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Markovitch O, Wu J, Otto S. Binding of Precursors to Replicator Assemblies Can Improve Replication Fidelity and Mediate Error Correction. Angew Chem Int Ed Engl 2024; 63:e202317997. [PMID: 38380789 DOI: 10.1002/anie.202317997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/06/2024] [Accepted: 02/14/2024] [Indexed: 02/22/2024]
Abstract
Copying information is vital for life's propagation. Current life forms maintain a low error rate in replication, using complex machinery to prevent and correct errors. However, primitive life had to deal with higher error rates, limiting its ability to evolve. Discovering mechanisms to reduce errors would alleviate this constraint. Here, we introduce a new mechanism that decreases error rates and corrects errors in synthetic self-replicating systems driven by self-assembly. Previous work showed that macrocycle replication occurs through the accumulation of precursor material on the sides of the fibrous replicator assemblies. Stochastic simulations now reveal that selective precursor binding to the fiber surface enhances replication fidelity and error correction. Centrifugation experiments show that replicator fibers can exhibit the necessary selectivity in precursor binding. Our results suggest that synthetic replicator systems are more evolvable than previously thought, encouraging further evolution-focused experiments.
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Affiliation(s)
- Omer Markovitch
- Stratingh Institute, Centre for Systems Chemistry, University of Groningen, Groningen, The Netherlands
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
- Blue Marble Space Institute of Science, Seattle, Washington, USA
| | - Juntian Wu
- Stratingh Institute, Centre for Systems Chemistry, University of Groningen, Groningen, The Netherlands
| | - Sijbren Otto
- Stratingh Institute, Centre for Systems Chemistry, University of Groningen, Groningen, The Netherlands
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2
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Santos TCB, Futerman AH. The fats of the matter: Lipids in prebiotic chemistry and in origin of life studies. Prog Lipid Res 2023; 92:101253. [PMID: 37659458 DOI: 10.1016/j.plipres.2023.101253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/04/2023]
Abstract
The unique biophysical and biochemical properties of lipids render them crucial in most models of the origin of life (OoL). Many studies have attempted to delineate the prebiotic pathways by which lipids were formed, how micelles and vesicles were generated, and how these micelles and vesicles became selectively permeable towards the chemical precursors required to initiate and support biochemistry and inheritance. Our analysis of a number of such studies highlights the extremely narrow and limited range of conditions by which an experiment is considered to have successfully modeled a role for lipids in an OoL experiment. This is in line with a recent proposal that bias is introduced into OoL studies by the extent and the kind of human intervention. It is self-evident that OoL studies can only be performed by human intervention, and we now discuss the possibility that some assumptions and simplifications inherent in such experimental approaches do not permit determination of mechanistic insight into the roles of lipids in the OoL. With these limitations in mind, we suggest that more nuanced experimental approaches than those currently pursued may be required to elucidate the generation and function of lipids, micelles and vesicles in the OoL.
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Affiliation(s)
- Tania C B Santos
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Anthony H Futerman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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3
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Vitas M, Dobovišek A. Is Darwinian selection a retrograde driving force of evolution? Biosystems 2023; 233:105031. [PMID: 37734699 DOI: 10.1016/j.biosystems.2023.105031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023]
Abstract
Modern science has still not provided a satisfactory empirical explanation for the increasing complexity of living organisms through evolutionary history. As no agreed-upon definitions of the complexity exist, the working definition of biological complexity has been formulated. There is no theoretical reason to expect evolutionary lineages to increase in complexity over time, and there is no empirical evidence that they do so. In our discussion we have assumed the hypothesis that at the origins of life, evolution had to first involve autocatalytic systems that only subsequently acquired the capacity of genetic heredity. We discuss the role of Darwinian selection in evolution and pose the hypothesis that Darwinian selection acts predominantly as a retrograde driving force of evolution. In this context we understand the term retrograde evolution as a degeneration of living systems from higher complexity towards living systems with lower complexity. With the proposed hypothesis we have closed the gap between Darwinism and Lamarckism early in the evolutionary process. By Lamarckism, the action of a special principle called complexification force is understood here rather than inheritance of acquired characteristics.
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Affiliation(s)
- Marko Vitas
- Laze pri Borovnici 38, 1353, Borovnica, Slovenia.
| | - Andrej Dobovišek
- University of Maribor, Faculty of Natural Sciences and Mathematics, Koroška Cesta 160, 2000, Maribor, Slovenia; University of Maribor, Faculty of Medicine, Taborska Ulica 6B, 2000, Maribor, Slovenia.
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4
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Baum DA, Peng Z, Dolson E, Smith E, Plum AM, Gagrani P. The ecology-evolution continuum and the origin of life. J R Soc Interface 2023; 20:20230346. [PMID: 37907091 PMCID: PMC10618062 DOI: 10.1098/rsif.2023.0346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/10/2023] [Indexed: 11/02/2023] Open
Abstract
Prior research on evolutionary mechanisms during the origin of life has mainly assumed the existence of populations of discrete entities with information encoded in genetic polymers. Recent theoretical advances in autocatalytic chemical ecology establish a broader evolutionary framework that allows for adaptive complexification prior to the emergence of bounded individuals or genetic encoding. This framework establishes the formal equivalence of cells, ecosystems and certain localized chemical reaction systems as autocatalytic chemical ecosystems (ACEs): food-driven (open) systems that can grow due to the action of autocatalytic cycles (ACs). When ACEs are organized in meta-ecosystems, whether they be populations of cells or sets of chemically similar environmental patches, evolution, defined as change in AC frequency over time, can occur. In cases where ACs are enriched because they enhance ACE persistence or dispersal ability, evolution is adaptive and can build complexity. In particular, adaptive evolution can explain the emergence of self-bounded units (e.g. protocells) and genetic inheritance mechanisms. Recognizing the continuity between ecological and evolutionary change through the lens of autocatalytic chemical ecology suggests that the origin of life should be seen as a general and predictable outcome of driven chemical ecosystems rather than a phenomenon requiring specific, rare conditions.
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Affiliation(s)
- David A. Baum
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53705, USA
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA
| | - Zhen Peng
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA
- Department of Geoscience, University of Wisconsin, Madison, WI 53706, USA
| | - Emily Dolson
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
- Ecology, Evolution and Behavior, Michigan State University, East Lansing, MI 48824, USA
| | - Eric Smith
- Department of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
- Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Alex M. Plum
- Department of Physics, University of California, San Diego, CA 92093, USA
| | - Praful Gagrani
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53705, USA
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5
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Mandal R, Ghosh A, Rout NK, Prasad M, Hazra B, Sar S, Das S, Datta A, Tarafdar PK. Self-assembled prebiotic amphiphile-mixture exhibits tunable catalytic properties. Org Biomol Chem 2023; 21:4473-4481. [PMID: 37194351 DOI: 10.1039/d3ob00606a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Protocellular surface formation via the self-assembly of amphiphiles, and catalysis by simple peptides/proto-RNA are two important pillars in the evolution of protocells. To hunt for prebiotic self-assembly-supported catalytic reactions, we thought that amino-acid-based amphiphiles might play an important role. In this paper, we investigate the formation of histidine-based and serine-based amphiphiles under mild prebiotic conditions from amino acid : fatty alcohol and amino acid : fatty acid mixtures. The histidine-based amphiphiles were able to catalyze hydrolytic reactions at the self-assembled surface (with a rate increase of ∼1000-fold), and the catalytic ability can be tuned by linkage of the fatty carbon part to histidine (N-acylated vs. O-acylated). Moreover, the presence of cationic serine-based amphiphiles on the surface enhances the catalytic efficiency by another ∼2-fold, whereas the presence of anionic aspartic acid-based amphiphiles reduces the catalytic activity. Ester partitioning into the surface, reactivity, and the accumulation of liberated fatty acid explain the substrate selectivity of the catalytic surface, where the hexyl esters were found to be more hydrolytic than other fatty acyl esters. Di-methylation of the -NH2 of OLH increases the catalytic efficacy by a further ∼2-fold, whereas trimethylation reduces the catalytic ability. The self-assembly, charge-charge repulsion, and the H-bonding to the ester carbonyl are likely to be responsible for the superior (∼2500-fold higher rate than the pre-micellar OLH) catalytic efficiency of O-lauryl dimethyl histidine (OLDMH). Thus, prebiotic amino-acid-based surfaces served as an efficient catalyst that exhibits regulation of catalytic function, substrate selectivity, and further adaptability to perform bio-catalysis.
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Affiliation(s)
- Raki Mandal
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Anupam Ghosh
- Indian Association for the Cultivation of Science, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Nilesh K Rout
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Mahesh Prasad
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Bibhas Hazra
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Sanu Sar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Subrata Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Ayan Datta
- Indian Association for the Cultivation of Science, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Pradip K Tarafdar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
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Subbotin V, Fiksel G. Exploring the Lipid World Hypothesis: A Novel Scenario of Self-Sustained Darwinian Evolution of the Liposomes. ASTROBIOLOGY 2023; 23:344-357. [PMID: 36716277 PMCID: PMC9986030 DOI: 10.1089/ast.2021.0161] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 12/03/2022] [Indexed: 06/18/2023]
Abstract
According to the Lipid World hypothesis, life on Earth originated with the emergence of amphiphilic assemblies in the form of lipid micelles and vesicles (liposomes). However, the mechanism of appearance of the information molecules (ribozymes/RNA) accompanying that process, considered obligatory for Darwinian evolution, is unclear. We propose a novel scenario of self-sustained Darwinian evolution of the liposomes driven by ever-present natural phenomena: solar UV radiation, day/night cycle, gravity, and the formation of liposomes in an aqueous media. The central tenet of this scenario is the liposomes' encapsulation of the heavy solutes, followed by their gravitational submerging in the water. The submerged liposomes, being protected from the damaging UV radiation, acquire the longevity necessary for autocatalytic replication of amphiphiles, their mutation, and the selection of those amphiphilic assemblies that provide the greatest membrane stability. These two sets of adaptive compositional information (heavy content and amphiphilic assemblies design) generate a population of liposomes with self-replication/reproduction properties, which are amendable to mutation, inheritance, and selection, thereby establishing Darwinian progression. Temporary and spatial expansion of this liposomal population will provide the basis for the next evolutionary step-a transition of accidentally entrapped RNA precursor molecules into complex functional molecules, such as ribozymes/RNA.
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Affiliation(s)
- Vladimir Subbotin
- Department of Human Oncology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Gennady Fiksel
- Department of Nuclear Engineering and Radiological Sciences, University of Michigan, Ann Arbor, Michigan, USA
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7
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Bartlett S, Louapre D. Provenance of life: Chemical autonomous agents surviving through associative learning. Phys Rev E 2022; 106:034401. [PMID: 36266823 DOI: 10.1103/physreve.106.034401] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/21/2022] [Indexed: 06/16/2023]
Abstract
We present a benchmark study of autonomous, chemical agents exhibiting associative learning of an environmental feature. Associative learning systems have been widely studied in cognitive science and artificial intelligence but are most commonly implemented in highly complex or carefully engineered systems, such as animal brains, artificial neural networks, DNA computing systems, and gene regulatory networks, among others. The ability to encode environmental information and use it to make simple predictions is a benchmark of biological resilience and underpins a plethora of adaptive responses in the living hierarchy, spanning prey animal species anticipating the arrival of predators to epigenetic systems in microorganisms learning environmental correlations. Given the ubiquitous and essential presence of learning behaviors in the biosphere, we aimed to explore whether simple, nonliving dissipative structures could also exhibit associative learning. Inspired by previous modeling of associative learning in chemical networks, we simulated simple systems composed of long- and short-term memory chemical species that could encode the presence or absence of temporal correlations between two external species. The ability to learn this association was implemented in Gray-Scott reaction-diffusion spots, emergent chemical patterns that exhibit self-replication and homeostasis. With the novel ability of associative learning, we demonstrate that simple chemical patterns can exhibit a broad repertoire of lifelike behavior, paving the way for in vitro studies of autonomous chemical learning systems, with potential relevance to artificial life, origins of life, and systems chemistry. The experimental realization of these learning behaviors in protocell or coacervate systems could advance a new research direction in astrobiology, since our system significantly reduces the lower bound on the required complexity for autonomous chemical learning.
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Affiliation(s)
- Stuart Bartlett
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California 91125, USA and Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - David Louapre
- Ubisoft Entertainment, 94160 Saint-Mandé, France and Science Étonnante, 75014 Paris, France†
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8
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Prosdocimi F, de Farias ST, José MV. Prebiotic chemical refugia: multifaceted scenario for the formation of biomolecules in primitive Earth. Theory Biosci 2022; 141:339-347. [PMID: 36042123 DOI: 10.1007/s12064-022-00377-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/17/2022] [Indexed: 11/25/2022]
Abstract
The origin of life was a cosmic event happened on primitive Earth. A critical problem to better understand the origins of life in Earth is the search for chemical scenarios on which the basic building blocks of biological molecules could be produced. Classic works in pre-biotic chemistry frequently considered early Earth as an homogeneous atmosphere constituted by chemical elements such as methane (CH4), ammonia (NH3), water (H2O), hydrogen (H2) and hydrogen sulfide (H2S). Under that scenario, Stanley Miller was capable to produce amino acids and solved the question about the abiotic origin of proteins. Conversely, the origin of nucleic acids has tricked scientists for decades once nucleotides are complex, though necessary molecules to allow the existence of life. Here we review possible chemical scenarios that allowed not only the formation of nucleotides but also other significant biomolecules. We aim to provide a theoretical solution for the origin of biomolecules at specific sites named "Prebiotic Chemical Refugia." Prebiotic chemical refugium should therefore be understood as a geographic site in prebiotic Earth on which certain chemical elements were accumulated in higher proportion than expected, facilitating the production of basic building blocks for biomolecules. This higher proportion should not be understood as static, but dynamic; once the physicochemical conditions of our planet changed periodically. These different concentration of elements, together with geochemical and astronomical changes along days, synodic months and years provided somewhat periodic changes in temperature, pressure, electromagnetic fields, and conditions of humidity, among other features. Recent and classic works suggesting most likely prebiotic refugia on which the main building blocks for biological molecules might be accumulated are reviewed and discussed.
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Affiliation(s)
- Francisco Prosdocimi
- Laboratório de Biologia Teórica E de Sistemas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal Do Rio de Janeiro, 21.941-902, Rio de Janeiro, Brazil. .,Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, CDMX, Mexico.
| | - Sávio Torres de Farias
- Laboratório de Genética Evolutiva Paulo Leminsk, Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | - Marco V José
- Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, CDMX, Mexico.
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9
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Kumar Bandela A, Sadihov‐Hanoch H, Cohen‐Luria R, Gordon C, Blake A, Poppitz G, Lynn DG, Ashkenasy G. The Systems Chemistry of Nucleic‐acid‐Peptide Networks. Isr J Chem 2022. [DOI: 10.1002/ijch.202200030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anil Kumar Bandela
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Hava Sadihov‐Hanoch
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Rivka Cohen‐Luria
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Christella Gordon
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Alexis Blake
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - George Poppitz
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - David G. Lynn
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Gonen Ashkenasy
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
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10
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Mishra P, Sankar SHH, Gosavi N, Bharathavikru RS. RNA nucleoprotein complexes in biological systems. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2022. [DOI: 10.1007/s43538-022-00087-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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11
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Suzuki N. Understanding nonlinear composition dependency of enantioselectivity in chiral separation using mixed micelle. J Colloid Interface Sci 2022; 627:578-586. [PMID: 35878457 DOI: 10.1016/j.jcis.2022.07.086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 10/17/2022]
Abstract
HYPOTHESIS Mixtures of chiral and achiral building blocks of supramolecules exhibit interesting cooperative phenomena, indicated by the nonlinear composition dependence of the chiral properties. However, the nonlinear composition dependence of the enantioselectivity of mixed micelles is not well understood. It was hypothesized that in-depth understanding can be achieved by carefully investigating the composition dependence of the properties. EXPERIMENTS In this work, the nonlinear composition dependence of the enantioselectivity was found for the mixed micelle of achiral and chiralN-acyl amino acids by micellar electrokinetic chromatography (MEKC). Capillary electrophoresis, circular dichroism (CD) spectroscopy, surface tension measurement, and fluorescence spectroscopy were used to investigate the mechanisms. FINDINGS Four mechanisms that could be causing the nonlinearity were investigated: (i) synergistic and antagonistic interactions of the surfactants; (ii) the chiral transfer from chiral to achiral surfactant; (iii) differences in the retention factor; and (iv) cooperative chiral recognition of the chiral and achiral surfactant. The investigation of the composition dependency of critical micelle concentration (CMC) and molar circular dichroism revealed that the effect of (i) and (ii) was negligibly small. The newly derived equations for (iii) and (iv) revealed that (iii) and (iv) have a major or medium effect on the nonlinear enantioselectivity.
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Affiliation(s)
- Nozomu Suzuki
- Department of Chemistry, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima, Tokyo 171-8501, Japan; Department of Human Studies, Faculty of Arts and Humanities, Shikoku Gakuin University, 3-2-1 Bunkyo-cho, Zentsuji, Kagawa 765-8505, Japan.
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12
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Imai M, Sakuma Y, Kurisu M, Walde P. From vesicles toward protocells and minimal cells. SOFT MATTER 2022; 18:4823-4849. [PMID: 35722879 DOI: 10.1039/d1sm01695d] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In contrast to ordinary condensed matter systems, "living systems" are unique. They are based on molecular compartments that reproduce themselves through (i) an uptake of ingredients and energy from the environment, and (ii) spatially and timely coordinated internal chemical transformations. These occur on the basis of instructions encoded in information molecules (DNAs). Life originated on Earth about 4 billion years ago as self-organised systems of inorganic compounds and organic molecules including macromolecules (e.g. nucleic acids and proteins) and low molar mass amphiphiles (lipids). Before the first living systems emerged from non-living forms of matter, functional molecules and dynamic molecular assemblies must have been formed as prebiotic soft matter systems. These hypothetical cell-like compartment systems often are called "protocells". Other systems that are considered as bridging units between non-living and living systems are called "minimal cells". They are synthetic, autonomous and sustainable reproducing compartment systems, but their constituents are not limited to prebiotic substances. In this review, we focus on both membrane-bounded (vesicular) protocells and minimal cells, and provide a membrane physics background which helps to understand how morphological transformations of vesicle systems might have happened and how vesicle reproduction might be coupled with metabolic reactions and information molecules. This research, which bridges matter and life, is a great challenge in which soft matter physics, systems chemistry, and synthetic biology must take joined efforts to better understand how the transformation of protocells into living systems might have occurred at the origin of life.
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Affiliation(s)
- Masayuki Imai
- Department of Physics, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba, Sendai 980-8578, Japan.
| | - Yuka Sakuma
- Department of Physics, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba, Sendai 980-8578, Japan.
| | - Minoru Kurisu
- Department of Physics, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba, Sendai 980-8578, Japan.
| | - Peter Walde
- Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, CH-8093 Zürich, Switzerland
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13
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Kahana A, Lancet D, Palmai Z. Micellar Composition Affects Lipid Accretion Kinetics in Molecular Dynamics Simulations: Support for Lipid Network Reproduction. LIFE (BASEL, SWITZERLAND) 2022; 12:life12070955. [PMID: 35888044 PMCID: PMC9325298 DOI: 10.3390/life12070955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/02/2022] [Accepted: 06/21/2022] [Indexed: 11/25/2022]
Abstract
Mixed lipid micelles were proposed to facilitate life through their documented growth dynamics and catalytic properties. Our previous research predicted that micellar self-reproduction involves catalyzed accretion of lipid molecules by the residing lipids, leading to compositional homeostasis. Here, we employ atomistic Molecular Dynamics simulations, beginning with 54 lipid monomers, tracking an entire course of micellar accretion. This was done to examine the self-assembly of variegated lipid clusters, allowing us to measure entry and exit rates of monomeric lipids into pre-micelles with different compositions and sizes. We observe considerable rate-modifications that depend on the assembly composition and scrutinize the underlying mechanisms as well as the energy contributions. Lastly, we describe the measured potential for compositional homeostasis in our simulated mixed micelles. This affirms the basis for micellar self-reproduction, with implications for the study of the origin of life.
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14
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Gözen I, Köksal ES, Põldsalu I, Xue L, Spustova K, Pedrueza-Villalmanzo E, Ryskulov R, Meng F, Jesorka A. Protocells: Milestones and Recent Advances. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2106624. [PMID: 35322554 DOI: 10.1002/smll.202106624] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/06/2022] [Indexed: 06/14/2023]
Abstract
The origin of life is still one of humankind's great mysteries. At the transition between nonliving and living matter, protocells, initially featureless aggregates of abiotic matter, gain the structure and functions necessary to fulfill the criteria of life. Research addressing protocells as a central element in this transition is diverse and increasingly interdisciplinary. The authors review current protocell concepts and research directions, address milestones, challenges and existing hypotheses in the context of conditions on the early Earth, and provide a concise overview of current protocell research methods.
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Affiliation(s)
- Irep Gözen
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Oslo, 0318, Norway
| | - Elif Senem Köksal
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Oslo, 0318, Norway
| | - Inga Põldsalu
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Oslo, 0318, Norway
| | - Lin Xue
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Oslo, 0318, Norway
| | - Karolina Spustova
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Oslo, 0318, Norway
| | - Esteban Pedrueza-Villalmanzo
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Göteborg, SE-412 96, Sweden
- Department of Physics, University of Gothenburg, Universitetsplatsen 1, Gothenburg, 40530, Sweden
| | - Ruslan Ryskulov
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Göteborg, SE-412 96, Sweden
| | - Fanda Meng
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Göteborg, SE-412 96, Sweden
- School of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250000, China
| | - Aldo Jesorka
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Göteborg, SE-412 96, Sweden
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15
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Fiore M, Chieffo C, Lopez A, Fayolle D, Ruiz J, Soulère L, Oger P, Altamura E, Popowycz F, Buchet R. Synthesis of Phospholipids Under Plausible Prebiotic Conditions and Analogies with Phospholipid Biochemistry for Origin of Life Studies. ASTROBIOLOGY 2022; 22:598-627. [PMID: 35196460 DOI: 10.1089/ast.2021.0059] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Phospholipids are essential components of biological membranes and are involved in cell signalization, in several enzymatic reactions, and in energy metabolism. In addition, phospholipids represent an evolutionary and non-negligible step in life emergence. Progress in the past decades has led to a deeper understanding of these unique hydrophobic molecules and their most pertinent functions in cell biology. Today, a growing interest in "prebiotic lipidomics" calls for a new assessment of these relevant biomolecules.
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Affiliation(s)
- Michele Fiore
- Université de Lyon, Université Claude Bernard Lyon 1, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, UMR 5246, CNRS, CPE, Villeurbanne, France
| | - Carolina Chieffo
- Université de Lyon, Université Claude Bernard Lyon 1, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, UMR 5246, CNRS, CPE, Villeurbanne, France
| | - Augustin Lopez
- Université de Lyon, Université Claude Bernard Lyon 1, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, UMR 5246, CNRS, CPE, Villeurbanne, France
| | - Dimitri Fayolle
- Université de Lyon, Université Claude Bernard Lyon 1, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, UMR 5246, CNRS, CPE, Villeurbanne, France
| | - Johal Ruiz
- Université de Lyon, Université Claude Bernard Lyon 1, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, UMR 5246, CNRS, CPE, Villeurbanne, France
- Institut National Des Sciences Appliquées, INSA Lyon, Villeurbanne, France
| | - Laurent Soulère
- Université de Lyon, Université Claude Bernard Lyon 1, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, UMR 5246, CNRS, CPE, Villeurbanne, France
- Institut National Des Sciences Appliquées, INSA Lyon, Villeurbanne, France
| | - Philippe Oger
- Microbiologie, Adaptation et Pathogénie, UMR 5240, Université de Lyon, Claude Bernard Lyon 1, Villeurbanne, France
| | - Emiliano Altamura
- Chemistry Department, Università degli studi di Bari "Aldo Moro," Bari, Italy
| | - Florence Popowycz
- Université de Lyon, Université Claude Bernard Lyon 1, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, UMR 5246, CNRS, CPE, Villeurbanne, France
- Institut National Des Sciences Appliquées, INSA Lyon, Villeurbanne, France
| | - René Buchet
- Université de Lyon, Université Claude Bernard Lyon 1, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, UMR 5246, CNRS, CPE, Villeurbanne, France
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16
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Barge LM, Rodriguez LE, Weber JM, Theiling BP. Determining the "Biosignature Threshold" for Life Detection on Biotic, Abiotic, or Prebiotic Worlds. ASTROBIOLOGY 2022; 22:481-493. [PMID: 34898272 DOI: 10.1089/ast.2021.0079] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The field of prebiotic chemistry has demonstrated that complex organic chemical systems that exhibit various life-like properties can be produced abiotically in the laboratory. Understanding these chemical systems is important for astrobiology and life detection since we do not know the extent to which prebiotic chemistry might exist or have existed on other worlds. Nor do we know what signatures are diagnostic of an extant or "failed" prebiotic system. On Earth, biology has suppressed most abiotic organic chemistry and overprints geologic records of prebiotic chemistry; therefore, it is difficult to validate whether chemical signatures from future planetary missions are remnant or extant prebiotic systems. The "biosignature threshold" between whether a chemical signature is more likely to be produced by abiotic versus biotic chemistry on a given world could vary significantly, depending on the particular environment, and could change over time, especially if life were to emerge and diversify on that world. To interpret organic signatures detected during a planetary mission, we advocate for (1) gaining a more complete understanding of prebiotic/abiotic chemical possibilities in diverse planetary environments and (2) involving experimental prebiotic samples as analogues when generating comparison libraries for "life-detection" mission instruments.
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Affiliation(s)
- Laura M Barge
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Laura E Rodriguez
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Jessica M Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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17
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Jia TZ, Nishikawa S, Fujishima K. Sequencing the Origins of Life. BBA ADVANCES 2022; 2:100049. [PMID: 37082609 PMCID: PMC10074849 DOI: 10.1016/j.bbadva.2022.100049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 01/10/2023] Open
Abstract
One goal of origins of life research is to understand how primitive informational and catalytic biopolymers emerged and evolved. Recently, a number of sequencing techniques have been applied to analysis of replicating and evolving primitive biopolymer systems, providing a sequence-specific and high-resolution view of primitive chemical processes. Here, we review application of sequencing techniques to analysis of synthetic and primitive nucleic acids and polypeptides. This includes next-generation sequencing of primitive polymerization and evolution processes, followed by discussion of other novel biochemical techniques that could contribute to sequence analysis of primitive biopolymer driven chemical systems. Further application of sequencing to origins of life research, perhaps as a life detection technology, could provide insight into the origin and evolution of informational and catalytic biopolymers on early Earth or elsewhere.
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Affiliation(s)
- Tony Z. Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Blue Marble Space Institute of Science, 600 1st Ave, Floor 1, Seattle, WA 98104, USA
- Corresponding author
| | - Shota Nishikawa
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa-shi, Kanagawa 252-0882, Japan
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18
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Sithamparam M, Satthiyasilan N, Chen C, Jia TZ, Chandru K. A material-based panspermia hypothesis: The potential of polymer gels and membraneless droplets. Biopolymers 2022; 113:e23486. [PMID: 35148427 DOI: 10.1002/bip.23486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 01/08/2023]
Abstract
The Panspermia hypothesis posits that either life's building blocks (molecular Panspermia) or life itself (organism-based Panspermia) may have been interplanetarily transferred to facilitate the origins of life (OoL) on a given planet, complementing several current OoL frameworks. Although many spaceflight experiments were performed in the past to test for potential terrestrial organisms as Panspermia seeds, it is uncertain whether such organisms will likely "seed" a new planet even if they are able to survive spaceflight. Therefore, rather than using organisms, using abiotic chemicals as seeds has been proposed as part of the molecular Panspermia hypothesis. Here, as an extension of this hypothesis, we introduce and review the plausibility of a polymeric material-based Panspermia seed (M-BPS) as a theoretical concept, where the type of polymeric material that can function as a M-BPS must be able to: (1) survive spaceflight and (2) "function", i.e., contingently drive chemical evolution toward some form of abiogenesis once arriving on a foreign planet. We use polymeric gels as a model example of a potential M-BPS. Polymeric gels that can be prebiotically synthesized on one planet (such as polyester gels) could be transferred to another planet via meteoritic transfer, where upon landing on a liquid bearing planet, can assemble into structures containing cellular-like characteristics and functionalities. Such features presupposed that these gels can assemble into compartments through phase separation to accomplish relevant functions such as encapsulation of primitive metabolic, genetic and catalytic materials, exchange of these materials, motion, coalescence, and evolution. All of these functions can result in the gels' capability to alter local geochemical niches on other planets, thereby allowing chemical evolution to lead to OoL events.
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Affiliation(s)
- Mahendran Sithamparam
- Space Science Center (ANGKASA), Institute of Climate Change, National University of Malaysia (UKM), Bangi, Selangor, Malaysia
| | - Nirmell Satthiyasilan
- Space Science Center (ANGKASA), Institute of Climate Change, National University of Malaysia (UKM), Bangi, Selangor, Malaysia
| | - Chen Chen
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Tony Z Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Blue Marble Space Institute of Science, Seattle, Washington, USA
| | - Kuhan Chandru
- Space Science Center (ANGKASA), Institute of Climate Change, National University of Malaysia (UKM), Bangi, Selangor, Malaysia
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19
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Kondratyeva LG, Dyachkova MS, Galchenko AV. The Origin of Genetic Code and Translation in the Framework of Current Concepts on the Origin of Life. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:150-169. [PMID: 35508902 DOI: 10.1134/s0006297922020079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The origin of genetic code and translation system is probably the central and most difficult problem in the investigations on the origin of life and one of the most complex problems in the evolutionary biology in general. There are multiple hypotheses on the emergence and development of existing genetic systems that propose the mechanisms for the origin and early evolution of genetic code, as well as for the emergence of replication and translation. Here, we discuss the most well-known of these hypotheses, although none of them provides a description of the early evolution of genetic systems without gaps and assumptions. The RNA world hypothesis is a currently prevailing scientific idea on the early evolution of biological and pre-biological structures, the main advantage of which is the assumption that RNAs as the first living systems were self-sufficient, i.e., capable of functioning as both catalysts and templates. However, this hypothesis has also significant limitations. In particular, no ribozymes with processive polymerase activity have been yet discovered or synthesized. Taking into account the mutual need of proteins and nucleic acids in each other in the current world, many authors propose the early evolution scenarios based on the co-evolution of these two classes of organic molecules. They postulate that the emergence of translation was necessary for the replication of nucleic acids, in contrast to the RNA world hypothesis, according to which the emergence of translation was preceded by the era of self-replicating RNAs. Although such scenarios are less parsimonious from the evolutionary point of view, since they require simultaneous emergence and evolution of two classes of organic molecules, as well as the emergence of synchronized replication and translation, their major advantage is that they explain the development of processive and much more accurate protein-dependent replication.
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Affiliation(s)
- Liya G Kondratyeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | | | - Alexey V Galchenko
- Peoples' Friendship University of Russia (RUDN University), Moscow, 117198, Russia.
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20
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Abstract
As the remit of chemistry expands beyond molecules to systems, new synthetic targets appear on the horizon. Among these, life represents perhaps the ultimate synthetic challenge. Building on an increasingly detailed understanding of the inner workings of living systems and advances in organic synthesis and supramolecular chemistry, the de novo synthesis of life (i.e., the construction of a new form of life based on completely synthetic components) is coming within reach. This Account presents our first steps in the journey toward this long-term goal. The synthesis of life requires the functional integration of different subsystems that harbor the different characteristics that are deemed essential to life. The most important of these are self-replication, metabolism, and compartmentalization. Integrating these features into a single system, maintaining this system out of equilibrium, and allowing it to undergo Darwinian evolution should ideally result in the emergence of life. Our journey toward de novo life started with the serendipitous discovery of a new mechanism of self-replication. We found that self-assembly in a mixture of interconverting oligomers is a general way of achieving self-replication, where the assembly process drives the synthesis of the very molecules that assemble. Mechanically induced breakage of the growing replicating assemblies resulted in their exponential growth, which is an important enabler for achieving Darwinian evolution. Through this mechanism, the self-replication of compounds containing peptides, nucleobases, and fully synthetic molecules was achieved. Several examples of evolutionary dynamics have been observed in these systems, including the spontaneous diversification of replicators allowing them to specialize on different food sets, history dependence of replicator composition, and the spontaneous emergence of parasitic behavior. Peptide-based replicator assemblies were found to organize their peptide units in space in a manner that, inadvertently, gives rise to microenvironments that are capable of catalysis of chemical reactions or binding-induced activation of cofactors. Among the reactions that can be catalyzed by the replicators are ones that produce the precursors from which these replicators grow, amounting to the first examples of the assimilation of a proto-metabolism. Operating these replicators in a chemically fueled out-of-equilibrium replication-destruction regime was found to promote an increase in their molecular complexity. Fueling counteracts the inherent tendency of replicators to evolve toward lower complexity (caused by the fact that smaller replicators tend to replicate faster). Among the remaining steps on the road to de novo life are now to assimilate compartmentalization and achieve open-ended evolution of the resulting system. Success in the synthesis of de novo life, once obtained, will have far-reaching implications for our understanding of what life is, for the search for extraterrestrial life, for how life may have originated on earth, and for every-day life by opening up new vistas in the form living technology and materials.
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Affiliation(s)
- Sijbren Otto
- Centre for Systems Chemistry, Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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21
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Kahana A, Maslov S, Lancet D. Dynamic lipid aptamers: non-polymeric chemical path to early life. Chem Soc Rev 2021; 50:11741-11746. [PMID: 34541591 DOI: 10.1039/d1cs00633a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A widespread dogma asserts that life could not have emerged without biopolymers - RNA and proteins. However, the widely acknowledged implausibility of a spontaneous appearance and proliferation of these complex molecules in primordial messy chemistry casts doubt on this scenario. A proposed alternative is "Lipid-First", based on the evidence that lipid assemblies may spontaneously emerge in heterogeneous environments, and are shown to undergo growth and fission, and to portray autocatalytic self-copying. What seems undecided is whether lipid assemblies have protein-like capacities for stereospecific interactions, a sine qua non of life processes. This Viewpoint aims to alleviate such doubts, pointing to growing experimental evidence that lipid aggregates possess dynamic surface configurations capable of stereospecific molecular recognition. Such findings help support a possible key role of lipids in seeding life's origin.
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Affiliation(s)
- Amit Kahana
- Dept. of Molecular Genetics, the Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Svetlana Maslov
- Dept. of Molecular Genetics, the Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Doron Lancet
- Dept. of Molecular Genetics, the Weizmann Institute of Science, Rehovot 7610001, Israel.
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22
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Kahana A, Lancet D. Self-reproducing catalytic micelles as nanoscopic protocell precursors. Nat Rev Chem 2021; 5:870-878. [PMID: 37117387 DOI: 10.1038/s41570-021-00329-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2021] [Indexed: 12/31/2022]
Abstract
Protocells at life's origin are often conceived as bilayer-enclosed precursors of life, whose self-reproduction rests on the early advent of replicating catalytic biopolymers. This Perspective describes an alternative scenario, wherein reproducing nanoscopic lipid micelles with catalytic capabilities were forerunners of biopolymer-containing protocells. This postulate gains considerable support from experiments describing micellar catalysis and autocatalytic proliferation, and, more recently, from reports on cross-catalysis in mixed micelles that lead to life-like steady-state dynamics. Such results, along with evidence for micellar prebiotic compatibility, synergize with predictions of our chemically stringent computer-simulated model, illustrating how mutually catalytic lipid networks may enable micellar compositional reproduction that could underlie primal selection and evolution. Finally, we highlight studies on how endogenously catalysed lipid modifications could guide further protocellular complexification, including micelle to vesicle transition and monomer to biopolymer progression. These portrayals substantiate the possibility that protocellular evolution could have been seeded by pre-RNA lipid assemblies.
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23
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Howlett M, Scanes RJH, Fletcher SP. Selection between Competing Self-Reproducing Lipids: Succession and Dynamic Activation. JACS AU 2021; 1:1355-1361. [PMID: 34604845 PMCID: PMC8479773 DOI: 10.1021/jacsau.1c00138] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Indexed: 06/09/2023]
Abstract
Models of chemical evolution are central to advancing origins of life research. To design more lifelike systems, we must expand our understanding of molecular selection mechanisms. Here, we show two selection modes that produce evolving populations of self-reproducing species, formed through thiol-disulfide exchange. Competition between thiol precursors can give clear succession patterns based on steric factors, an intrinsic property. A separate, emergent selection mechanism-dynamic activating metathesis-was found when exploring competing disulfide precursors. These experiments reveal that additional species generated in the mixture open up alternative reaction pathways to form self-reproducing products. Thus, increased compositional complexity provides certain species with a unique competitive advantage at the expense of others.
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Affiliation(s)
- Michael
G. Howlett
- Department of Chemistry,
Chemistry Research Laboratory, University
of Oxford, Oxford OX1 3TA, United Kingdom
| | - Robert J. H. Scanes
- Department of Chemistry,
Chemistry Research Laboratory, University
of Oxford, Oxford OX1 3TA, United Kingdom
| | - Stephen P. Fletcher
- Department of Chemistry,
Chemistry Research Laboratory, University
of Oxford, Oxford OX1 3TA, United Kingdom
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24
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Gözen İ. Did Solid Surfaces Enable the Origin of Life? Life (Basel) 2021; 11:795. [PMID: 34440539 PMCID: PMC8399221 DOI: 10.3390/life11080795] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 12/01/2022] Open
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 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.
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Affiliation(s)
- İrep Gözen
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, 0318 Oslo, Norway;
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Oslo, 0315 Oslo, Norway
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25
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Abstract
Natural selection successfully explains how organisms accumulate adaptive change despite that traits acquired over a lifetime are eliminated at the end of each generation. However, in some domains that exhibit cumulative, adaptive change-e.g. cultural evolution, and earliest life-acquired traits are retained; these domains do not face the problem that Darwin's theory was designed to solve. Lack of transmission of acquired traits occurs when germ cells are protected from environmental change, due to a self-assembly code used in two distinct ways: (i) actively interpreted during development to generate a soma, and (ii) passively copied without interpretation during reproduction to generate germ cells. Early life and cultural evolution appear not to involve a self-assembly code used in these two ways. We suggest that cumulative, adaptive change in these domains is due to a lower-fidelity evolutionary process, and model it using reflexively autocatalytic and foodset-generated networks. We refer to this more primitive evolutionary process as self-other reorganization (SOR) because it involves internal self-organizing and self-maintaining processes within entities, as well as interaction between entities. SOR encompasses learning but in general operates across groups. We discuss the relationship between SOR and Lamarckism, and illustrate a special case of SOR without variation.
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Affiliation(s)
- Liane Gabora
- Department of Psychology, University of British Columbia, Kelowna British Columbia, Canada
| | - Mike Steel
- Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand
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26
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Caliari A, Xu J, Yomo T. The requirement of cellularity for abiogenesis. Comput Struct Biotechnol J 2021; 19:2202-2212. [PMID: 33995913 PMCID: PMC8099592 DOI: 10.1016/j.csbj.2021.04.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/10/2021] [Accepted: 04/13/2021] [Indexed: 11/22/2022] Open
Abstract
The history of modern biochemistry started with the cellular theory of life. By putting aside the holistic protoplasmic theory, scientists of the XX century were able to advance the functional classification of cellular components significantly. The cell became the unit of the living. Current theories on the abiogenesis of life must account for a moment in evolution (chemical or biological) when this was not the case. Investigating the role of compartments and membranes along chemical and biotic evolution can lead a more generalised idea of living organisms that is fundamental to advance our efforts in astrobiology, origin of life and artificial life studies. Furthermore, it may provide insights in unexplained evolutionary features such as the lipid divide between Archaea and Eubacteria. By surveying our current understanding of the involvement of compartments in abiogenesis and evolution, the idea of cells as atomistic units of a general theory of biology will be discussed. The aim is not to undermine the validity of the cellular theory of life, but rather to elucidate possible biases with regards to cellularity and the origin of life. An open discussion in these regards could show the inherent limitations of non-cellular compartmentalization that may lead to the necessity of cellular structures to support complex life.
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Affiliation(s)
- Adriano Caliari
- School of Software Engineering, East China Normal University, Shanghai 200062, PR China
| | - Jian Xu
- Laboratory of Biology and Information Science, Biomedical Synthetic Biology Research Center, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Tetsuya Yomo
- Laboratory of Biology and Information Science, Biomedical Synthetic Biology Research Center, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
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27
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Can coacervation unify disparate hypotheses in the origin of cellular life? Curr Opin Colloid Interface Sci 2021. [DOI: 10.1016/j.cocis.2020.101415] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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28
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Ameta S, Matsubara YJ, Chakraborty N, Krishna S, Thutupalli S. Self-Reproduction and Darwinian Evolution in Autocatalytic Chemical Reaction Systems. Life (Basel) 2021; 11:308. [PMID: 33916135 PMCID: PMC8066523 DOI: 10.3390/life11040308] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/25/2021] [Accepted: 03/27/2021] [Indexed: 11/18/2022] Open
Abstract
Understanding the emergence of life from (primitive) abiotic components has arguably been one of the deepest and yet one of the most elusive scientific questions. Notwithstanding the lack of a clear definition for a living system, it is widely argued that heredity (involving self-reproduction) along with compartmentalization and metabolism are key features that contrast living systems from their non-living counterparts. A minimal living system may be viewed as "a self-sustaining chemical system capable of Darwinian evolution". It has been proposed that autocatalytic sets of chemical reactions (ACSs) could serve as a mechanism to establish chemical compositional identity, heritable self-reproduction, and evolution in a minimal chemical system. Following years of theoretical work, autocatalytic chemical systems have been constructed experimentally using a wide variety of substrates, and most studies, thus far, have focused on the demonstration of chemical self-reproduction under specific conditions. While several recent experimental studies have raised the possibility of carrying out some aspects of experimental evolution using autocatalytic reaction networks, there remain many open challenges. In this review, we start by evaluating theoretical studies of ACSs specifically with a view to establish the conditions required for such chemical systems to exhibit self-reproduction and Darwinian evolution. Then, we follow with an extensive overview of experimental ACS systems and use the theoretically established conditions to critically evaluate these empirical systems for their potential to exhibit Darwinian evolution. We identify various technical and conceptual challenges limiting experimental progress and, finally, conclude with some remarks about open questions.
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Affiliation(s)
- Sandeep Ameta
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Yoshiya J. Matsubara
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Nayan Chakraborty
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Sandeep Krishna
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Shashi Thutupalli
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
- International Centre for Theoretical Sciences, Tata Institute of Fundamental Research, Bangalore 560089, India
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29
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Affiliation(s)
- Dragana Despotovic
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot 7610001 Israel
| | - Dan S. Tawfik
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot 7610001 Israel
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30
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Salvador López JM, Van Bogaert INA. Microbial fatty acid transport proteins and their biotechnological potential. Biotechnol Bioeng 2021; 118:2184-2201. [PMID: 33638355 DOI: 10.1002/bit.27735] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 01/08/2021] [Accepted: 02/24/2021] [Indexed: 12/11/2022]
Abstract
Fatty acid metabolism has been widely studied in various organisms. However, fatty acid transport has received less attention, even though it plays vital physiological roles, such as export of toxic free fatty acids or uptake of exogenous fatty acids. Hence, there are important knowledge gaps in how fatty acids cross biological membranes, and many mechanisms and proteins involved in these processes still need to be determined. The lack of information is more predominant in microorganisms, even though the identification of fatty acids transporters in these cells could lead to establishing new drug targets or improvements in microbial cell factories. This review provides a thorough analysis of the current information on fatty acid transporters in microorganisms, including bacteria, yeasts and microalgae species. Most available information relates to the model organisms Escherichia coli and Saccharomyces cerevisiae, but transport systems of other species are also discussed. Intracellular trafficking of fatty acids and their transport through organelle membranes in eukaryotic organisms is described as well. Finally, applied studies and engineering efforts using fatty acids transporters are presented to show the applied potential of these transporters and to stress the need for further identification of new transporters and their engineering.
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Affiliation(s)
- José M Salvador López
- BioPort Group, Faculty of Bioscience Engineering, Centre for Synthetic Biology (CSB), Ghent University, Ghent, Belgium
| | - Inge N A Van Bogaert
- BioPort Group, Faculty of Bioscience Engineering, Centre for Synthetic Biology (CSB), Ghent University, Ghent, Belgium
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31
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Carter CW, Wills PR. Reciprocally-Coupled Gating: Strange Loops in Bioenergetics, Genetics, and Catalysis. Biomolecules 2021; 11:265. [PMID: 33670192 PMCID: PMC7916928 DOI: 10.3390/biom11020265] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/04/2021] [Accepted: 02/06/2021] [Indexed: 12/12/2022] Open
Abstract
Bioenergetics, genetic coding, and catalysis are all difficult to imagine emerging without pre-existing historical context. That context is often posed as a "Chicken and Egg" problem; its resolution is concisely described by de Grasse Tyson: "The egg was laid by a bird that was not a chicken". The concision and generality of that answer furnish no details-only an appropriate framework from which to examine detailed paradigms that might illuminate paradoxes underlying these three life-defining biomolecular processes. We examine experimental aspects here of five examples that all conform to the same paradigm. In each example, a paradox is resolved by coupling "if, and only if" conditions for reciprocal transitions between levels, such that the consequent of the first test is the antecedent for the second. Each condition thus restricts fluxes through, or "gates" the other. Reciprocally-coupled gating, in which two gated processes constrain one another, is self-referential, hence maps onto the formal structure of "strange loops". That mapping uncovers two different kinds of forces that may help unite the axioms underlying three phenomena that distinguish biology from chemistry. As a physical analog for Gödel's logic, biomolecular strange-loops provide a natural metaphor around which to organize a large body of experimental data, linking biology to information, free energy, and the second law of thermodynamics.
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Affiliation(s)
- Charles W. Carter
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7260, USA
| | - Peter R. Wills
- Department of Physics and Te Ao Marama Centre for Fundamental Inquiry, University of Auckland, PB 92019, Auckland 1142, New Zealand;
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32
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Ameta S, Arsène S, Foulon S, Saudemont B, Clifton BE, Griffiths AD, Nghe P. Darwinian properties and their trade-offs in autocatalytic RNA reaction networks. Nat Commun 2021; 12:842. [PMID: 33558542 PMCID: PMC7870898 DOI: 10.1038/s41467-021-21000-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 01/08/2021] [Indexed: 12/18/2022] Open
Abstract
Discovering autocatalytic chemistries that can evolve is a major goal in systems chemistry and a critical step towards understanding the origin of life. Autocatalytic networks have been discovered in various chemistries, but we lack a general understanding of how network topology controls the Darwinian properties of variation, differential reproduction, and heredity, which are mediated by the chemical composition. Using barcoded sequencing and droplet microfluidics, we establish a landscape of thousands of networks of RNAs that catalyze their own formation from fragments, and derive relationships between network topology and chemical composition. We find that strong variations arise from catalytic innovations perturbing weakly connected networks, and that growth increases with global connectivity. These rules imply trade-offs between reproduction and variation, and between compositional persistence and variation along trajectories of network complexification. Overall, connectivity in reaction networks provides a lever to balance variation (to explore chemical states) with reproduction and heredity (persistence being necessary for selection to act), as required for chemical evolution.
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Affiliation(s)
- Sandeep Ameta
- Laboratoire de Biochimie, ESPCI Paris, Université PSL, CNRS UMR 8231, 10 Rue Vauquelin, Paris, France
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences (TIFR), Bangalore, India
| | - Simon Arsène
- Laboratoire de Biochimie, ESPCI Paris, Université PSL, CNRS UMR 8231, 10 Rue Vauquelin, Paris, France
| | - Sophie Foulon
- Laboratoire de Biochimie, ESPCI Paris, Université PSL, CNRS UMR 8231, 10 Rue Vauquelin, Paris, France
| | - Baptiste Saudemont
- Laboratoire de Biochimie, ESPCI Paris, Université PSL, CNRS UMR 8231, 10 Rue Vauquelin, Paris, France
| | - Bryce E Clifton
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Andrew D Griffiths
- Laboratoire de Biochimie, ESPCI Paris, Université PSL, CNRS UMR 8231, 10 Rue Vauquelin, Paris, France.
| | - Philippe Nghe
- Laboratoire de Biochimie, ESPCI Paris, Université PSL, CNRS UMR 8231, 10 Rue Vauquelin, Paris, France.
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33
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Is it possible that cells have had more than one origin? Biosystems 2021; 202:104371. [PMID: 33524470 DOI: 10.1016/j.biosystems.2021.104371] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 01/03/2023]
Abstract
Cells occupy a prominent place in the history of life in Earth. The central role of cellular organization can be understood by the fact that "cellular life" is often used as a synonym for life itself. Thus, most characteristics used to define cell overlap with those ones used to define life. However, innovative scenarios for the origin of life are bringing alternative views to describe how cells may have evolved from the open biological systems named progenotes. Here, using a logical and conceptual analysis, we re-evaluate the characteristics used to infer a single origin for cells. We argue that some evidences used to support cell monophyly, such as the presence of elements from the translation mechanism together with the universality of the genetic code, actually indicate a unique origin for all "biological systems", a term used to define not only cells, but also viruses and progenotes. Besides, we present evidence that at least two biochemical pathways as important as (i) DNA replication and (ii) lipid biosynthesis are not homologous between Bacteria and Archaea. The identities observed between the proteins involved in those pathways along representatives of these two ancestral domains of life are too low to indicate common genic ancestry. Altogether these facts can be seen as an indication that cellular organization has possibly evolved two or more times and that LUCA (the Last Universal Common Ancestor) may not have existed as a cellular entity. Thus, we aim to consider the possibility that different strategies acquired by biological systems to exist, such as viral, bacterial and archaeal were most likely originated independently from the evolution of different progenote populations.
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34
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Slijepcevic P. Serial Endosymbiosis Theory: From biology to astronomy and back to the origin of life. Biosystems 2021; 202:104353. [PMID: 33453317 DOI: 10.1016/j.biosystems.2021.104353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 12/20/2022]
Abstract
Serial Endosymbiosis Theory, or SET, was conceived and developed by Lynn Margulis, to explain the greatest discontinuity in the history of life, the origin of eukaryotic cells. Some predictions of SET, namely the origin of mitochondria and chloroplasts, withstood the test of the most recent evidence from a variety of disciplines including phylogenetics, biochemistry, and cell biology. Even though some other predictions fared less well, SET remains a seminal theory in biology. In this paper, I focus on two aspects of SET. First, using the concept of "universal symbiogenesis", developed by Freeman Dyson to search for commonalities in astronomy and biology, I propose that SET can be extended beyond eukaryogenesis. The extension refers to the possibility that even prokaryotic organisms, themselves subject to the process of symbiogenesis in SET, could have emerged symbiotically. Second, I contrast a recent "viral eukaryogenesis" hypothesis, according to which the nucleus evolved from a complex DNA virus, with a view closer to SET, according to which the nucleus evolved through the interplay of the archaeal host, the eubacterial symbiont, and a non-LTR transposon, or telomerase. Viruses joined in later, through the process of viral endogenization, to shape eukaryotic chromosomes in the process of karyotype evolution. These two proposals based on SET are a testament to its longevity as a scientific theory.
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Affiliation(s)
- Predrag Slijepcevic
- Department of Life Sciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UB8 3PH, United Kingdom.
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35
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Abstract
How did life begin on Earth? And is there life elsewhere in the Cosmos? Challenging questions, indeed. The series of conferences established by NoR CEL in 2013 addresses these very questions. This paper comprises a summary report of oral presentations that were delivered by NoR CEL’s network members during the 2018 Athens conference and, as such, disseminates the latest research which they have put forward. More in depth material can be found by consulting the contributors referenced papers. Overall, the outcome of this conspectus on the conference demonstrates a case for the existence of “probable chemistry” during the prebiotic epoch.
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36
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Abstract
Thresholds are widespread in origin of life scenarios, from the emergence of chirality, to the appearance of vesicles, of autocatalysis, all the way up to Darwinian evolution. Here, we analyze the “error threshold,” which poses a condition for sustaining polymer replication, and generalize the threshold approach to other properties of prebiotic systems. Thresholds provide theoretical predictions, prescribe experimental tests, and integrate interdisciplinary knowledge. The coupling between systems and their environment determines how thresholds can be crossed, leading to different categories of prebiotic transitions. Articulating multiple thresholds reveals evolutionary properties in prebiotic scenarios. Overall, thresholds indicate how to assess, revise, and compare origin of life scenarios.
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Affiliation(s)
- Cyrille Jeancolas
- Laboratoire de Biochimie, UMR CNRS-ESPCI 8231 Chimie Biologie Innovation, PSL University, ESPCI Paris, 10 rue Vauquelin, 75005 Paris, France.,Laboratoire d'Anthropologie Sociale, Collège de France, 52 rue du Cardinal Lemoine, 75005 Paris, France
| | - Christophe Malaterre
- Département de Philosophie and Centre de Recherche Interuniversitaire sur la Science et la Technologie (CIRST), Université du Québec à Montréal (UQAM), 455 boulevard René-Lévesque Est, Montréal, QC H3C 3P8, Canada
| | - Philippe Nghe
- Laboratoire de Biochimie, UMR CNRS-ESPCI 8231 Chimie Biologie Innovation, PSL University, ESPCI Paris, 10 rue Vauquelin, 75005 Paris, France
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37
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Lopez A, Fayolle D, Fiore M, Strazewski P. Chemical Analysis of Lipid Boundaries after Consecutive Growth and Division of Supported Giant Vesicles. iScience 2020; 23:101677. [PMID: 33163935 PMCID: PMC7609504 DOI: 10.1016/j.isci.2020.101677] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/21/2020] [Accepted: 10/09/2020] [Indexed: 11/17/2022] Open
Abstract
The reproduction of the shape of giant vesicles usually results in the increase of their "population" size. This may be achieved on giant vesicles by appropriately supplying "mother" vesicles with membranogenic amphiphiles. The next "generation" of "daughter" vesicles obtained from this "feeding" is inherently difficult to distinguish from the original mothers. Here we report on a method for the consecutive feeding with different fatty acids that each provoke membrane growth and detachment of daughter vesicles from glass microsphere-supported phospholipidic mother vesicles. We discovered that a saturated fatty acid was carried over to the next generation of mothers better than two unsaturated congeners. This has an important bearing on the growth and replication of primitive compartments at the early stages of life. Microsphere-supported vesicles are also a precise analytical tool.
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Affiliation(s)
- Augustin Lopez
- Université de Lyon, Université Claude Bernard Lyon 1, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Bâtiment Edgar Lederer, 1 Rue Victor Grignard, 69622 Villeurbanne Cedex, France
| | - Dimitri Fayolle
- Université de Lyon, Université Claude Bernard Lyon 1, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Bâtiment Edgar Lederer, 1 Rue Victor Grignard, 69622 Villeurbanne Cedex, France
| | - Michele Fiore
- Université de Lyon, Université Claude Bernard Lyon 1, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Bâtiment Edgar Lederer, 1 Rue Victor Grignard, 69622 Villeurbanne Cedex, France
| | - Peter Strazewski
- Université de Lyon, Université Claude Bernard Lyon 1, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Bâtiment Edgar Lederer, 1 Rue Victor Grignard, 69622 Villeurbanne Cedex, France
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38
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Sarkar S, Das S, Dagar S, Joshi MP, Mungi CV, Sawant AA, Patki GM, Rajamani S. Prebiological Membranes and Their Role in the Emergence of Early Cellular Life. J Membr Biol 2020; 253:589-608. [PMID: 33200235 DOI: 10.1007/s00232-020-00155-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/08/2020] [Indexed: 01/30/2023]
Abstract
Membrane compartmentalization is a fundamental feature of contemporary cellular life. Given this, it is rational to assume that at some stage in the early origins of life, membrane compartments would have potentially emerged to form a dynamic semipermeable barrier in primitive cells (protocells), protecting them from their surrounding environment. It is thought that such prebiological membranes would likely have played a crucial role in the emergence and evolution of life on the early Earth. Extant biological membranes are highly organized and complex, which is a consequence of a protracted evolutionary history. On the other hand, prebiotic membrane assemblies, which are thought to have preceded sophisticated contemporary membranes, are hypothesized to have been relatively simple and composed of single chain amphiphiles. Recent studies indicate that the evolution of prebiotic membranes potentially resulted from interactions between the membrane and its physicochemical environment. These studies have also speculated on the origin, composition, function and influence of environmental conditions on protocellular membranes as the niche parameters would have directly influenced their composition and biophysical properties. Nonetheless, the evolutionary pathways involved in the transition from prebiological membranes to contemporary membranes are largely unknown. This review critically evaluates existing research on prebiotic membranes in terms of their probable origin, composition, energetics, function and evolution. Notably, we outline new approaches that can further our understanding about how prebiotic membranes might have evolved in response to relevant physicochemical parameters that would have acted as pertinent selection pressures on the early Earth.
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Affiliation(s)
- Susovan Sarkar
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Souradeep Das
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Shikha Dagar
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Manesh Prakash Joshi
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Chaitanya V Mungi
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Anupam A Sawant
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Gauri M Patki
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Sudha Rajamani
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India.
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39
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Kunnev D. Origin of Life: The Point of No Return. Life (Basel) 2020; 10:life10110269. [PMID: 33153087 PMCID: PMC7693465 DOI: 10.3390/life10110269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/01/2020] [Accepted: 11/01/2020] [Indexed: 12/13/2022] Open
Abstract
Origin of life research is one of the greatest scientific frontiers of mankind. Many hypotheses have been proposed to explain how life began. Although different hypotheses emphasize different initial phenomena, all of them agree around one important concept: at some point, along with the chain of events toward life, Darwinian evolution emerged. There is no consensus, however, how this occurred. Frequently, the mechanism leading to Darwinian evolution is not addressed and it is assumed that this problem could be solved later, with experimental proof of the hypothesis. Here, the author first defines the minimum components required for Darwinian evolution and then from this standpoint, analyzes some of the hypotheses for the origin of life. Distinctive features of Darwinian evolution and life rooted in the interaction between information and its corresponding structure/function are then reviewed. Due to the obligatory dependency of the information and structure subject to Darwinian evolution, these components must be locked in their origin. One of the most distinctive characteristics of Darwinian evolution in comparison with all other processes is the establishment of a fundamentally new level of matter capable of evolving and adapting. Therefore, the initiation of Darwinian evolution is the "point of no return" after which life begins. In summary: a definition and a mechanism for Darwinian evolution are provided together with a critical analysis of some of the hypotheses for the origin of life.
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Affiliation(s)
- Dimiter Kunnev
- Department of Oral Biology, University at Buffalo, Buffalo, NY 14263, USA
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40
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Hansen JS, Tran TH, Cavalera M, Paul S, Chaudhuri A, Lindkvist-Petersson K, Ho JCS, Svanborg C. Peptide-Oleate Complexes Create Novel Membrane-Bound Compartments. Mol Biol Evol 2020; 37:3083-3093. [PMID: 32521018 DOI: 10.1093/molbev/msaa138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A challenging question in evolutionary theory is the origin of cell division and plausible molecular mechanisms involved. Here, we made the surprising observation that complexes formed by short alpha-helical peptides and oleic acid can create multiple membrane-enclosed spaces from a single lipid vesicle. The findings suggest that such complexes may contain the molecular information necessary to initiate and sustain this process. Based on these observations, we propose a new molecular model to understand protocell division.
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Affiliation(s)
- Jesper S Hansen
- Department of Microbiology, Immunology and Glycobiology, Institute of Laboratory Medicine, Lund University, Lund, Sweden.,Experimental Medical Science, Medical Structural Biology, Lund University, Lund, Sweden
| | - Tuan Hiep Tran
- Department of Microbiology, Immunology and Glycobiology, Institute of Laboratory Medicine, Lund University, Lund, Sweden
| | - Michele Cavalera
- Department of Microbiology, Immunology and Glycobiology, Institute of Laboratory Medicine, Lund University, Lund, Sweden
| | - Sanchari Paul
- Department of Microbiology, Immunology and Glycobiology, Institute of Laboratory Medicine, Lund University, Lund, Sweden
| | - Arunima Chaudhuri
- Department of Microbiology, Immunology and Glycobiology, Institute of Laboratory Medicine, Lund University, Lund, Sweden
| | | | - James C S Ho
- Department of Microbiology, Immunology and Glycobiology, Institute of Laboratory Medicine, Lund University, Lund, Sweden.,Centre for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Catharina Svanborg
- Department of Microbiology, Immunology and Glycobiology, Institute of Laboratory Medicine, Lund University, Lund, Sweden
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41
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Bell T, Feng K, Calvin G, Van Winkle DH, Lenhert S. Organic Composomes as Supramolecular Aptamers. ACS OMEGA 2020; 5:27393-27400. [PMID: 33134702 PMCID: PMC7594120 DOI: 10.1021/acsomega.0c03799] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/29/2020] [Indexed: 06/11/2023]
Abstract
Information contained in the sequences of biological polymers such as DNA and protein is crucial to determining their function. Lipids are not generally thought of as information-containing molecules. However, from a supramolecular perspective, the number of possible combinations of lipids in a mixture is comparable to the complexity of DNA or proteins. Here, we test the idea that an organic composome can exhibit molecular recognition. We use water/octanol as a model two-phase system and investigate the effect of organic solutes in different combinations in the organic phase on selective partitioning of two water-soluble dyes (Brilliant Blue FCF and Allura Red AC) from the aqueous phase into the organic phase. We found that variation in the concentration of the surfactant cetyltrimethylamonium bromide (CTAB) in the octanol phase alone was sufficient to cause a switch in selectivity, with low CTAB concentrations being selective for the red dye and high CTAB concentrations being selective for the blue dye. Other organic components were added to the organic phase to introduce molecular diversity into the composome and directed evolution was used to optimize the relative concentrations of the solutes. An improvement of selective partitioning in the heterogeneous system over the pure CTAB solution was observed. The results indicate that supramolecular composomes are sufficient for molecular recognition processes in a way analogous to nucleic acid aptamers.
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Affiliation(s)
- Tracey
N. Bell
- Department
of Biological Science and Integrative NanoScience Institute, Florida State University, Biology Unit 1, 89 Chieftan Way, Tallahassee, Florida 32306, United States
| | - Keke Feng
- Department
of Physics, Florida State University, 77 Chieftan Way, Tallahassee, Florida 32306, United States
| | - Gabriel Calvin
- Department
of Biological Science and Integrative NanoScience Institute, Florida State University, Biology Unit 1, 89 Chieftan Way, Tallahassee, Florida 32306, United States
| | - David H. Van Winkle
- Department
of Physics, Florida State University, 77 Chieftan Way, Tallahassee, Florida 32306, United States
| | - Steven Lenhert
- Department
of Biological Science and Integrative NanoScience Institute, Florida State University, Biology Unit 1, 89 Chieftan Way, Tallahassee, Florida 32306, United States
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42
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Abstract
Autocatalysis is essential for the origin of life and chemical evolution. However, the lack of a unified framework so far prevents a systematic study of autocatalysis. Here, we derive, from basic principles, general stoichiometric conditions for catalysis and autocatalysis in chemical reaction networks. This allows for a classification of minimal autocatalytic motifs called cores. While all known autocatalytic systems indeed contain minimal motifs, the classification also reveals hitherto unidentified motifs. We further examine conditions for kinetic viability of such networks, which depends on the autocatalytic motifs they contain and is notably increased by internal catalytic cycles. Finally, we show how this framework extends the range of conceivable autocatalytic systems, by applying our stoichiometric and kinetic analysis to autocatalysis emerging from coupled compartments. The unified approach to autocatalysis presented in this work lays a foundation toward the building of a systems-level theory of chemical evolution.
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43
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Abstract
Either stereo reactants or stereo catalysis from achiral or chiral molecules are a prerequisite to obtain pure enantiomeric lipid derivatives. We reviewed a few plausibly organic syntheses of phospholipids under prebiotic conditions with special attention paid to the starting materials as pro-chiral dihydroxyacetone and dihydroxyacetone phosphate (DHAP), which are the key molecules to break symmetry in phospholipids. The advantages of homochiral membranes compared to those of heterochiral membranes were analysed in terms of specific recognition, optimal functions of enzymes, membrane fluidity and topological packing. All biological membranes contain enantiomerically pure lipids in modern bacteria, eukarya and archaea. The contemporary archaea, comprising of methanogens, halobacteria and thermoacidophiles, are living under extreme conditions reminiscent of primitive environment and may indicate the origin of one ancient evolution path of lipid biosynthesis. The analysis of the known lipid metabolism reveals that all modern cells including archaea synthetize enantiomerically pure lipid precursors from prochiral DHAP. Sn-glycerol-1-phosphate dehydrogenase (G1PDH), usually found in archaea, catalyses the formation of sn-glycerol-1-phosphate (G1P), while sn-glycerol-3-phosphate dehydrogenase (G3PDH) catalyses the formation of sn-glycerol-3-phosphate (G3P) in bacteria and eukarya. The selective enzymatic activity seems to be the main strategy that evolution retained to obtain enantiomerically pure lipids. The occurrence of two genes encoding for G1PDH and G3PDH served to build up an evolutionary tree being the basis of our hypothesis article focusing on the evolution of these two genes. Gene encoding for G3PDH in eukarya may originate from G3PDH gene found in rare archaea indicating that archaea appeared earlier in the evolutionary tree than eukarya. Archaea and bacteria evolved probably separately, due to their distinct respective genes coding for G1PDH and G3PDH. We propose that prochiral DHAP is an essential molecule since it provides a convergent link between G1DPH and G3PDH. The synthesis of enantiopure phospholipids from DHAP appeared probably firstly in the presence of chemical catalysts, before being catalysed by enzymes which were the products of later Darwinian selection. The enzymes were probably selected for their efficient catalytic activities during evolution from large libraries of vesicles containing amino acids, carbohydrates, nucleic acids, lipids, and meteorite components that induced symmetry imbalance.
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44
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Hanopolskyi AI, Smaliak VA, Novichkov AI, Semenov SN. Autocatalysis: Kinetics, Mechanisms and Design. CHEMSYSTEMSCHEM 2020. [DOI: 10.1002/syst.202000026] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Anton I. Hanopolskyi
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
| | - Viktoryia A. Smaliak
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
| | - Alexander I. Novichkov
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
| | - Sergey N. Semenov
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
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45
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Post EAJ, Fletcher SP. Dissipative self-assembly, competition and inhibition in a self-reproducing protocell model. Chem Sci 2020; 11:9434-9442. [PMID: 34094210 PMCID: PMC8162124 DOI: 10.1039/d0sc02768e] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/07/2020] [Indexed: 12/14/2022] Open
Abstract
The bottom-up synthesis of artificial, life-like systems promises to enable the study of emergent properties distinctive to life. Here, we report protocell systems generated from phase-separated building blocks. Vesicle protocells self-reproduce through a phase-transfer mechanism, catalysing their own formation. Dissipative self-assembly by the protocells is achieved when a hydrolysis step to destroy the surfactant is introduced. Competition between micelle and vesicle based replicators for a common feedstock shows that environmental conditions can control what species predominates: under basic conditions vesicles predominate, but in a neutral medium micelles are selected for via a mechanism which inhibits vesicle formation. Finally, the protocells enable orthogonal reactivity by catalysing in situ formation of an amphiphilic organocatalyst, which after incorporation into the vesicle bilayer enantioselectively forms a secondary product.
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Affiliation(s)
- Elias A J Post
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Stephen P Fletcher
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
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46
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Maity S, Ottelé J, Santiago GM, Frederix PWJM, Kroon P, Markovitch O, Stuart MCA, Marrink SJ, Otto S, Roos WH. Caught in the Act: Mechanistic Insight into Supramolecular Polymerization-Driven Self-Replication from Real-Time Visualization. J Am Chem Soc 2020; 142:13709-13717. [PMID: 32786814 PMCID: PMC7426903 DOI: 10.1021/jacs.0c02635] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Self-assembly features
prominently in fields ranging from materials
science to biophysical chemistry. Assembly pathways, often passing
through transient intermediates, can control the outcome of assembly
processes. Yet, the mechanisms of self-assembly remain largely obscure
due to a lack of experimental tools for probing these pathways at
the molecular level. Here, the self-assembly of self-replicators into
fibers is visualized in real-time by high-speed atomic force microscopy
(HS-AFM). Fiber growth requires the conversion of precursor molecules
into six-membered macrocycles, which constitute the fibers. HS-AFM
experiments, supported by molecular dynamics simulations, revealed
that aggregates of precursor molecules accumulate at the sides of
the fibers, which then diffuse to the fiber ends where growth takes
place. This mechanism of precursor reservoir formation, followed by
one-dimensional diffusion, which guides the precursor molecules to
the sites of growth, reduces the entropic penalty associated with
colocalizing precursors and growth sites and constitutes a new mechanism
for supramolecular polymerization.
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Affiliation(s)
- Sourav Maity
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
| | - Jim Ottelé
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
| | - Guillermo Monreal Santiago
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
| | - Pim W J M Frederix
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands
| | - Peter Kroon
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands
| | - Omer Markovitch
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands.,Origins Center, Nijenborgh 7, Groningen 9747 AG, The Netherlands
| | - Marc C A Stuart
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
| | - Wouter H Roos
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
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47
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Liu Y, Hjerpe D, Lundh T. Side Reactions Do Not Completely Disrupt Linear Self-Replicating Chemical Reaction Systems. ARTIFICIAL LIFE 2020; 26:327-337. [PMID: 32697159 DOI: 10.1162/artl_a_00327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A crucial question within the fields of origins of life and metabolic networks is whether or not a self-replicating chemical reaction system is able to persist in the presence of side reactions. Due to the strong nonlinear effects involved in such systems, they are often difficult to study analytically. There are however certain conditions that allow for a wide range of these reaction systems to be well described by a set of linear ordinary differential equations. In this article, we elucidate these conditions and present a method to construct and solve such equations. For those linear self-replicating systems, we quantitatively find that the growth rate of the system is simply proportional to the sum of all the rate constants of the reactions that constitute the system (but is nontrivially determined by the relative values). We also give quantitative descriptions of how strongly side reactions need to be coupled with the system in order to completely disrupt the system.
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Affiliation(s)
| | | | - Torbjörn Lundh
- Institut Mittag-Leffler
- Chalmers University of Technology
- University of Gothenburg, Mathematical Sciences
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48
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Muchowska KB, Varma SJ, Moran J. Nonenzymatic Metabolic Reactions and Life's Origins. Chem Rev 2020; 120:7708-7744. [PMID: 32687326 DOI: 10.1021/acs.chemrev.0c00191] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Prebiotic chemistry aims to explain how the biochemistry of life as we know it came to be. Most efforts in this area have focused on provisioning compounds of importance to life by multistep synthetic routes that do not resemble biochemistry. However, gaining insight into why core metabolism uses the molecules, reactions, pathways, and overall organization that it does requires us to consider molecules not only as synthetic end goals. Equally important are the dynamic processes that build them up and break them down. This perspective has led many researchers to the hypothesis that the first stage of the origin of life began with the onset of a primitive nonenzymatic version of metabolism, initially catalyzed by naturally occurring minerals and metal ions. This view of life's origins has come to be known as "metabolism first". Continuity with modern metabolism would require a primitive version of metabolism to build and break down ketoacids, sugars, amino acids, and ribonucleotides in much the same way as the pathways that do it today. This review discusses metabolic pathways of relevance to the origin of life in a manner accessible to chemists, and summarizes experiments suggesting several pathways might have their roots in prebiotic chemistry. Finally, key remaining milestones for the protometabolic hypothesis are highlighted.
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Affiliation(s)
| | - Sreejith J Varma
- University of Strasbourg, CNRS, ISIS UMR 7006, 67000 Strasbourg, France
| | - Joseph Moran
- University of Strasbourg, CNRS, ISIS UMR 7006, 67000 Strasbourg, France
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49
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Danchin A, Sekowska A, You C. One-carbon metabolism, folate, zinc and translation. Microb Biotechnol 2020; 13:899-925. [PMID: 32153134 PMCID: PMC7264889 DOI: 10.1111/1751-7915.13550] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 02/17/2020] [Indexed: 12/16/2022] Open
Abstract
The translation process, central to life, is tightly connected to the one-carbon (1-C) metabolism via a plethora of macromolecule modifications and specific effectors. Using manual genome annotations and putting together a variety of experimental studies, we explore here the possible reasons of this critical interaction, likely to have originated during the earliest steps of the birth of the first cells. Methionine, S-adenosylmethionine and tetrahydrofolate dominate this interaction. Yet, 1-C metabolism is unlikely to be a simple frozen accident of primaeval conditions. Reactive 1-C species (ROCS) are buffered by the translation machinery in a way tightly associated with the metabolism of iron-sulfur clusters, zinc and potassium availability, possibly coupling carbon metabolism to nitrogen metabolism. In this process, the highly modified position 34 of tRNA molecules plays a critical role. Overall, this metabolic integration may serve both as a protection against the deleterious formation of excess carbon under various growth transitions or environmental unbalanced conditions and as a regulator of zinc homeostasis, while regulating input of prosthetic groups into nascent proteins. This knowledge should be taken into account in metabolic engineering.
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Affiliation(s)
- Antoine Danchin
- AMAbiotics SASInstitut Cochin24 rue du Faubourg Saint‐Jacques75014ParisFrance
- School of Biomedical SciencesLi Ka Shing Faculty of MedicineThe University of Hong KongS.A.R. Hong KongChina
| | - Agnieszka Sekowska
- AMAbiotics SASInstitut Cochin24 rue du Faubourg Saint‐Jacques75014ParisFrance
| | - Conghui You
- Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Sciences and OceanologyShenzhen University1066 Xueyuan Rd518055ShenzhenChina
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50
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Seligmann H. First arrived, first served: competition between codons for codon-amino acid stereochemical interactions determined early genetic code assignments. Naturwissenschaften 2020; 107:20. [PMID: 32367155 DOI: 10.1007/s00114-020-01676-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/10/2020] [Accepted: 04/05/2020] [Indexed: 12/12/2022]
Abstract
Stereochemical nucleotide-amino acid interactions, in the form of noncovalent nucleotide-amino acid interactions, potentially produced the genetic code's codon-amino acid assignments. Empirical estimates of single nucleotide-amino acid affinities on surfaces and in solution are used to test whether trinucleotide-amino acid affinities determined genetic code assignments pending the principle "first arrived, first served": presumed early amino acids have greater codon-amino acid affinities than ulterior ones. Here, these single nucleotide affinities are used to approximate all 64 × 20 trinucleotide-amino acid affinities. Analyses show that (1) on surfaces, genetic code codon-amino acid assignments tend to match high affinities for the amino acids that integrated earliest the genetic code (according to Wong's metabolic coevolution hypothesis between nucleotides and amino acids) and (2) in solution, the same principle holds for the anticodon-amino acid assignments. Affinity analyses match best genetic code assignments when assuming that trinucleotides competed for amino acids, rather than amino acids for trinucleotides. Codon-amino acid affinities stick better to genetic code assignments than anticodon-amino acid affinities. Presumably, two independent coding systems, on surfaces and in solution, converged, and formed the current translation system. Proto-translation on surfaces by direct codon-amino acid interactions without tRNA-like adaptors coadapted with a system emerging in solution by proto-tRNA anticodon-amino acid interactions. These systems assigned identical or similar cognates to codons on surfaces and to anticodons in solution. Results indicate that a prebiotic metabolism predated genetic code self-organization.
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Affiliation(s)
- Hervé Seligmann
- The National Natural History Collections, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel. .,Faculty of Medicine, Université Grenoble Alpes, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecoms4Health, F-38700, La Tronche, France.
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