambert, Louis M. P. Ter-Ovanessian, Jacques Vergne, Guy Hervé and Marie-Christine Maurel
Life 2022, 12(11), 1689; https://0-doi-org.brum.beds.ac.uk/10.3390/life12111689 - 24 Oct 2022
Cited by 2 | Viewed by 1235
Abstract
The role of minerals in the chemical evolution of RNA molecules is an important issue when considering the early stage of the Hadean Earth. In particular, the interaction between functional ribozymes and ancient minerals under simulated primitive conditions is a recent research focus. [...] Read more.
The role of minerals in the chemical evolution of RNA molecules is an important issue when considering the early stage of the Hadean Earth. In particular, the interaction between functional ribozymes and ancient minerals under simulated primitive conditions is a recent research focus. We are currently attempting to design a primitive RNA metabolic network which would function with minerals, and believe that the simulated chemical network of RNA molecules would be useful for evaluation of the chemical evolution from a simple RNA mixture to an RNA-based life-like system. First, we measured the binding interactions of oligonucleotides with four types of minerals; Aerosil silica, zirconium silicate, sepiolite, and montmorillonite. Oligonucleotides bound zirconium silicate and montmorillonite in the presence of MgCl2, and bound sepiolite both in the presence and absence of MgCl2, but they did not bind Aerosil. Based on the binding behavior, we attempted the self-cleavage reaction of the hammerhead ribozyme from an avocado viroid. This reaction was strongly inhibited by zirconium silicate, a compound regarded as mineral evidence for the existence of water. The present study suggests that the chemical evolution of functional RNA molecules requires specific conformational binding, resulting in efficient ribozyme function as well as zirconium silicate for the chemical evolution of biomolecules. Full article
(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Systems Chemistry Perspective)
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11 pages, 2546 KiB  
Article
Oxidative Phosphorus Chemistry Perturbed by Minerals
by Arthur Omran, Josh Abbatiello, Tian Feng and Matthew A. Pasek
Life 2022, 12(2), 198; https://0-doi-org.brum.beds.ac.uk/10.3390/life12020198 - 28 Jan 2022
Cited by 6 | Viewed by 2925
Abstract
Life is a complex, open chemical system that must be supported with energy inputs. If one fathoms how simple early life must have been, the complexity of modern-day life is staggering by comparison. A minimally complex system that could plausibly provide pyrophosphates for [...] Read more.
Life is a complex, open chemical system that must be supported with energy inputs. If one fathoms how simple early life must have been, the complexity of modern-day life is staggering by comparison. A minimally complex system that could plausibly provide pyrophosphates for early life could be the oxidation of reduced phosphorus sources such as hypophosphite and phosphite. Like all plausible prebiotic chemistries, this system would have been altered by minerals and rocks in close contact with the evolving solutions. This study addresses the different types of perturbations that minerals might have on this chemical system. This study finds that minerals may inhibit the total production of oxidized phosphorus from reduced phosphorus species, they may facilitate the production of phosphate, or they may facilitate the production of pyrophosphate. This study concludes with the idea that mineral perturbations from the environment increase the chemical complexity of this system. Full article
(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Systems Chemistry Perspective)
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13 pages, 4838 KiB  
Article
Membrane Structure Obtained in an Experimental Evolution Process
by María J. Dávila and Christian Mayer
Life 2022, 12(2), 145; https://0-doi-org.brum.beds.ac.uk/10.3390/life12020145 - 20 Jan 2022
Cited by 4 | Viewed by 2068
Abstract
Recently, an evolution experiment was carried out in a cyclic process, which involved periodic vesicle formation in combination with peptide and vesicle selection. As an outcome, an octapeptide (KSPFPFAA) was identified which rapidly integrated into the vesicle membrane and, according to its significant [...] Read more.
Recently, an evolution experiment was carried out in a cyclic process, which involved periodic vesicle formation in combination with peptide and vesicle selection. As an outcome, an octapeptide (KSPFPFAA) was identified which rapidly integrated into the vesicle membrane and, according to its significant accumulation, is obviously connected to a particular advantage of the corresponding functionalized vesicle. Here we report a molecular dynamics study of the structural details of the functionalized vesicle membrane, which was a product of this evolution process and is connected to several survival mechanisms. In order to elucidate the particular advantage of this structure, we performed all-atom molecular dynamics simulations to examine structural changes and interactions of the peptide (KSPFPFAA) with the given octadecanoic acid/octadecylamine (1:1) bilayer under acidic conditions. The calculations clearly demonstrate the specific interactions between the peptide and the membrane and reveal the mechanisms leading to the improved vesicle survival. Full article
(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Systems Chemistry Perspective)
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15 pages, 3168 KiB  
Article
Influence of Metal Ions on Model Protoamphiphilic Vesicular Systems: Insights from Laboratory and Analogue Studies
by Manesh Prakash Joshi, Luke Steller, Martin J. Van Kranendonk and Sudha Rajamani
Life 2021, 11(12), 1413; https://0-doi-org.brum.beds.ac.uk/10.3390/life11121413 - 16 Dec 2021
Cited by 6 | Viewed by 3431
Abstract
Metal ions strongly affect the self-assembly and stability of membranes composed of prebiotically relevant amphiphiles (protoamphiphiles). Therefore, evaluating the behavior of such amphiphiles in the presence of ions is a crucial step towards assessing their potential as model protocell compartments. We have recently [...] Read more.
Metal ions strongly affect the self-assembly and stability of membranes composed of prebiotically relevant amphiphiles (protoamphiphiles). Therefore, evaluating the behavior of such amphiphiles in the presence of ions is a crucial step towards assessing their potential as model protocell compartments. We have recently reported vesicle formation by N-acyl amino acids (NAAs), an interesting class of protoamphiphiles containing an amino acid linked to a fatty acid via an amide linkage. Herein, we explore the effect of ions on the self-assembly and stability of model N-oleoyl glycine (NOG)-based membranes. Microscopic analysis showed that the blended membranes of NOG and Glycerol 1-monooleate (GMO) were more stable than pure NOG vesicles, both in the presence of monovalent and divalent cations, with the overall vesicle stability being 100-fold higher in the presence of a monovalent cation. Furthermore, both pure NOG and NOG + GMO mixed systems were able to self-assemble into vesicles in natural water samples containing multiple ions that were collected from active hot spring sites. Our study reveals that several aspects of the metal ion stability of NAA-based membranes are comparable to those of fatty acid-based systems, while also confirming the robustness of compositionally heterogeneous membranes towards high metal ion concentrations. Pertinently, the vesicle formation by NAA-based systems in terrestrial hot spring samples indicates the conduciveness of these low ionic strength freshwater systems for facilitating prebiotic membrane-assembly processes. This further highlights their potential to serve as a plausible niche for the emergence of cellular life on the early Earth. Full article
(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Systems Chemistry Perspective)
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15 pages, 1565 KiB  
Article
Racemate Resolution of Alanine and Leucine on Homochiral Quartz, and Its Alteration by Strong Radiation Damage
by Adrien D. Garcia, Cornelia Meinert, Friedrich Finger, Uwe J. Meierhenrich and Ewald Hejl
Life 2021, 11(11), 1222; https://0-doi-org.brum.beds.ac.uk/10.3390/life11111222 - 11 Nov 2021
Cited by 3 | Viewed by 1612
Abstract
Homochiral proteins orchestrate biological functions throughout all domains of life, but the origin of the uniform l-stereochemistry of amino acids remains unknown. Here, we describe enantioselective adsorption experiments of racemic alanine and leucine onto homochiral d- and l-quartz as a [...] Read more.
Homochiral proteins orchestrate biological functions throughout all domains of life, but the origin of the uniform l-stereochemistry of amino acids remains unknown. Here, we describe enantioselective adsorption experiments of racemic alanine and leucine onto homochiral d- and l-quartz as a possible mechanism for the abiotic emergence of biological homochirality. Substantial racemate resolution with enantiomeric excesses of up to 55% are demonstrated to potentially occur in interstitial pores, along grain boundaries or small fractures in local quartz-bearing environments. Our previous hypothesis on the enhanced enantioselectivity due to uranium-induced fission tracks could not be validated. Such capillary tubes in the near-surface structure of quartz have been proposed to increase the overall chromatographic separation of enantiomers, but no systematic positive correlation of accumulated radiation damage and enantioselective adsorption was observed in this study. In general, the natural l-quartz showed stronger enantioselective adsorption affinities than synthetic d-quartz without any significant trend in amino acid selectivity. Moreover, the l-enantiomer of both investigated amino acids alanine and leucine was preferably adsorbed regardless of the handedness of the enantiomorphic quartz sand. This lack of mirror symmetry breaking is probably due to the different crystal habitus of the synthetic z-bar of d-quartz and the natural mountain crystals of l-quartz used in our experiments. Full article
(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Systems Chemistry Perspective)
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23 pages, 2728 KiB  
Article
Thermodynamics of Potential CHO Metabolites in a Reducing Environment
by Jeremy Kua, Alexandra L. Hernandez and Danielle N. Velasquez
Life 2021, 11(10), 1025; https://0-doi-org.brum.beds.ac.uk/10.3390/life11101025 - 29 Sep 2021
Cited by 2 | Viewed by 2293
Abstract
How did metabolism arise and evolve? What chemical compounds might be suitable to support and sustain a proto-metabolism before the advent of more complex co-factors? We explore these questions by using first-principles quantum chemistry to calculate the free energies of CHO compounds in [...] Read more.
How did metabolism arise and evolve? What chemical compounds might be suitable to support and sustain a proto-metabolism before the advent of more complex co-factors? We explore these questions by using first-principles quantum chemistry to calculate the free energies of CHO compounds in aqueous solution, allowing us to probe the thermodynamics of core extant cycles and their closely related chemical cousins. By framing our analysis in terms of the simplest feasible cycle and its permutations, we analyze potentially favorable thermodynamic cycles for CO2 fixation with H2 as a reductant. We find that paying attention to redox states illuminates which reactions are endergonic or exergonic. Our results highlight the role of acetate in proto-metabolic cycles, and its connection to other prebiotic molecules such as glyoxalate, glycolaldehyde, and glycolic acid. Full article
(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Systems Chemistry Perspective)
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12 pages, 659 KiB  
Article
The Combinatorial Fusion Cascade to Generate the Standard Genetic Code
by Alexander Nesterov-Mueller and Roman Popov
Life 2021, 11(9), 975; https://0-doi-org.brum.beds.ac.uk/10.3390/life11090975 - 16 Sep 2021
Cited by 2 | Viewed by 2305
Abstract
Combinatorial fusion cascade was proposed as a transition stage between prebiotic chemistry and early forms of life. The combinatorial fusion cascade consists of three stages: eight initial complimentary pairs of amino acids, four protocodes, and the standard genetic code. The initial complimentary pairs [...] Read more.
Combinatorial fusion cascade was proposed as a transition stage between prebiotic chemistry and early forms of life. The combinatorial fusion cascade consists of three stages: eight initial complimentary pairs of amino acids, four protocodes, and the standard genetic code. The initial complimentary pairs and the protocodes are divided into dominant and recessive entities. The transitions between these stages obey the same combinatorial fusion rules for all amino acids. The combinatorial fusion cascade mathematically describes the codon assignments in the standard genetic code. It explains the availability of amino acids with the even and odd numbers of codons, the appearance of stop codons, inclusion of novel canonical amino acids, exceptional high numbers of codons for amino acids arginine, leucine, and serine, and the temporal order of amino acid inclusion into the genetic code. The temporal order of amino acids within the cascade is congruent with the consensus temporal order previously derived from the similarities between the available hypotheses. The control over the combinatorial fusion cascades would open the road for a novel technology to develop artificial microorganisms. Full article
(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Systems Chemistry Perspective)
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26 pages, 5888 KiB  
Article
When Is a Reaction Network a Metabolism? Criteria for Simple Metabolisms That Support Growth and Division of Protocells
by Paul G. Higgs
Life 2021, 11(9), 966; https://0-doi-org.brum.beds.ac.uk/10.3390/life11090966 - 14 Sep 2021
Cited by 9 | Viewed by 2495
Abstract
With the aim of better understanding the nature of metabolism in the first cells and the relationship between the origin of life and the origin of metabolism, we propose three criteria that a chemical reaction system must satisfy in order to constitute a [...] Read more.
With the aim of better understanding the nature of metabolism in the first cells and the relationship between the origin of life and the origin of metabolism, we propose three criteria that a chemical reaction system must satisfy in order to constitute a metabolism that would be capable of sustaining growth and division of a protocell. (1) Biomolecules produced by the reaction system must be maintained at high concentration inside the cell while they remain at low or zero concentration outside. (2) The total solute concentration inside the cell must be higher than outside, so there is a positive osmotic pressure that drives cell growth. (3) The metabolic rate (i.e., the rate of mass throughput) must be higher inside the cell than outside. We give examples of small-molecule reaction systems that satisfy these criteria, and others which do not, firstly considering fixed-volume compartments, and secondly, lipid vesicles that can grow and divide. If the criteria are satisfied, and if a supply of lipid is available outside the cell, then continued growth of membrane surface area occurs alongside the increase in volume of the cell. If the metabolism synthesizes more lipid inside the cell, then the membrane surface area can increase proportionately faster than the cell volume, in which case cell division is possible. The three criteria can be satisfied if the reaction system is bistable, because different concentrations can exist inside and out while the rate constants of all the reactions are the same. If the reaction system is monostable, the criteria can only be satisfied if there is a reason why the rate constants are different inside and out (for example, the decay rates of biomolecules are faster outside, or the formation rates of biomolecules are slower outside). If this difference between inside and outside does not exist, a monostable reaction system cannot sustain cell growth and division. We show that a reaction system for template-directed RNA polymerization can satisfy the requirements for a metabolism, even if the small-molecule reactions that make the single nucleotides do not. Full article
(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Systems Chemistry Perspective)
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9 pages, 1389 KiB  
Article
Plausibility of Early Life in a Relatively Wide Temperature Range: Clues from Simulated Metabolic Network Expansion
by Xin-Yi Chu, Si-Ming Chen, Ke-Wei Zhao, Tian Tian, Jun Gao and Hong-Yu Zhang
Life 2021, 11(8), 738; https://0-doi-org.brum.beds.ac.uk/10.3390/life11080738 - 24 Jul 2021
Cited by 2 | Viewed by 1525
Abstract
The debate on the temperature of the environment where life originated is still inconclusive. Metabolic reactions constitute the basis of life, and may be a window to the world where early life was born. Temperature is an important parameter of reaction thermodynamics, which [...] Read more.
The debate on the temperature of the environment where life originated is still inconclusive. Metabolic reactions constitute the basis of life, and may be a window to the world where early life was born. Temperature is an important parameter of reaction thermodynamics, which determines whether metabolic reactions can proceed. In this study, the scale of the prebiotic metabolic network at different temperatures was examined by a thermodynamically constrained network expansion simulation. It was found that temperature has limited influence on the scale of the simulated metabolic networks, implying that early life may have occurred in a relatively wide temperature range. Full article
(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Systems Chemistry Perspective)
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11 pages, 2387 KiB  
Article
Effect of the Membrane Composition of Giant Unilamellar Vesicles on Their Budding Probability: A Trade-Off between Elasticity and Preferred Area Difference
by Ylenia Miele, Gábor Holló, István Lagzi and Federico Rossi
Life 2021, 11(7), 634; https://0-doi-org.brum.beds.ac.uk/10.3390/life11070634 - 29 Jun 2021
Cited by 5 | Viewed by 2220
Abstract
The budding and division of artificial cells engineered from vesicles and droplets have gained much attention in the past few decades due to an increased interest in designing stimuli-responsive synthetic systems. Proper control of the division process is one of the main challenges [...] Read more.
The budding and division of artificial cells engineered from vesicles and droplets have gained much attention in the past few decades due to an increased interest in designing stimuli-responsive synthetic systems. Proper control of the division process is one of the main challenges in the field of synthetic biology and, especially in the context of the origin of life studies, it would be helpful to look for the simplest chemical and physical processes likely at play in prebiotic conditions. Here we show that pH-sensitive giant unilamellar vesicles composed of mixed phospholipid/fatty acid membranes undergo a budding process, internally fuelled by the urea–urease enzymatic reaction, only for a given range of the membrane composition. A gentle interplay between the effects of the membrane composition on the elasticity and the preferred area difference of the bilayer is responsible for the existence of a narrow range of membrane composition yielding a high probability for budding of the vesicles. Full article
(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Systems Chemistry Perspective)
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45 pages, 5581 KiB  
Article
Origin of Life on Mars: Suitability and Opportunities
by Benton C. Clark, Vera M. Kolb, Andrew Steele, Christopher H. House, Nina L. Lanza, Patrick J. Gasda, Scott J. VanBommel, Horton E. Newsom and Jesús Martínez-Frías
Life 2021, 11(6), 539; https://0-doi-org.brum.beds.ac.uk/10.3390/life11060539 - 09 Jun 2021
Cited by 19 | Viewed by 10347
Abstract
Although the habitability of early Mars is now well established, its suitability for conditions favorable to an independent origin of life (OoL) has been less certain. With continued exploration, evidence has mounted for a widespread diversity of physical and chemical conditions on Mars [...] Read more.
Although the habitability of early Mars is now well established, its suitability for conditions favorable to an independent origin of life (OoL) has been less certain. With continued exploration, evidence has mounted for a widespread diversity of physical and chemical conditions on Mars that mimic those variously hypothesized as settings in which life first arose on Earth. Mars has also provided water, energy sources, CHNOPS elements, critical catalytic transition metal elements, as well as B, Mg, Ca, Na and K, all of which are elements associated with life as we know it. With its highly favorable sulfur abundance and land/ocean ratio, early wet Mars remains a prime candidate for its own OoL, in many respects superior to Earth. The relatively well-preserved ancient surface of planet Mars helps inform the range of possible analogous conditions during the now-obliterated history of early Earth. Continued exploration of Mars also contributes to the understanding of the opportunities for settings enabling an OoL on exoplanets. Favoring geochemical sediment samples for eventual return to Earth will enhance assessments of the likelihood of a Martian OoL. Full article
(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Systems Chemistry Perspective)
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9 pages, 1043 KiB  
Article
Prebiotic Peptides Based on the Glycocodon Theory Analyzed with FRET
by Jozef Nahalka and Eva Hrabarova
Life 2021, 11(5), 380; https://0-doi-org.brum.beds.ac.uk/10.3390/life11050380 - 23 Apr 2021
Cited by 2 | Viewed by 1788
Abstract
In modern protein–carbohydrate interactions, carbohydrate–aromatic contact with CH–π interactions are used. Currently, they are considered driving forces of this complexation. In these contacts, tryptophan, tyrosine, and histidine are preferred. In this study, we focus on primary prebiotic chemistry when only glycine, alanine, aspartic [...] Read more.
In modern protein–carbohydrate interactions, carbohydrate–aromatic contact with CH–π interactions are used. Currently, they are considered driving forces of this complexation. In these contacts, tryptophan, tyrosine, and histidine are preferred. In this study, we focus on primary prebiotic chemistry when only glycine, alanine, aspartic acid, and valine are available in polypeptides. In this situation, when the aromatic acids are not available, hydrogen-bonding aspartic acid must be used for monosaccharide complexation. It is shown here that (DAA)n polypeptides play important roles in primary “protein”–glucose recognition, that (DGG)n plays an important role in “protein”–ribose recognition, and that (DGA)n plays an important role in “protein”–galactose recognition. Glucose oxidase from Aspergillus niger, which still has some ancient prebiotic sequences, is chosen here as an example for discussion. Full article
(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Systems Chemistry Perspective)
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8 pages, 893 KiB  
Communication
Formation of Thiophene under Simulated Volcanic Hydrothermal Conditions on Earth—Implications for Early Life on Extraterrestrial Planets?
by Thomas Geisberger, Jessica Sobotta, Wolfgang Eisenreich and Claudia Huber
Life 2021, 11(2), 149; https://0-doi-org.brum.beds.ac.uk/10.3390/life11020149 - 16 Feb 2021
Cited by 5 | Viewed by 3252
Abstract
Thiophene was detected on Mars during the Curiosity mission in 2018. The compound was even suggested as a biomarker due to its possible origin from diagenesis or pyrolysis of biological material. In the laboratory, thiophene can be synthesized at 400 °C by reacting [...] Read more.
Thiophene was detected on Mars during the Curiosity mission in 2018. The compound was even suggested as a biomarker due to its possible origin from diagenesis or pyrolysis of biological material. In the laboratory, thiophene can be synthesized at 400 °C by reacting acetylene and hydrogen sulfide on alumina. We here show that thiophene and thiophene derivatives are also formed abiotically from acetylene and transition metal sulfides such as NiS, CoS and FeS under simulated volcanic, hydrothermal conditions on Early Earth. Exactly the same conditions were reported earlier to have yielded a plethora of organic molecules including fatty acids and other components of extant metabolism. It is therefore tempting to suggest that thiophenes from abiotic formation could indicate sites and conditions well-suited for the evolution of metabolism and potentially for the origin-of-life on extraterrestrial planets. Full article
(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Systems Chemistry Perspective)
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19 pages, 1082 KiB  
Article
Combinatorial Fusion Rules to Describe Codon Assignment in the Standard Genetic Code
by Alexander Nesterov-Mueller, Roman Popov and Hervé Seligmann
Life 2021, 11(1), 4; https://0-doi-org.brum.beds.ac.uk/10.3390/life11010004 - 23 Dec 2020
Cited by 3 | Viewed by 3074
Abstract
We propose combinatorial fusion rules that describe the codon assignment in the standard genetic code simply and uniformly for all canonical amino acids. These rules become obvious if the origin of the standard genetic code is considered as a result of a fusion [...] Read more.
We propose combinatorial fusion rules that describe the codon assignment in the standard genetic code simply and uniformly for all canonical amino acids. These rules become obvious if the origin of the standard genetic code is considered as a result of a fusion of four protocodes: Two dominant AU and GC protocodes and two recessive AU and GC protocodes. The biochemical meaning of the fusion rules consists of retaining the complementarity between cognate codons of the small hydrophobic amino acids and large charged or polar amino acids within the protocodes. The proto tRNAs were assembled in form of two kissing hairpins with 9-base and 10-base loops in the case of dominant protocodes and two 9-base loops in the case of recessive protocodes. The fusion rules reveal the connection between the stop codons, the non-canonical amino acids, pyrrolysine and selenocysteine, and deviations in the translation of mitochondria. Using fusion rules, we predicted the existence of additional amino acids that are essential for the development of the standard genetic code. The validity of the proposed partition of the genetic code into dominant and recessive protocodes is considered referring to state-of-the-art hypotheses. The formation of two aminoacyl-tRNA synthetase classes is compatible with four-protocode partition. Full article
(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Systems Chemistry Perspective)
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14 pages, 2789 KiB  
Article
Further Characterization of the Pseudo-Symmetrical Ribosomal Region
by Mario Rivas and George E. Fox
Life 2020, 10(9), 201; https://0-doi-org.brum.beds.ac.uk/10.3390/life10090201 - 14 Sep 2020
Cited by 8 | Viewed by 2804
Abstract
The peptidyl transferase center of the modern ribosome has been found to encompass an area of twofold pseudosymmetry (SymR). This observation strongly suggests that the very core of the ribosome arose from a dimerization event between two modest-sized RNAs. It was previously shown [...] Read more.
The peptidyl transferase center of the modern ribosome has been found to encompass an area of twofold pseudosymmetry (SymR). This observation strongly suggests that the very core of the ribosome arose from a dimerization event between two modest-sized RNAs. It was previously shown that at least four non-standard interactions exist between the two halves of SymR. Herein, we verify that the structure of the SymR is highly conserved with respect to both ribosome transition state and phylogenetic diversity. These comparisons also reveal two additional sites of interaction between the two halves of SymR and refine our understanding of the previously known interactions. In addition, the possible role that magnesium may have in the coordination, stabilization, association, and evolutionary history of the two halves (A-region and P-region) was examined. Together, the results identify a likely site where structural elements and Mg2+ ions may have facilitated the ligation of two aboriginal RNAs into a single unit. Full article
(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Systems Chemistry Perspective)
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Review

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13 pages, 3212 KiB  
Review
Questions and Answers Related to the Prebiotic Production of Oligonucleotide Sequences from 3′,5′ Cyclic Nucleotide Precursors
by Judit E. Šponer, Jiří Šponer, Aleš Kovařík, Ondrej Šedo, Zbyněk Zdráhal, Giovanna Costanzo and Ernesto Di Mauro
Life 2021, 11(8), 800; https://0-doi-org.brum.beds.ac.uk/10.3390/life11080800 - 08 Aug 2021
Cited by 4 | Viewed by 2420
Abstract
Template-free nonenzymatic polymerization of 3′,5′ cyclic nucleotides is an emerging topic of the origin of life research. In the last ten years, a number of papers have been published addressing various aspects of this process. These works evoked a vivid discussion among scientists [...] Read more.
Template-free nonenzymatic polymerization of 3′,5′ cyclic nucleotides is an emerging topic of the origin of life research. In the last ten years, a number of papers have been published addressing various aspects of this process. These works evoked a vivid discussion among scientists working in the field of prebiotic chemistry. The aim of the current review is to answer the most frequently raised questions related to the detection and characterization of oligomeric products as well as to the geological context of this chemistry. Full article
(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Systems Chemistry Perspective)
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8 pages, 208 KiB  
Review
How Was Nature Able to Discover Its Own Laws—Twice?
by Addy Pross
Life 2021, 11(7), 679; https://0-doi-org.brum.beds.ac.uk/10.3390/life11070679 - 12 Jul 2021
Cited by 3 | Viewed by 2484
Abstract
The central thesis of the modern scientific revolution is that nature is objective. Yet, somehow, out of that objective reality, projective systems emerged—cognitive and purposeful. More remarkably, through nature’s objective laws, chemical systems emerged and evolved to take advantage of those laws. Even [...] Read more.
The central thesis of the modern scientific revolution is that nature is objective. Yet, somehow, out of that objective reality, projective systems emerged—cognitive and purposeful. More remarkably, through nature’s objective laws, chemical systems emerged and evolved to take advantage of those laws. Even more inexplicably, nature uncovered those laws twice—once unconsciously, once consciously. Accordingly, one could rephrase the origin of life question as follows: how was nature able to become self-aware and discover its own laws? What is the law of nature that enabled nature to discover its own laws? Addressing these challenging questions in physical-chemical terms may be possible through the newly emergent field of systems chemistry. Full article
(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Systems Chemistry Perspective)
22 pages, 2612 KiB  
Review
Astrochemical Pathways to Complex Organic and Prebiotic Molecules: Experimental Perspectives for In Situ Solid-State Studies
by Daniele Fulvio, Alexey Potapov, Jiao He and Thomas Henning
Life 2021, 11(6), 568; https://0-doi-org.brum.beds.ac.uk/10.3390/life11060568 - 17 Jun 2021
Cited by 9 | Viewed by 3491
Abstract
A deep understanding of the origin of life requires the physical, chemical, and biological study of prebiotic systems and the comprehension of the mechanisms underlying their evolutionary steps. In this context, great attention is paid to the class of interstellar molecules known as [...] Read more.
A deep understanding of the origin of life requires the physical, chemical, and biological study of prebiotic systems and the comprehension of the mechanisms underlying their evolutionary steps. In this context, great attention is paid to the class of interstellar molecules known as “Complex Organic Molecules” (COMs), considered as possible precursors of prebiotic species. Although COMs have already been detected in different astrophysical environments (such as interstellar clouds, protostars, and protoplanetary disks) and in comets, the physical–chemical mechanisms underlying their formation are not yet fully understood. In this framework, a unique contribution comes from laboratory experiments specifically designed to mimic the conditions found in space. We present a review of experimental studies on the formation and evolution of COMs in the solid state, i.e., within ices of astrophysical interest, devoting special attention to the in situ detection and analysis techniques commonly used in laboratory astrochemistry. We discuss their main strengths and weaknesses and provide a perspective view on novel techniques, which may help in overcoming the current experimental challenges. Full article
(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Systems Chemistry Perspective)
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Other

11 pages, 912 KiB  
Concept Paper
Viroids and Viroid-like Circular RNAs: Do They Descend from Primordial Replicators?
by Benjamin D. Lee and Eugene V. Koonin
Life 2022, 12(1), 103; https://0-doi-org.brum.beds.ac.uk/10.3390/life12010103 - 12 Jan 2022
Cited by 11 | Viewed by 7659
Abstract
Viroids are a unique class of plant pathogens that consist of small circular RNA molecules, between 220 and 450 nucleotides in size. Viroids encode no proteins and are the smallest known infectious agents. Viroids replicate via the rolling circle mechanism, producing multimeric intermediates [...] Read more.
Viroids are a unique class of plant pathogens that consist of small circular RNA molecules, between 220 and 450 nucleotides in size. Viroids encode no proteins and are the smallest known infectious agents. Viroids replicate via the rolling circle mechanism, producing multimeric intermediates which are cleaved to unit length either by ribozymes formed from both polarities of the viroid genomic RNA or by coopted host RNAses. Many viroid-like small circular RNAs are satellites of plant RNA viruses. Ribozyviruses, represented by human hepatitis delta virus, are larger viroid-like circular RNAs that additionally encode the viral nucleocapsid protein. It has been proposed that viroids are direct descendants of primordial RNA replicons that were present in the hypothetical RNA world. We argue, however, that much later origin of viroids, possibly, from recently discovered mobile genetic elements known as retrozymes, is a far more parsimonious evolutionary scenario. Nevertheless, viroids and viroid-like circular RNAs are minimal replicators that are likely to be close to the theoretical lower limit of replicator size and arguably comprise the paradigm for replicator emergence. Thus, although viroid-like replicators are unlikely to be direct descendants of primordial RNA replicators, the study of the diversity and evolution of these ultimate genetic parasites can yield insights into the earliest stages of the evolution of life. Full article
(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Systems Chemistry Perspective)
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9 pages, 1666 KiB  
Perspective
Did Solid Surfaces Enable the Origin of Life?
by İrep Gözen
Life 2021, 11(8), 795; https://0-doi-org.brum.beds.ac.uk/10.3390/life11080795 - 05 Aug 2021
Cited by 4 | Viewed by 3793
Abstract
In this perspective article, I discuss whether and how solid surfaces could have played a key role in the formation of membranous primitive cells on the early Earth. I argue why surface energy could have been used by prebiotic amphiphile assemblies for unique [...] Read more.
In this perspective article, I discuss whether and how solid surfaces could have played a key role in the formation of membranous primitive cells on the early Earth. I argue why surface energy could have been used by prebiotic amphiphile assemblies for unique morphological transformations, and present recent experimental findings showing the surface-dependent formation and behavior of sophisticated lipid membrane structures. Finally, I discuss the possible unique contributions of such surface-adhered architectures to the transition from prebiotic matter to living systems. Full article
(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Systems Chemistry Perspective)
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