Life | Special Issue : The Origin and Early Evolution of Life: Prebiotic Chemistry Perspective

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15 pages, 2129 KiB

Open AccessArticle

Mineral-Mediated Oligoribonucleotide Condensation: Broadening the Scope of Prebiotic Possibilities on the Early Earth

by Vincent S. Riggi, E. Bruce Watson, Andrew Steele and Karyn L. Rogers

Life 2023, 13(9), 1899; https://doi.org/10.3390/life13091899 - 12 Sep 2023

Cited by 1 | Viewed by 1566

Abstract

The origin of life on earth requires the synthesis of protobiopolymers in realistic geologic environments along strictly abiotic pathways that rely on inorganic phases (such as minerals) instead of cellular machinery to promote condensation. One such class of polymer central to biochemistry is [...] Read more.

The origin of life on earth requires the synthesis of protobiopolymers in realistic geologic environments along strictly abiotic pathways that rely on inorganic phases (such as minerals) instead of cellular machinery to promote condensation. One such class of polymer central to biochemistry is the polynucleotides, and oligomerization of activated ribonucleotides has been widely studied. Nonetheless, the range of laboratory conditions tested to date is limited and the impact of realistic early Earth conditions on condensation reactions remains unexplored. Here, we investigate the potential for a variety of minerals to enhance oligomerization using ribonucleotide monomers as one example to model condensation under plausible planetary conditions. The results show that several minerals differing in both structure and composition enhance oligomerization. Sulfide minerals yielded oligomers of comparable lengths to those formed in the presence of clays, with galena being the most effective, yielding oligonucleotides up to six bases long. Montmorillonite continues to excel beyond other clays. Chemical pretreatment of the clay was not required, though maximum oligomer lengths decreased from ~11 to 6 bases. These results demonstrate the diversity of mineral phases that can impact condensation reactions and highlight the need for greater consideration of environmental context when assessing prebiotic synthesis and the origin of life. Full article

(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Chemistry Perspective)

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23 pages, 7456 KiB

Open AccessArticle

Prebiotic Synthesis of Aspartate Using Life’s Metabolism as a Guide

by Stuart A. Harrison, William L. Webb, Hanadi Rammu and Nick Lane

Life 2023, 13(5), 1177; https://doi.org/10.3390/life13051177 - 12 May 2023

Cited by 4 | Viewed by 2472

Abstract

A protometabolic approach to the origins of life assumes that the conserved biochemistry of metabolism has direct continuity with prebiotic chemistry. One of the most important amino acids in modern biology is aspartic acid, serving as a nodal metabolite for the synthesis of [...] Read more.

A protometabolic approach to the origins of life assumes that the conserved biochemistry of metabolism has direct continuity with prebiotic chemistry. One of the most important amino acids in modern biology is aspartic acid, serving as a nodal metabolite for the synthesis of many other essential biomolecules. Aspartate’s prebiotic synthesis is complicated by the instability of its precursor, oxaloacetate. In this paper, we show that the use of the biologically relevant cofactor pyridoxamine, supported by metal ion catalysis, is sufficiently fast to offset oxaloacetate’s degradation. Cu²⁺-catalysed transamination of oxaloacetate by pyridoxamine achieves around a 5% yield within 1 h, and can operate across a broad range of pH, temperature, and pressure. In addition, the synthesis of the downstream product β-alanine may also take place in the same reaction system at very low yields, directly mimicking an archaeal synthesis route. Amino group transfer supported by pyridoxal is shown to take place from aspartate to alanine, but the reverse reaction (alanine to aspartate) shows a poor yield. Overall, our results show that the nodal metabolite aspartate and related amino acids can indeed be synthesised via protometabolic pathways that foreshadow modern metabolism in the presence of the simple cofactor pyridoxamine and metal ions. Full article

(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Chemistry Perspective)

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20 pages, 2984 KiB

Open AccessArticle

Biophysical Interactions Underpin the Emergence of Information in the Genetic Code

by Aaron Halpern, Lilly R. Bartsch, Kaan Ibrahim, Stuart A. Harrison, Minkoo Ahn, John Christodoulou and Nick Lane

Life 2023, 13(5), 1129; https://doi.org/10.3390/life13051129 - 4 May 2023

Cited by 3 | Viewed by 2379

Abstract

The genetic code conceals a ‘code within the codons’, which hints at biophysical interactions between amino acids and their cognate nucleotides. Yet, research over decades has failed to corroborate systematic biophysical interactions across the code. Using molecular dynamics simulations and NMR, we have [...] Read more.

The genetic code conceals a ‘code within the codons’, which hints at biophysical interactions between amino acids and their cognate nucleotides. Yet, research over decades has failed to corroborate systematic biophysical interactions across the code. Using molecular dynamics simulations and NMR, we have analysed interactions between the 20 standard proteinogenic amino acids and 4 RNA mononucleotides in 3 charge states. Our simulations show that 50% of amino acids bind best with their anticodonic middle base in the −1 charge state common to the backbone of RNA, while 95% of amino acids interact most strongly with at least 1 of their codonic or anticodonic bases. Preference for the cognate anticodonic middle base was greater than 99% of randomised assignments. We verify a selection of our results using NMR, and highlight challenges with both techniques for interrogating large numbers of weak interactions. Finally, we extend our simulations to a range of amino acids and dinucleotides, and corroborate similar preferences for cognate nucleotides. Despite some discrepancies between the predicted patterns and those observed in biology, the existence of weak stereochemical interactions means that random RNA sequences could template non-random peptides. This offers a compelling explanation for the emergence of genetic information in biology. Full article

(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Chemistry Perspective)

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15 pages, 3147 KiB

Open AccessArticle

Screening for Primordial RNA–Peptide Interactions Using High-Density Peptide Arrays

by Felix Jenne, Ivan Berezkin, Frank Tempel, Dimitry Schmidt, Roman Popov and Alexander Nesterov-Mueller

Life 2023, 13(3), 796; https://doi.org/10.3390/life13030796 - 15 Mar 2023

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Abstract

RNA–peptide interactions are an important factor in the origin of the modern mechanism of translation and the genetic code. Despite great progress in the bioinformatics of RNA–peptide interactions due to the rapid growth in the number of known RNA–protein complexes, there is no [...] Read more.

RNA–peptide interactions are an important factor in the origin of the modern mechanism of translation and the genetic code. Despite great progress in the bioinformatics of RNA–peptide interactions due to the rapid growth in the number of known RNA–protein complexes, there is no comprehensive experimental method to take into account the influence of individual amino acids on non-covalent RNA–peptide bonds. First, we designed the combinatorial libraries of primordial peptides according to the combinatorial fusion rules based on Watson–Crick mutations. Next, we used high-density peptide arrays to investigate the interaction of primordial peptides with their cognate homo-oligonucleotides. We calculated the interaction scores of individual peptide fragments and evaluated the influence of the peptide length and its composition on the strength of RNA binding. The analysis shows that the amino acids phenylalanine, tyrosine, and proline contribute significantly to the strong binding between peptides and homo-oligonucleotides, while the sum charge of the peptide does not have a significant effect. We discuss the physicochemical implications of the combinatorial fusion cascade, a hypothesis that follows from the amino acid partition used in the work. Full article

(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Chemistry Perspective)

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15 pages, 3464 KiB

Open AccessArticle

by Dominic Papineau, Kevin Devine and Bernardo Albuquerque Nogueira

Life 2023, 13(2), 551; https://doi.org/10.3390/life13020551 - 16 Feb 2023

Cited by 3 | Viewed by 2042

Abstract

The origin of life must have included an abiotic stage of carbon redox reactions that involved electron transport chains and the production of lifelike patterns. Chemically oscillating reactions (COR) are abiotic, spontaneous, out-of-equilibrium, and redox reactions that involve the decarboxylation of carboxylic acids [...] Read more.

The origin of life must have included an abiotic stage of carbon redox reactions that involved electron transport chains and the production of lifelike patterns. Chemically oscillating reactions (COR) are abiotic, spontaneous, out-of-equilibrium, and redox reactions that involve the decarboxylation of carboxylic acids with strong oxidants and strong acids to produce CO₂ and characteristic self-similar patterns. Those patterns have circular concentricity, radial geometries, characteristic circular twins, colour gradients, cavity structures, and branching to parallel alignment. We propose that COR played a role during the prebiotic cycling of carboxylic acids, furthering the new model for geology where COR can also explain the patterns of diagenetic spheroids in sediments. The patterns of COR in Petri dishes are first considered and compared to those observed in some eukaryotic lifeforms. The molecular structures and functions of reactants in COR are then compared to key biological metabolic processes. We conclude that the newly recognised similarities in compositions and patterns warrant future research to better investigate the role of halogens in biochemistry; COR in life-forms, including in humans; and the COR-stage of prebiotic carbon cycling on other planets, such as Mars. Full article

(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Chemistry Perspective)

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Review

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16 pages, 1821 KiB

Open AccessReview

Spectroscopic Detection of Biosignatures in Natural Ice Samples as a Proxy for Icy Moons

by Francisco Calapez, Rodrigo Dias, Rute Cesário, Diogo Gonçalves, Bruno Pedras, João Canário and Zita Martins

Life 2023, 13(2), 478; https://doi.org/10.3390/life13020478 - 9 Feb 2023

Cited by 1 | Viewed by 3030

Abstract

Some of the icy moons of the solar system with a subsurface ocean, such as Europa and Enceladus, are the targets of future space missions that search for potential extraterrestrial life forms. While the ice shells that envelop these moons have been studied [...] Read more.

Some of the icy moons of the solar system with a subsurface ocean, such as Europa and Enceladus, are the targets of future space missions that search for potential extraterrestrial life forms. While the ice shells that envelop these moons have been studied by several spacecrafts, the oceans beneath them remain unreachable. To better constrain the habitability conditions of these moons, we must understand the interactions between their frozen crusts, liquid layers, and silicate mantles. To that end, astrobiologists rely on planetary field analogues, for which the polar regions of Earth have proven to be great candidates. This review shows how spectroscopy is a powerful tool in space missions to detect potential biosignatures, in particular on the aforementioned moons, and how the polar regions of the Earth are being used as planetary field analogues for these extra-terrestrial environments. Full article

(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Chemistry Perspective)

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20 pages, 6861 KiB

Open AccessReview

Spark of Life: Role of Electrotrophy in the Emergence of Life

by Guillaume Pillot, Óscar Santiago, Sven Kerzenmacher and Pierre-Pol Liebgott

Life 2023, 13(2), 356; https://doi.org/10.3390/life13020356 - 28 Jan 2023

Viewed by 2022

Abstract

The emergence of life has been a subject of intensive research for decades. Different approaches and different environmental “cradles” have been studied, from space to the deep sea. Since the recent discovery of a natural electrical current through deep-sea hydrothermal vents, a new [...] Read more.

The emergence of life has been a subject of intensive research for decades. Different approaches and different environmental “cradles” have been studied, from space to the deep sea. Since the recent discovery of a natural electrical current through deep-sea hydrothermal vents, a new energy source is considered for the transition from inorganic to organic. This energy source (electron donor) is used by modern microorganisms via a new trophic type, called electrotrophy. In this review, we draw a parallel between this metabolism and a new theory for the emergence of life based on this electrical electron flow. Each step of the creation of life is revised in the new light of this prebiotic electrochemical context, going from the evaluation of similar electrical current during the Hadean, the CO₂ electroreduction into a prebiotic primordial soup, the production of proto-membranes, the energetic system inspired of the nitrate reduction, the proton gradient, and the transition to a planktonic proto-cell. Finally, this theory is compared to the two other theories in hydrothermal context to assess its relevance and overcome the limitations of each. Many critical factors that were limiting each theory can be overcome given the effect of electrochemical reactions and the environmental changes produced. Full article

(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Chemistry Perspective)

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Other

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12 pages, 482 KiB

Open AccessPerspective

On the Chemical Origin of Biological Cognition

by Robert Pascal and Addy Pross

Life 2022, 12(12), 2016; https://doi.org/10.3390/life12122016 - 3 Dec 2022

Cited by 4 | Viewed by 2000

Abstract

One of life’s most striking characteristics is its mental dimension, one whose very existence within a material system has long been a deep scientific mystery. Given the current scientific view that life emerged from non-life, how was it possible for ‘dead’ matter to [...] Read more.

One of life’s most striking characteristics is its mental dimension, one whose very existence within a material system has long been a deep scientific mystery. Given the current scientific view that life emerged from non-life, how was it possible for ‘dead’ matter to have taken on mental capabilities? In this Perspective we describe the existence of a recently discovered non-equilibrium state of matter, an energized dynamic kinetic state, and demonstrate how particular chemical systems once activated into that kinetic state could manifest rudimentary cognitive behavior. Thus, contrary to a common view that biology is not reducible to physics and chemistry, recent findings in both chemistry and biology suggest that life’s mental state is an outcome of its physical state, and therefore may be explicable in physical/chemical terms. Such understanding offers added insight into the physico-chemical process by which life was able to emerge from non-life and the perennial ‘what is life?’ question. Most remarkably, it appears that Darwin, through his deep understanding of the evolutionary process, already sensed the existence of a connection between life’s physical and mental states. Full article

(This article belongs to the Special Issue The Origin and Early Evolution of Life: Prebiotic Chemistry Perspective)

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