From prebiotic chemistry to cellular metabolism—The chemical evolution of metabolism before Darwinian natural selection

The very specific thermodynamic instability and kinetic stability of phosphate esters and anhydrides impart them invaluable properties in living organisms in which highly efficient enzyme catalysts compensate for their low intrinsic reactivity. Considering their role in protein biosynthesis, these properties raise a paradox about early stages: How could these species be selected in the absence of enzymes? This review is aimed at demonstrating that considering mixed anhydrides or other species more reactive than esters and anhydrides can help in solving the paradox. The consequences of this approach for chemical evolution and early stages of life are analysed.

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Natural selection in chemical evolution

Journal of Theoretical Biology ◽

10.1016/j.jtbi.2007.01.028 ◽

2007 ◽

Vol 247 (1) ◽

pp. 152-167 ◽

Cited By ~ 36

Author(s):

Chrisantha Fernando ◽

Jonathan Rowe

Keyword(s):

Natural Selection ◽

Chemical Evolution

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Tracing Molecular Properties Throughout Evolution: A Chemoinformatic Approach.

10.26434/chemrxiv.12654512.v2 ◽

2020 ◽

Author(s):

Marcelo Otero ◽

Silvina Sarno ◽

Sofía Acebedo ◽

Javier Alberto Ramirez

Keyword(s):

Natural Selection ◽

Evolutionary Process ◽

Population Level ◽

Complex Compounds ◽

Point Of View ◽

Molecular Properties ◽

Machine Learning Techniques ◽

Complex Process ◽

Learning Techniques ◽

Evolution Of Metabolism

<p>Evolution of metabolism is a longstanding yet unresolved question, and several hypotheses were proposed to address this complex process from a Darwinian point of view. Modern statistical bioinformatic approaches targeted to the comparative analysis of genomes are being used to detect signatures of natural selection at the gene and population level, as an attempt to understand the origin of primordial metabolism and its expansion. These studies, however, are still mainly centered on genes and the proteins they encode, somehow neglecting the small organic chemicals that support life processes. In this work, we selected steroids as an ancient family of metabolites widely distributed in all eukaryotes and applied unsupervised machine learning techniques to reveal the traits that natural selection has imprinted on molecular properties throughout the evolutionary process. Our results clearly show that sterols, the primal steroids that first appeared, have more conserved properties and that, from then on, more complex compounds with increasingly diverse properties have emerged, suggesting that chemical diversification parallels the expansion of biological complexity. In a wider context, these findings highlight the worth of chemoinformatic approaches to a better understanding the evolution of metabolism.</p>

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Tracing Molecular Properties Throughout Evolution: A Chemoinformatic Approach.

10.26434/chemrxiv.12654512.v3 ◽

2021 ◽

Author(s):

Marcelo Otero ◽

Silvina Sarno ◽

Sofía Acebedo ◽

Javier Alberto Ramirez

Keyword(s):

Natural Selection ◽

Evolutionary Process ◽

Population Level ◽

Complex Compounds ◽

Point Of View ◽

Molecular Properties ◽

Machine Learning Techniques ◽

Complex Process ◽

Learning Techniques ◽

Evolution Of Metabolism

<p>Evolution of metabolism is a longstanding yet unresolved question, and several hypotheses were proposed to address this complex process from a Darwinian point of view. Modern statistical bioinformatic approaches targeted to the comparative analysis of genomes are being used to detect signatures of natural selection at the gene and population level, as an attempt to understand the origin of primordial metabolism and its expansion. These studies, however, are still mainly centered on genes and the proteins they encode, somehow neglecting the small organic chemicals that support life processes. In this work, we selected steroids as an ancient family of metabolites widely distributed in all eukaryotes and applied unsupervised machine learning techniques to reveal the traits that natural selection has imprinted on molecular properties throughout the evolutionary process. Our results clearly show that sterols, the primal steroids that first appeared, have more conserved properties and that, from then on, more complex compounds with increasingly diverse properties have emerged, suggesting that chemical diversification parallels the expansion of biological complexity. In a wider context, these findings highlight the worth of chemoinformatic approaches to a better understanding the evolution of metabolism.</p>

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4. The chemistry of life

Organic Chemistry: A Very Short Introduction ◽

10.1093/actrade/9780198759775.003.0004 ◽

2017 ◽

pp. 50-70

Author(s):

Graham Patrick

Keyword(s):

Amino Acids ◽

Natural Products ◽

Nucleic Acids ◽

Chemical Evolution ◽

Prebiotic Chemistry ◽

Building Blocks ◽

Complex Structures ◽

Dna And Rna ◽

Molecular Building Blocks ◽

Commercial Applications

From very simple molecular building blocks, life has created an astonishing diversity of molecules, some of which are extremely complex structures that prove very difficult to synthesize in a laboratory. ‘The chemistry of life’ describes how proteins, which serve a myriad of purposes, and nucleic acids, another form of biopolymer, are constructed from molecular building blocks called amino acids and nucleotides respectively. It goes on to explain the polymerization processes involved in the biosynthesis of many other natural products; the functions of proteins, DNA, and RNA; and the different theories proposed to explain chemical evolution, or prebiotic chemistry. Enzymes and nucleic acids are increasingly being used in commercial applications.

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Polyesters as a Model System for Building Primitive Biologies from Non-Biological Prebiotic Chemistry

Life ◽

10.3390/life10010006 ◽

2020 ◽

Vol 10 (1) ◽

pp. 6 ◽

Cited By ~ 4

Author(s):

Chandru ◽

Mamajanov ◽

Cleaves ◽

Jia

Keyword(s):

Chemical Evolution ◽

Hot Springs ◽

Prebiotic Chemistry ◽

Chemical Reactivity ◽

Structural Diversity ◽

Building Blocks ◽

Chemical Diversity ◽

Prebiotic Chemical ◽

Small Set ◽

Prebiotic Earth

A variety of organic chemicals were likely available on prebiotic Earth. These derived from diverse processes including atmospheric and geochemical synthesis and extraterrestrial input, and were delivered to environments including oceans, lakes, and subaerial hot springs. Prebiotic chemistry generates both molecules used by modern organisms, such as proteinaceous amino acids, as well as many molecule types not used in biochemistry. As prebiotic chemical diversity was likely high, and the core of biochemistry uses a rather small set of common building blocks, the majority of prebiotically available organic compounds may not have been those used in modern biochemistry. Chemical evolution was unlikely to have been able to discriminate which molecules would eventually be used in biology, and instead, interactions among compounds were governed simply by abundance and chemical reactivity. Previous work has shown that likely prebiotically available α-hydroxy acids can combinatorially polymerize into polyesters that self-assemble to create new phases which are able to compartmentalize other molecule types. The unexpectedly rich complexity of hydroxy acid chemistry and the likely enormous structural diversity of prebiotic organic chemistry suggests chemical evolution could have been heavily influenced by molecules not used in contemporary biochemistry, and that there is a considerable amount of prebiotic chemistry which remains unexplored.

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The natural selection of metabolism explains curvature in allometric scaling

10.1101/090191 ◽

2016 ◽

Cited By ~ 3

Author(s):

Lars Witting

Keyword(s):

Natural Selection ◽

Time Scale ◽

Generation Time ◽

Allometric Scaling ◽

Exponential Increase ◽

Wide Range ◽

Order Of Magnitude ◽

Evolution Of Metabolism ◽

Over Time ◽

Selection Of

AbstractI simulate the evolution of metabolism and mass to explain the curvature in the metabolic allometry for placental and marsupial mammals. I assume that the release of inter-specific competition by the extinction of dinosaurs 65 million years ago made it possible for each clade to diversity into a multitude of species across a wide range of niches. The natural selection of metabolism and mass was then fitted to explain the maximum observed body masses over time, as well as the current inter-specific allometry for metabolism. The estimated selection of mass specific metabolism was found to bend the metabolic allometry over time, with the strongest curvature in the placental clade. The rate of exponential increase in mass specific metabolism for placentals was estimated to 9.3 × 10−9 (95% CI:7.3 × 10−9 − 1.1 × 10−8) on the per generation time-scale. This is an order of magnitude larger than the estimate for marsupials, in agreement with an average metabolism that is 30% larger in placentals relative to marsupials of similar size.

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Prebiotic chemistry: chemical evolution of organics on the primitive Earth under simulated prebiotic conditions

Photochemical & Photobiological Sciences ◽

10.1039/b709813h ◽

2007 ◽

Vol 6 (11) ◽

pp. 1210 ◽

Cited By ~ 8

Author(s):

Daniele Dondi ◽

Daniele Merli ◽

Luca Pretali ◽

Maurizio Fagnoni ◽

Angelo Albini ◽

...

Keyword(s):

Chemical Evolution ◽

Prebiotic Chemistry ◽

Primitive Earth

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Submarine hydrothermal vent systems: the relevance of dynamic systems in chemical evolution and prebiotic chemistry experiments

International Journal of Astrobiology ◽

10.1017/s1473550421000331 ◽

2021 ◽

pp. 1-8

Author(s):

Saúl A. Villafañe-Barajas ◽

María Colín-García

Keyword(s):

Chemical Evolution ◽

Dynamic Systems ◽

Hydrothermal Vent ◽

Redox Reactions ◽

Prebiotic Chemistry ◽

Ph Gradients ◽

Dissolved Ions ◽

Geochemical Variables ◽

Specific Part ◽

Hydrothermal Fields

Abstract Since their discovery, submarine hydrothermal vent systems have been pointed out as important places where chemical evolution on Earth could have occurred; and their role in the process has been highlighted. Similarly, some hypotheses have considered these systems in origin of life scenarios. In this way, many experiments have been developed, and the knowledge about these systems has increased. Due to their complexity, many experimental simulations have only included a few of the geochemical variables present in these environments, pressure and temperature. Other main variables have hardly been included, such as mineralogy, thermal and pH gradients, dissolved ions and/or redox reactions. As it has been understood, the dynamism and heterogeneity of these environments are huge, and it comprises different scales, from single vents to full hydrothermal fields. However, the vast majority of experiments focus on a specific part of these systems and do not include salinity, mineralogy and pH gradients. For this reason, in this paper, we pointed out some considerations about how this dynamism can be interpreted, and included in some models, as well their importance in prebiotic chemistry experiments and their extrapolations regarding the hypothesis about the origins of life.

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