Life | Special Issue : Feature Papers in Origins of Life

Editorial

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3 pages, 146 KiB

Open AccessEditorial

Various Viewpoints to Investigate the Origins of Life Are Needed

by Tony Z. Jia and Kuhan Chandru

Life 2024, 14(10), 1324; https://doi.org/10.3390/life14101324 - 18 Oct 2024

Viewed by 923

Abstract

How life first arose on Earth is a mystery that humankind has sought to understand for millennia, and includes scientific, philosophical, societal, and religious aspects, amongst others [...] Full article

(This article belongs to the Special Issue Feature Papers in Origins of Life)

Research

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13 pages, 4647 KiB

Open AccessArticle

New Estimates of Nitrogen Fixation on Early Earth

by Madeline Christensen, Danica Adams, Michael L. Wong, Patrick Dunn and Yuk L. Yung

Life 2024, 14(5), 601; https://doi.org/10.3390/life14050601 - 8 May 2024

Cited by 1 | Viewed by 1307

Abstract

Fixed nitrogen species generated by the early Earth’s atmosphere are thought to be critical to the emergence of life and the sustenance of early metabolisms. A previous study estimated nitrogen fixation in the Hadean Earth’s N₂/CO₂-dominated atmosphere; however, that [...] Read more.

Fixed nitrogen species generated by the early Earth’s atmosphere are thought to be critical to the emergence of life and the sustenance of early metabolisms. A previous study estimated nitrogen fixation in the Hadean Earth’s N₂/CO₂-dominated atmosphere; however, that previous study only considered a limited chemical network that produces NO_x species (i.e., no HCN formation) via the thermochemical dissociation of N₂ and CO₂ in lightning flashes, followed by photochemistry. Here, we present an updated model of nitrogen fixation on Hadean Earth. We use the Chemical Equilibrium with Applications (CEA) thermochemical model to estimate lightning-induced NO and HCN formation and an updated version of KINETICS, the 1-D Caltech/JPL photochemical model, to assess the photochemical production of fixed nitrogen species that rain out into the Earth’s early ocean. Our updated photochemical model contains hydrocarbon and nitrile chemistry, and we use a Geant4 simulation platform to consider nitrogen fixation stimulated by solar energetic particle deposition throughout the atmosphere. We study the impact of a novel reaction pathway for generating HCN via HCN₂, inspired by the experimental results which suggest that reactions with CH radicals (from CH₄ photolysis) may facilitate the incorporation of N into the molecular structure of aerosols. When the HCN₂ reactions are added, we find that the HCN rainout rate rises by a factor of five in our 1-bar case and is about the same in our 2- and 12-bar cases. Finally, we estimate the equilibrium concentration of fixed nitrogen species under a kinetic steady state in the Hadean ocean, considering loss by hydrothermal vent circulation, photoreduction, and hydrolysis. These results inform our understanding of environments that may have been relevant to the formation of life on Earth, as well as processes that could lead to the emergence of life elsewhere in the universe. Full article

(This article belongs to the Special Issue Feature Papers in Origins of Life)

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14 pages, 2867 KiB

Open AccessArticle

Microfluidics-Based Drying–Wetting Cycles to Investigate Phase Transitions of Small Molecules Solutions

by Ajay Verma, Tiphaine Mateo, Juan Quintero Botero, Nishanth Mohankumar and Tommaso P. Fraccia

Life 2024, 14(4), 472; https://doi.org/10.3390/life14040472 - 4 Apr 2024

Cited by 1 | Viewed by 1309

Abstract

Drying–wetting cycles play a crucial role in the investigation of the origin of life as processes that both concentrate and induce the supramolecular assembly and polymerization of biomolecular building blocks, such as nucleotides and amino acids. Here, we test different microfluidic devices to [...] Read more.

Drying–wetting cycles play a crucial role in the investigation of the origin of life as processes that both concentrate and induce the supramolecular assembly and polymerization of biomolecular building blocks, such as nucleotides and amino acids. Here, we test different microfluidic devices to study the dehydration–hydration cycles of the aqueous solutions of small molecules, and to observe, by optical microscopy, the insurgence of phase transitions driven by self-assembly, exploiting water pervaporation through polydimethylsiloxane (PDMS). As a testbed, we investigate solutions of the chromonic dye Sunset Yellow (SSY), which self-assembles into face-to-face columnar aggregates and produces nematic and columnar liquid crystal (LC) phases as a function of concentration. We show that the LC temperature–concentration phase diagram of SSY can be obtained with a fair agreement with previous reports, that droplet hydration–dehydration can be reversibly controlled and automated, and that the simultaneous incubation of samples with different final water contents, corresponding to different phases, can be implemented. These methods can be further extended to study the assembly of diverse prebiotically relevant small molecules and to characterize their phase transitions. Full article

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17 pages, 2503 KiB

Open AccessArticle

The GARD Prebiotic Reproduction Model Described in Order and Complexity

by Christian Mayer, Doron Lancet and Omer Markovitch

Life 2024, 14(3), 288; https://doi.org/10.3390/life14030288 - 21 Feb 2024

Cited by 1 | Viewed by 1379

Abstract

Early steps in the origin of life were necessarily connected to the unlikely formation of self-reproducing structures from chaotic chemistry. Simulations of chemical kinetics based on the graded autocatalysis replication domain (GARD) model demonstrate the ability of a micellar system to become self-reproducing [...] Read more.

Early steps in the origin of life were necessarily connected to the unlikely formation of self-reproducing structures from chaotic chemistry. Simulations of chemical kinetics based on the graded autocatalysis replication domain (GARD) model demonstrate the ability of a micellar system to become self-reproducing units away from equilibrium. Even though they may be very rare in the initial state of the system, the property of their endogenous mutually catalytic networks being dynamic attractors greatly enhanced reproduction propensity, revealing their potential for selection and Darwinian evolution processes. In parallel, order and complexity have been shown to be crucial parameters in successful evolution. Here, we probe these parameters in the dynamics of GARD-governed entities in an attempt to identify characteristic mechanisms of their development in non-covalent molecular assemblies. Using a virtual random walk perspective, a value for consecutive order is defined based on statistical thermodynamics. The complexity, on the other hand, is determined by the size of a minimal algorithm fully describing the statistical properties of the random walk. By referring to a previously published diagonal line in an order/complexity diagram that represents the progression of evolution, it is shown that the GARD model has the potential to advance in this direction. These results can serve as a solid foundation for identifying general criteria for future analyses of evolving systems. Full article

(This article belongs to the Special Issue Feature Papers in Origins of Life)

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32 pages, 10331 KiB

Open AccessArticle

From the RNA-Peptide World: Prebiotic Reaction Conditions Compatible with Lipid Membranes for the Formation of Lipophilic Random Peptides in the Presence of Short Oligonucleotides, and More

by Augustin Lopez, Antoine Vauchez, Ghinwa Ajram, Anastasiia Shvetsova, Gabrielle Leveau, Michele Fiore and Peter Strazewski

Life 2024, 14(1), 108; https://doi.org/10.3390/life14010108 - 9 Jan 2024

Cited by 1 | Viewed by 2369

Abstract

Deciphering the origins of life on a molecular level includes unravelling the numerous interactions that could occur between the most important biomolecules being the lipids, peptides and nucleotides. They were likely all present on the early Earth and all necessary for the emergence [...] Read more.

Deciphering the origins of life on a molecular level includes unravelling the numerous interactions that could occur between the most important biomolecules being the lipids, peptides and nucleotides. They were likely all present on the early Earth and all necessary for the emergence of cellular life. In this study, we intended to explore conditions that were at the same time conducive to chemical reactions critical for the origins of life (peptide–oligonucleotide couplings and templated ligation of oligonucleotides) and compatible with the presence of prebiotic lipid vesicles. For that, random peptides were generated from activated amino acids and analysed using NMR and MS, whereas short oligonucleotides were produced through solid-support synthesis, manually deprotected and purified using HPLC. After chemical activation in prebiotic conditions, the resulting mixtures were analysed using LC-MS. Vesicles could be produced through gentle hydration in similar conditions and observed using epifluorescence microscopy. Despite the absence of coupling or ligation, our results help to pave the way for future investigations on the origins of life that may gather all three types of biomolecules rather than studying them separately, as it is still too often the case. Full article

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22 pages, 4811 KiB

Open AccessArticle

Gamma-Ray-Induced Amino Acid Formation during Aqueous Alteration in Small Bodies: The Effects of Compositions of Starting Solutions

by Akari Ishikawa, Yoko Kebukawa, Kensei Kobayashi and Isao Yoda

Life 2024, 14(1), 103; https://doi.org/10.3390/life14010103 - 9 Jan 2024

Cited by 2 | Viewed by 1553

Abstract

Organic compounds, such as amino acids, are essential for the origin of life, and they may have been delivered to the prebiotic Earth from extra-terrestrial sources, such as carbonaceous chondrites. In the parent bodies of carbonaceous chondrites, the radioactive decays of short-lived radionuclides, [...] Read more.

Organic compounds, such as amino acids, are essential for the origin of life, and they may have been delivered to the prebiotic Earth from extra-terrestrial sources, such as carbonaceous chondrites. In the parent bodies of carbonaceous chondrites, the radioactive decays of short-lived radionuclides, such as ²⁶Al, cause the melting of ice, and aqueous alteration occurs in the early stages of solar system formation. Many experimental studies have shown that complex organic matter, including amino acids and high-molecular-weight organic compounds, is produced by such hydrothermal processes. On the other hand, radiation, particularly gamma rays from radionuclides, can contribute to the formation of amino acids from simple molecules such as formaldehyde and ammonia. In this study, we investigated the details of gamma-ray-induced amino acid formation, focusing on the effects of different starting materials on aqueous solutions of formaldehyde, ammonia, methanol, and glycolaldehyde with various compositions, as well as hexamethylenetetramine. Alanine and glycine were the most abundantly formed amino acids after acid hydrolysis of gamma-ray-irradiated products. Amino acid formation increased with increasing gamma-ray irradiation doses. Lower amounts of ammonia relative to formaldehyde produced more amino acids. Glycolaldehyde significantly increased amino acid yields. Our results indicated that glycolaldehyde formation from formaldehyde enhanced by gamma rays is key for the subsequent production of amino acids. Full article

(This article belongs to the Special Issue Feature Papers in Origins of Life)

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12 pages, 921 KiB

Open AccessArticle

Influence of the Weak Nuclear Force on Metal-Promoted Autocatalytic Strecker Synthesis of Amino Acids: Formation of a Chiral Pool of Precursors for Prebiotic Peptide and Protein Synthesis

by J. A. Cowan

Life 2024, 14(1), 66; https://doi.org/10.3390/life14010066 - 30 Dec 2023

Cited by 4 | Viewed by 1561

Abstract

Natural chiral amino acids typically adopt an L structural configuration. While a preference for specific molecular chiralities is observed throughout biology and cellular chemistry, the origins of this preference are unclear. In a previous report the origin of enantiomeric selectivity was analyzed in [...] Read more.

Natural chiral amino acids typically adopt an L structural configuration. While a preference for specific molecular chiralities is observed throughout biology and cellular chemistry, the origins of this preference are unclear. In a previous report the origin of enantiomeric selectivity was analyzed in terms of an “RNA World” model, and a pathway to a chiral preference for d-ribose was proposed based on the autocatalytic transformation of glyceraldehyde as a precursor to the formation of sugars. Metal-ion-promoted catalysis allows the parity non-conserving (PNC) weak nuclear interaction to influence the chirality of a nascent chiral carbon center. Since the PNC effect is the only natural property with an inherent handedness, it is an obvious candidate to influence enantiomeric preference from a catalytic reaction performed over geologically relevant time scales. The PNC influence requires and emphasizes the important role of catalytic metal ions in primordial chemistry. In this study, the impact of geologically available divalent calcium and higher Z alkaline earth elements are examined as mediators of chiral preference. Detailed calculations of the magnitude of the effect are presented, including the influence of time, temperature, pH, and metal ion identity. It is concluded that metal ions can direct chiral preference for amino acid synthesis via a metal-promoted autocatalytic Strecker reaction within a relatively short geological timeframe, thereby providing a pool of l-amino acids for catalytic chemistry evolving either from an RNA-world model of molecular evolution or alternative pathways to protein synthesis. Full article

(This article belongs to the Special Issue Feature Papers in Origins of Life)

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15 pages, 4663 KiB

Open AccessArticle

The Nature of the Spark Is a Pivotal Element in the Design of a Miller–Urey Experiment

by Sina Ravanbodshirazi, Timothée Boutfol, Neda Safaridehkohneh, Marc Finkler, Mina Mohammadi-Kambs and Albrecht Ott

Life 2023, 13(11), 2201; https://doi.org/10.3390/life13112201 - 12 Nov 2023

Cited by 2 | Viewed by 2185

Abstract

Miller and Urey applied electric sparks to a reducive mixture of CH₄, NH₃, and water to obtain a complex organic mixture including biomolecules. In this study, we examined the impact of temperature, initial pressure, ammonia concentration, and the spark [...] Read more.

Miller and Urey applied electric sparks to a reducive mixture of CH₄, NH₃, and water to obtain a complex organic mixture including biomolecules. In this study, we examined the impact of temperature, initial pressure, ammonia concentration, and the spark generator on the chemical profile of a Miller–Urey-type prebiotic broth. We analyzed the broth composition using Gas Chromatography combined with Mass Spectroscopy (GC/MS). The results point towards strong compositional changes with the nature of the spark. Ammonia exhibited catalytic properties even with non-nitrogen-containing compounds. A more elevated temperature led to a higher variety of substances. We conclude that to reproduce such a broth as well as possible, all the studied parameters need to be tightly controlled, the most difficult and important being spark generation. Full article

(This article belongs to the Special Issue Feature Papers in Origins of Life)

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7 pages, 2900 KiB

Open AccessCommunication

One-Pot Formation of Pairing Proto-RNA Nucleotides and Their Supramolecular Assemblies

by Tyler P. Roche, Pranav J. Nedumpurath, Suneesh C. Karunakaran, Gary B. Schuster and Nicholas V. Hud

Life 2023, 13(11), 2200; https://doi.org/10.3390/life13112200 - 12 Nov 2023

Cited by 3 | Viewed by 1760

Abstract

Most contemporary theories for the chemical origins of life include the prebiotic synthesis of informational polymers, including strong interpretations of the RNA World hypothesis. Existing challenges to the prebiotic emergence of RNA have encouraged exploration of the possibility that RNA was preceded by [...] Read more.

Most contemporary theories for the chemical origins of life include the prebiotic synthesis of informational polymers, including strong interpretations of the RNA World hypothesis. Existing challenges to the prebiotic emergence of RNA have encouraged exploration of the possibility that RNA was preceded by an ancestral informational polymer, or proto-RNA, that formed more easily on the early Earth. We have proposed that the proto-nucleobases of proto-RNA would have readily formed glycosides with ribose and that these proto-nucleosides would have formed base pairs as monomers in aqueous solution, two properties not exhibited by the extant nucleosides or nucleotides. Here we demonstrate that putative proto-nucleotides of the model proto-nucleobases barbituric acid and melamine can be formed in the same one-pot reaction with ribose-5-phosphate. Additionally, the proto-nucleotides formed in these reactions spontaneously form assemblies that are consistent with the presence of Watson–Crick-like base pairs. Together, these results provide further support for the possibility that heterocycles closely related to the extant bases of RNA facilitated the prebiotic emergence of RNA-like molecules, which were eventually replaced by RNA over the course of chemical and biological evolution. Full article

(This article belongs to the Special Issue Feature Papers in Origins of Life)

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18 pages, 2638 KiB

Open AccessArticle

The Genetic Code Assembles via Division and Fusion, Basic Cellular Events

by Michael Yarus

Life 2023, 13(10), 2069; https://doi.org/10.3390/life13102069 - 17 Oct 2023

Cited by 3 | Viewed by 1307

Abstract

Standard Genetic Code (SGC) evolution is quantitatively modeled in up to 2000 independent coding ‘environments’. Environments host multiple codes that may fuse or divide, with division yielding identical descendants. Code division may be selected—sophisticated gene products could be required for an orderly separation [...] Read more.

Standard Genetic Code (SGC) evolution is quantitatively modeled in up to 2000 independent coding ‘environments’. Environments host multiple codes that may fuse or divide, with division yielding identical descendants. Code division may be selected—sophisticated gene products could be required for an orderly separation that preserves the coding. Several unforeseen results emerge: more rapid evolution requires unselective code division rather than its selective form. Combining selective and unselective code division, with/without code fusion, with/without independent environmental coding tables, and with/without wobble defines 2⁵ = 32 possible pathways for SGC evolution. These 32 possible histories are compared, specifically, for evolutionary speed and code accuracy. Pathways differ greatly, for example, by ≈300-fold in time to evolve SGC-like codes. Eight of thirty-two pathways employing code division evolve quickly. Four of these eight that combine fusion and division also unite speed and accuracy. The two most precise, swiftest paths; thus the most likely routes to the SGC are similar, differing only in fusion with independent environmental codes. Code division instead of fusion with unrelated codes implies that exterior codes can be dispensable. Instead, a single ancestral code that divides and fuses can initiate fully encoded peptide biosynthesis. Division and fusion create a ‘crescendo of competent coding’, facilitating the search for the SGC and also assisting the advent of otherwise uniformly disfavored wobble coding. Code fusion can unite multiple codon assignment mechanisms. However, via code division and fusion, an SGC can emerge from a single primary origin via familiar cellular events. Full article

(This article belongs to the Special Issue Feature Papers in Origins of Life)

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15 pages, 3827 KiB

Open AccessArticle

Environmental Stability and Its Importance for the Emergence of Darwinian Evolution

by Khushi R. Daga, Mensura Feray Çoşar, Abigail Lowenkron, Jihua Hao and Joti Rouillard

Life 2023, 13(10), 1960; https://doi.org/10.3390/life13101960 - 25 Sep 2023

Cited by 1 | Viewed by 1916

Abstract

The emergence of Darwinian evolution represents a central point in the history of life as we know it. However, it is generally assumed that the environments in which life appeared were hydrothermal environments, with highly variable conditions in terms of pH, temperature or [...] Read more.

The emergence of Darwinian evolution represents a central point in the history of life as we know it. However, it is generally assumed that the environments in which life appeared were hydrothermal environments, with highly variable conditions in terms of pH, temperature or redox levels. Are evolutionary processes favored to appear in such settings, where the target of biological adaptation changes over time? How would the first evolving populations compete with non-evolving populations? Using a numerical model, we explore the effect of environmental variation on the outcome of the competition between evolving and non-evolving populations of protocells. Our study found that, while evolving protocells consistently outcompete non-evolving populations in stable environments, they are outcompeted in variable environments when environmental variations occur on a timescale similar to the average duration of a generation. This is due to the energetic burden represented by adaptation to the wrong environmental conditions. Since the timescale of temperature variation in natural hydrothermal settings overlaps with the average prokaryote generation time, the current work indicates that a solution must have been found by early life to overcome this threshold. Full article

(This article belongs to the Special Issue Feature Papers in Origins of Life)

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15 pages, 3420 KiB

Open AccessArticle

The Role of the CuCl Active Complex in the Stereoselectivity of the Salt-Induced Peptide Formation Reaction: Insights from Density Functional Theory Calculations

by Allison C. Fox, Jason D. Boettger, Eve L. Berger and Aaron S. Burton

Life 2023, 13(9), 1796; https://doi.org/10.3390/life13091796 - 23 Aug 2023

Cited by 1 | Viewed by 1350

Abstract

The salt-induced peptide formation (SIPF) reaction is a prebiotically plausible mechanism for the spontaneous polymerization of amino acids into peptides on early Earth. Experimental investigations of the SIPF reaction have found that in certain conditions, the l enantiomer is more reactive than the [...] Read more.

The salt-induced peptide formation (SIPF) reaction is a prebiotically plausible mechanism for the spontaneous polymerization of amino acids into peptides on early Earth. Experimental investigations of the SIPF reaction have found that in certain conditions, the l enantiomer is more reactive than the d enantiomer, indicating its potential role in the rise of biohomochirality. Previous work hypothesized that the distortion of the CuCl active complex toward a tetrahedral-like structure increases the central chirality on the Cu ion, which amplifies the inherent parity-violating energy differences between l- and d-amino acid enantiomers, leading to stereoselectivity. Computational evaluations of this theory have been limited to the protonated–neutral l + l forms of the CuCl active complex. Here, density functional theory methods were used to compare the energies and geometries of the homochiral (l + l and d + d) and heterochiral (l + d) CuCl–amino acid complexes for both the positive–neutral and neutral–neutral forms for alanine, valine, and proline. Significant energy differences were not observed between different chiral active complexes (i.e., d + d, l + l vs. l + d), and the distortions of active complexes between stereoselective systems and non-selective systems were not consistent, indicating that the geometry of the active complex is not the primary driver of the observed stereoselectivity of the SIPF reaction. Full article

(This article belongs to the Special Issue Feature Papers in Origins of Life)

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Review

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20 pages, 1882 KiB

Open AccessReview

Alternative Pathways in Astrobiology: Reviewing and Synthesizing Contingency and Non-Biomolecular Origins of Terrestrial and Extraterrestrial Life

by Kuhan Chandru, Christian Potiszil and Tony Z. Jia

Life 2024, 14(9), 1069; https://doi.org/10.3390/life14091069 - 27 Aug 2024

Cited by 1 | Viewed by 1817

Abstract

The pursuit of understanding the origins of life (OoL) on and off Earth and the search for extraterrestrial life (ET) are central aspects of astrobiology. Despite the considerable efforts in both areas, more novel and multifaceted approaches are needed to address these profound [...] Read more.

The pursuit of understanding the origins of life (OoL) on and off Earth and the search for extraterrestrial life (ET) are central aspects of astrobiology. Despite the considerable efforts in both areas, more novel and multifaceted approaches are needed to address these profound questions with greater detail and with certainty. The complexity of the chemical milieu within ancient geological environments presents a diverse landscape where biomolecules and non-biomolecules interact. This interaction could lead to life as we know it, dominated by biomolecules, or to alternative forms of life where non-biomolecules could play a pivotal role. Such alternative forms of life could be found beyond Earth, i.e., on exoplanets and the moons of Jupiter and Saturn. Challenging the notion that all life, including ET life, must use the same building blocks as life on Earth, the concept of contingency—when expanded beyond its macroevolution interpretation—suggests that non-biomolecules may have played essential roles at the OoL. Here, we review the possible role of contingency and non-biomolecules at the OoL and synthesize a conceptual model formally linking contingency with non-biomolecular OoL theories. This model emphasizes the significance of considering the role of non-biomolecules both at the OoL on Earth or beyond, as well as their potential as agnostic biosignatures indicative of ET Life. Full article

(This article belongs to the Special Issue Feature Papers in Origins of Life)

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12 pages, 1997 KiB

Open AccessReview

The Mystery of Homochirality on Earth

by Michael G. Weller

Life 2024, 14(3), 341; https://doi.org/10.3390/life14030341 - 6 Mar 2024

Cited by 3 | Viewed by 3421

Abstract

Homochirality is an obvious feature of life on Earth. On the other hand, extraterrestrial samples contain largely racemic compounds. The same is true for any common organic synthesis. Therefore, it has been a perplexing puzzle for decades how these racemates could have formed [...] Read more.

Homochirality is an obvious feature of life on Earth. On the other hand, extraterrestrial samples contain largely racemic compounds. The same is true for any common organic synthesis. Therefore, it has been a perplexing puzzle for decades how these racemates could have formed enantiomerically enriched fractions as a basis for the origin of homochiral life forms. Numerous hypotheses have been put forward as to how preferentially homochiral molecules could have formed and accumulated on Earth. In this article, it is shown that homochirality of the abiotic organic pool at the time of formation of the first self-replicating molecules is not necessary and not even probable. It is proposed to abandon the notion of a molecular ensemble and to focus on the level of individual molecules. Although the formation of the first self-replicating, most likely homochiral molecule, is a seemingly improbable event, on a closer look, it is almost inevitable that some homochiral molecules have formed simply on a statistical basis. In this case, the non-selective leap to homochirality would be one of the first steps in chemical evolution directly out of a racemic “ocean”. Moreover, most studies focus on the chirality of the primordial monomers with respect to an asymmetric carbon atom. However, any polymer with a minimal size that allows folding to a secondary structure would spontaneously lead to asymmetric higher structures (conformations). Most of the functions of these polymers would be influenced by this inherently asymmetric folding. Furthermore, a concept of physical compartmentalization based on rock nanopores in analogy to nanocavities of digital immunoassays is introduced to suggest that complex cell walls or membranes were also not required for the first steps of chemical evolution. To summarize, simple and universal mechanisms may have led to homochiral self-replicating systems in the context of chemical evolution. A homochiral monomer pool is deemed unnecessary and probably never existed on primordial Earth. Full article

(This article belongs to the Special Issue Feature Papers in Origins of Life)

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21 pages, 1037 KiB

Open AccessReview

Three Biopolymers and Origin of Life Scenarios

by Ilana Agmon

Life 2024, 14(2), 277; https://doi.org/10.3390/life14020277 - 18 Feb 2024

Cited by 6 | Viewed by 2542

Abstract

To track down the possible roots of life, various models for the initial living system composed of different combinations of the three extant biopolymers, RNA, DNA, and proteins, are presented. The suitability of each molecular set is assessed according to its ability to [...] Read more.

To track down the possible roots of life, various models for the initial living system composed of different combinations of the three extant biopolymers, RNA, DNA, and proteins, are presented. The suitability of each molecular set is assessed according to its ability to emerge autonomously, sustain, and evolve continuously towards life as we know it. The analysis incorporates current biological knowledge gained from high-resolution structural data and large sequence datasets, together with experimental results concerned with RNA replication and with the activity demonstrated by standalone constructs of the ribosomal Peptidyl Transferase Center region. The scrutiny excludes the DNA–protein combination and assigns negligible likelihood to the existence of an RNA–DNA world, as well as to an RNA world that contained a replicase made of RNA. It points to the precedence of an RNA–protein system, whose model of emergence suggests specific processes whereby a coded proto-ribosome ribozyme, specifically aminoacylated proto-tRNAs and a proto-polymerase enzyme, could have autonomously emerged, cross-catalyzing the formation of each other. This molecular set constitutes a feasible starting point for a continuous evolutionary path, proceeding via natural processes from the inanimate matter towards life as we know it. Full article

(This article belongs to the Special Issue Feature Papers in Origins of Life)

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25 pages, 2613 KiB

Open AccessReview

Opinion: The Key Steps in the Origin of Life to the Formation of the Eukaryotic Cell

by Clifford F. Brunk and Charles R. Marshall

Life 2024, 14(2), 226; https://doi.org/10.3390/life14020226 - 5 Feb 2024

Cited by 1 | Viewed by 5024

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Feature Papers in Origins of Life)

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24 pages, 733 KiB

Open AccessReview

Evolution at the Origins of Life?

by Ludo L. J. Schoenmakers, Thomas A. C. Reydon and Andreas Kirschning

Life 2024, 14(2), 175; https://doi.org/10.3390/life14020175 - 24 Jan 2024

Cited by 2 | Viewed by 6082

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, [...] Read more.

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. Full article

(This article belongs to the Special Issue Feature Papers in Origins of Life)

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31 pages, 7933 KiB

Open AccessReview

Xeno Amino Acids: A Look into Biochemistry as We Do Not Know It

by Sean M. Brown, Christopher Mayer-Bacon and Stephen Freeland

Life 2023, 13(12), 2281; https://doi.org/10.3390/life13122281 - 29 Nov 2023

Cited by 1 | Viewed by 3710

Abstract

Would another origin of life resemble Earth’s biochemical use of amino acids? Here, we review current knowledge at three levels: (1) Could other classes of chemical structure serve as building blocks for biopolymer structure and catalysis? Amino acids now seem both readily available [...] Read more.

Would another origin of life resemble Earth’s biochemical use of amino acids? Here, we review current knowledge at three levels: (1) Could other classes of chemical structure serve as building blocks for biopolymer structure and catalysis? Amino acids now seem both readily available to, and a plausible chemical attractor for, life as we do not know it. Amino acids thus remain important and tractable targets for astrobiological research. (2) If amino acids are used, would we expect the same L-alpha-structural subclass used by life? Despite numerous ideas, it is not clear why life favors L-enantiomers. It seems clearer, however, why life on Earth uses the shortest possible (alpha-) amino acid backbone, and why each carries only one side chain. However, assertions that other backbones are physicochemically impossible have relaxed into arguments that they are disadvantageous. (3) Would we expect a similar set of side chains to those within the genetic code? Many plausible alternatives exist. Furthermore, evidence exists for both evolutionary advantage and physicochemical constraint as explanatory factors for those encoded by life. Overall, as focus shifts from amino acids as a chemical class to specific side chains used by post-LUCA biology, the probable role of physicochemical constraint diminishes relative to that of biological evolution. Exciting opportunities now present themselves for laboratory work and computing to explore how changing the amino acid alphabet alters the universe of protein folds. Near-term milestones include: (a) expanding evidence about amino acids as attractors within chemical evolution; (b) extending characterization of other backbones relative to biological proteins; and (c) merging computing and laboratory explorations of structures and functions unlocked by xeno peptides. Full article

(This article belongs to the Special Issue Feature Papers in Origins of Life)

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20 pages, 6247 KiB

Open AccessReview

The 3 31 Nucleotide Minihelix tRNA Evolution Theorem and the Origin of Life

by Lei Lei and Zachary Frome Burton

Life 2023, 13(11), 2224; https://doi.org/10.3390/life13112224 - 19 Nov 2023

Cited by 4 | Viewed by 5865

Abstract

There are no theorems (proven theories) in the biological sciences. We propose that the 3 31 nt minihelix tRNA evolution theorem be universally accepted as one. The 3 31 nt minihelix theorem completely describes the evolution of type I and type II tRNAs [...] Read more.

There are no theorems (proven theories) in the biological sciences. We propose that the 3 31 nt minihelix tRNA evolution theorem be universally accepted as one. The 3 31 nt minihelix theorem completely describes the evolution of type I and type II tRNAs from ordered precursors (RNA repeats and inverted repeats). Despite the diversification of tRNAome sequences, statistical tests overwhelmingly support the theorem. Furthermore, the theorem relates the dominant pathway for the origin of life on Earth, specifically, how tRNAomes and the genetic code may have coevolved. Alternate models for tRNA evolution (i.e., 2 minihelix, convergent and accretion models) are falsified. In the context of the pre-life world, tRNA was a molecule that, via mutation, could modify anticodon sequences and teach itself to code. Based on the tRNA sequence, we relate the clearest history to date of the chemical evolution of life. From analysis of tRNA evolution, ribozyme-mediated RNA ligation was a primary driving force in the evolution of complexity during the pre-life-to-life transition. TRNA formed the core for the evolution of living systems on Earth. Full article

(This article belongs to the Special Issue Feature Papers in Origins of Life)

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31 pages, 6371 KiB

Open AccessReview

Organic Matter in the Asteroid Ryugu: What We Know So Far

by Christian Potiszil, Masahiro Yamanaka, Chie Sakaguchi, Tsutomu Ota, Hiroshi Kitagawa, Tak Kunihiro, Ryoji Tanaka, Katsura Kobayashi and Eizo Nakamura

Life 2023, 13(7), 1448; https://doi.org/10.3390/life13071448 - 26 Jun 2023

Cited by 6 | Viewed by 5887

Abstract

The Hayabusa2 mission was tasked with returning samples from the C-complex asteroid Ryugu (1999 JU3), in order to shed light on the formation, evolution and composition of such asteroids. One of the main science objectives was to understand whether such bodies could have [...] Read more.

The Hayabusa2 mission was tasked with returning samples from the C-complex asteroid Ryugu (1999 JU3), in order to shed light on the formation, evolution and composition of such asteroids. One of the main science objectives was to understand whether such bodies could have supplied the organic matter required for the origin of life on Earth. Here, a review of the studies concerning the organic matter within the Ryugu samples is presented. This review will inform the reader about the Hayabusa2 mission, the nature of the organic matter analyzed and the various interpretations concerning the analytical findings including those concerning the origin and evolution of organic matter from Ryugu. Finally, the review puts the findings and individual interpretations in the context of the current theories surrounding the formation and evolution of Ryugu. Overall, the summary provided here will help to inform those operating in a wide range of interdisciplinary fields, including planetary science, astrobiology, the origin of life and astronomy, about the most recent developments concerning the organic matter in the Ryugu return samples and their relevance to understanding our solar system and beyond. The review also outlines the issues that still remain to be solved and highlights potential areas for future work. Full article

(This article belongs to the Special Issue Feature Papers in Origins of Life)

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