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Singh A, Parvin P, Saha B, Das D. Non-equilibrium self-assembly for living matter-like properties. Nat Rev Chem 2024:10.1038/s41570-024-00640-z. [PMID: 39179623 DOI: 10.1038/s41570-024-00640-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2024] [Indexed: 08/26/2024]
Abstract
The soft and wet machines of life emerged as the spatially enclosed ensemble of biomolecules with replicating capabilities integrated with metabolic reaction cycles that operate at far-from-equilibrium. A thorough step-by-step synthetic integration of these elements, namely metabolic and replicative properties all confined and operating far-from-equilibrium, can set the stage from which we can ask questions related to the construction of chemical-based evolving systems with living matter-like properties - a monumental endeavour of systems chemistry. The overarching concept of this Review maps the discoveries on this possible integration of reaction networks, self-reproduction and compartmentalization under non-equilibrium conditions. We deconvolute the events of reaction networks and transient compartmentalization and extend the discussion towards self-reproducing systems that can be sustained under non-equilibrium conditions. Although enormous challenges lie ahead in terms of molecular diversity, information transfer, adaptation and selection that are required for open-ended evolution, emerging strategies to generate minimal metabolic cycles can extend our growing understanding of the chemical emergence of the biosphere of Earth.
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Affiliation(s)
- Abhishek Singh
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
| | - Payel Parvin
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
| | - Bapan Saha
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
| | - Dibyendu Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India.
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India.
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2
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Agrawal A, Radakovic A, Vonteddu A, Rizvi S, Huynh VN, Douglas JF, Tirrell MV, Karim A, Szostak JW. Did the exposure of coacervate droplets to rain make them the first stable protocells? SCIENCE ADVANCES 2024; 10:eadn9657. [PMID: 39167649 PMCID: PMC11338219 DOI: 10.1126/sciadv.adn9657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 07/17/2024] [Indexed: 08/23/2024]
Abstract
Membraneless coacervate microdroplets have long been proposed as model protocells as they can grow, divide, and concentrate RNA by natural partitioning. However, the rapid exchange of RNA between these compartments, along with their rapid fusion, both within minutes, means that individual droplets would be unable to maintain their separate genetic identities. Hence, Darwinian evolution would not be possible, and the population would be vulnerable to collapse due to the rapid spread of parasitic RNAs. In this study, we show that distilled water, mimicking rain/freshwater, leads to the formation of electrostatic crosslinks on the interface of coacervate droplets that not only suppress droplet fusion indefinitely but also allow the spatiotemporal compartmentalization of RNA on a timescale of days depending on the length and structure of RNA. We suggest that these nonfusing membraneless droplets could potentially act as protocells with the capacity to evolve compartmentalized ribozymes in prebiotic environments.
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Affiliation(s)
- Aman Agrawal
- William A. Brookshire Department of Chemical & Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Aleksandar Radakovic
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Anusha Vonteddu
- Materials Science and Engineering Program, University of Houston, Houston, TX 77204, USA
| | - Syed Rizvi
- William A. Brookshire Department of Chemical & Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
| | - Vivian N. Huynh
- William A. Brookshire Department of Chemical & Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
| | - Jack F. Douglas
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Matthew V. Tirrell
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
- Argonne National Laboratory, Lemont, IL, 60439 USA
| | - Alamgir Karim
- William A. Brookshire Department of Chemical & Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
- Materials Science and Engineering Program, University of Houston, Houston, TX 77204, USA
| | - Jack W. Szostak
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
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3
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Pascal R. Evolutionary Abilities of Minimalistic Physicochemical Models of Life Processes. Chemistry 2024; 30:e202401780. [PMID: 39074967 DOI: 10.1002/chem.202401780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Indexed: 07/31/2024]
Abstract
The ability of living organisms to persist, grow, evolve and invade environments seemingly challenges physical laws. Emerging Autonomous Systems representing autocatalytic cycles constituted of energized components in a state of Dynamic Kinetic Stability feature some of these properties. These simple theoretical models can grow, can be transferred but need an initiation to emerge and can collapse. Moreover, they can undergo kinetic selection in a way consistent with Darwinian behaviour, though they lack the ability to undergo change. The mere existence of these systems and their open-ended growth potential are proposed to constitute a transmissible factor of a non-coded kind. The onset and selection of epigenetic factors may therefore have preceded that of genetic polymers. Here is addressed the question of how these systems may arise from the diversity exhibited by abiotic organic matter, sometimes associated with intractable mixtures, which may actually be useful in providing initiators. The Darwinian description of evolution may therefore be merged without critical discontinuity within an origin scenario. Accordingly, such a theory would rests solely on physicochemical laws beginning with the potential of emerging autonomous systems to compete and invade the space dimension, and to further develop along other available dimensions including variability and, possibly, cognition.
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Affiliation(s)
- Robert Pascal
- Institut Origines, PIIM, service 232, Aix-Marseille Université - CNRS, Ave Escadrille Normandie Niemen, 13013, Marseille, France
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4
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Saha R, Choi JA, Chen IA. Protocell Effects on RNA Folding, Function, and Evolution. Acc Chem Res 2024; 57:2058-2066. [PMID: 39005057 PMCID: PMC11308369 DOI: 10.1021/acs.accounts.4c00174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/03/2024] [Accepted: 07/03/2024] [Indexed: 07/16/2024]
Abstract
ConspectusCreating a living system from nonliving matter is a great challenge in chemistry and biophysics. The early history of life can provide inspiration from the idea of the prebiotic "RNA World" established by ribozymes, in which all genetic and catalytic activities were executed by RNA. Such a system could be much simpler than the interdependent central dogma characterizing life today. At the same time, cooperative systems require a mechanism such as cellular compartmentalization in order to survive and evolve. Minimal cells might therefore consist of simple vesicles enclosing a prebiotic RNA metabolism.The internal volume of a vesicle is a distinctive environment due to its closed boundary, which alters diffusion and available volume for macromolecules and changes effective molecular concentrations, among other considerations. These physical effects are mechanistically distinct from chemical interactions, such as electrostatic repulsion, that might also occur between the membrane boundary and encapsulated contents. Both indirect and direct interactions between the membrane and RNA can give rise to nonintuitive, "emergent" behaviors in the model protocell system. We have been examining how encapsulation inside membrane vesicles would affect the folding and activity of entrapped RNA.Using biophysical techniques such as FRET, we characterized ribozyme folding and activity inside vesicles. Encapsulation inside model protocells generally promoted RNA folding, consistent with an excluded volume effect, independently of chemical interactions. This energetic stabilization translated into increased ribozyme activity in two different systems that were studied (hairpin ribozyme and self-aminoacylating RNAs). A particularly intriguing finding was that encapsulation could rescue the activity of mutant ribozymes, suggesting that encapsulation could affect not only folding and activity but also evolution. To study this further, we developed a high-throughput sequencing assay to measure the aminoacylation kinetics of many thousands of ribozyme variants in parallel. The results revealed an unexpected tendency for encapsulation to improve the better ribozyme variants more than worse variants. During evolution, this effect would create a tilted playing field, so to speak, that would give additional fitness gains to already-high-activity variants. According to Fisher's Fundamental Theorem of Natural Selection, the increased variance in fitness should manifest as faster evolutionary adaptation. This prediction was borne out experimentally during in vitro evolution, where we observed that the initially diverse ribozyme population converged more quickly to the most active sequences when they were encapsulated inside vesicles.The studies in this Account have expanded our understanding of emergent protocell behavior, by showing how simply entrapping an RNA inside a vesicle, which could occur spontaneously during vesicle formation, might profoundly affect the evolutionary landscape of the RNA. Because of the exponential dynamics of replication and selection, even small changes to activity and function could lead to major evolutionary consequences. By closely studying the details of minimal yet surprisingly complex protocells, we might one day trace a pathway from encapsulated RNA to a living system.
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Affiliation(s)
- Ranajay Saha
- Department of Chemical and Biomolecular
Engineering, Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095-1592, United States
| | - Jongseok A. Choi
- Department of Chemical and Biomolecular
Engineering, Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095-1592, United States
| | - Irene A. Chen
- Department of Chemical and Biomolecular
Engineering, Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095-1592, United States
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5
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Ding Y, Cardoso SSS, Cartwright JHE. Dynamics of the osmotic lysis of mineral protocells and its avoidance at the origins of life. GEOBIOLOGY 2024; 22:e12611. [PMID: 39020475 DOI: 10.1111/gbi.12611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 04/22/2024] [Accepted: 06/24/2024] [Indexed: 07/19/2024]
Abstract
The osmotic rupture of a cell, its osmotic lysis or cytolysis, is a phenomenon that active biological cell volume regulation mechanisms have evolved in the cell membrane to avoid. How then, at the origin of life, did the first protocells survive prior to such active processes? The pores of alkaline hydrothermal vents in the oceans form natural nanoreactors in which osmosis across a mineral membrane plays a fundamental role. Here, we discuss the dynamics of lysis and its avoidance in an abiotic system without any active mechanisms, reliant upon self-organized behaviour, similar to the first self-organized mineral membranes within which complex chemistry may have begun to evolve into metabolism. We show that such mineral nanoreactors could function as protocells without exploding because their self-organized dynamics have a large regime in parameter space where osmotic lysis does not occur and homeostasis is possible. The beginnings of Darwinian evolution in proto-biochemistry must have involved the survival of protocells that remained within such a safe regime.
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Affiliation(s)
- Yang Ding
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Silvana S S Cardoso
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Julyan H E Cartwright
- Instituto Andaluz de Ciencias de la Tierra, CSIC-Universidad de Granada, Granada, Spain
- Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada, Granada, Spain
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6
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Saha R, Poduval P, Baratam K, Nagesh J, Srivastava A. Membrane Catalyzed Formation of Nucleotide Clusters and Their Role in the Origins of Life: Insights from Molecular Simulations and Lattice Modeling. J Phys Chem B 2024; 128:3121-3132. [PMID: 38518175 DOI: 10.1021/acs.jpcb.3c08061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]
Abstract
One of the mysteries in studying the molecular "Origin of Life" is the emergence of RNA and RNA-based life forms, where nonenzymatic polymerization of nucleotides is a crucial hypothesis in formation of large RNA chains. The nonenzymatic polymerization can be mediated by various environmental settings, such as cycles of hydration and dehydration, temperature variations, and proximity to a variety of organizing matrices, such as clay, salt, fatty acids, lipid membrane, and mineral surface. In this work, we explore the influence of different phases of the lipid membrane toward nucleotide organization and polymerization in a simulated prebiotic setting. Our molecular simulations quantify the localization propensity of a mononucleotide, uridine monophosphate (UMP), in distinct membrane settings. We perform all-atom molecular dynamics (MD) simulations to estimate the role of the monophasic and biphasic membranes in modifying the behavior of UMPs localization and their clustering mechanism. Based on the interaction energy of mononucleotides with the membrane and their diffusion profile from our MD calculations, we developed a lattice-based model to explore the thermodynamic limits of the observations made from the MD simulations. The mathematical model substantiates our hypothesis that the lipid layers can act as unique substrates for "catalyzing" polymerization of mononucleotides due to the inherent spatiotemporal heterogeneity and phase change behavior.
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Affiliation(s)
- Rajlaxmi Saha
- Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata 741246, India
| | - Prathyush Poduval
- Department of Physics, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Krishnakanth Baratam
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Jayashree Nagesh
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
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7
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Li S, Wang D, Zhang M, Yang Y, Zhang X, Li J, Wu D. Design of oleic acid/alkyl glycoside composite vesicles as cosmetics carrier: stability, skin permeability and antioxidant activity. JOURNAL OF BIOMATERIALS SCIENCE. POLYMER EDITION 2024; 35:579-604. [PMID: 38217851 DOI: 10.1080/09205063.2024.2302632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 12/29/2023] [Indexed: 01/15/2024]
Abstract
Biocompatible fatty acids are natural biological materials which exhibit widespread biomedical applications. Nevertheless, their application in vesicle forms is hampered by strong pH sensitivity and poor stability to changes in ionic strength, temperature, and storage. In the investigation, the incorporation of alkyl glycoside (APG), a surfactant with non-ionic properties, into the oleic acid (OA) vesicles was undertaken as a means to address this issue. The newly formed OA/APG composite vesicles form in a pH range of between 5.4 and 7.4, which is close to the pH range of the physiological environment. The stability studies results showed that the OA/APG composite vesicles have excellent stability in terms of ionic strengths, temperature and storage. The formation of NAR-loaded OA/APG composite vesicles was demonstrated through FT-IR, DSC and XRD. In vitro topical delivery and skin retention studies confirmed that the composite vesicles improve skin permeation rate and have better skin permeation behavior. Antioxidant activity experiments confirmed that the antioxidant effect composite vesicles were significantly increased as compared to the naringenin (NAR). This finding has theoretical implications for the use of drug-loaded fatty acid vesicles in cosmetics industries and topical delivery systems.
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Affiliation(s)
- Siqi Li
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang, China
- Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi University, Jiamusi, China
| | - Di Wang
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang, China
| | - Meng Zhang
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang, China
| | - Ying Yang
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang, China
| | - Xiangyu Zhang
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang, China
- Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi University, Jiamusi, China
| | - Jinlian Li
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang, China
- Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi University, Jiamusi, China
| | - Dongmei Wu
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang, China
- Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi University, Jiamusi, China
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8
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Mikhailovsky GE. Life, its definition, origin, evolution, and four-dimensional hierarchical structure. Biosystems 2024; 237:105158. [PMID: 38382824 DOI: 10.1016/j.biosystems.2024.105158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 02/23/2024]
Abstract
The main unique features of biological systems are reviewed, and four necessary and sufficient attributes of life are formulated, based on the ideas of Ervin Bauer. The possibility of the occurrence of each of these attributes during the origin of life is analyzed. As a result, different scenarios for the origin of life are presented, with their pros and cons. Next, the mainstream of biological evolution is discussed, considering it as a special case of general complexification, and structuredness is defined as a quantitative measure of structural complexity. By introducing the concepts of post-dissipative structure and ratcheting process based on "frozen" patterns, their role in the generation of biological structures underlying biological evolution is demonstrated. Furthermore, it is proposed that all living things can be divided into micro- (unicellular) and macro- (multicellular) creatures, which differ from each other even more radically than the difference between prokaryotes and unicellular eukaryotes. Then the fifth, sufficient, but not necessary attribute of life, hierarchicality, is formulated, which is fully applicable only to macrolife. It is also shown that living organisms are primarily chemodynamic rather than thermodynamic systems, and three basic laws of biochemodynamics are formulated. Finally, fifteen basic features of living beings, grouped into four basic blocks, are summarized.
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9
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Girard C. The tri-flow adaptiveness of codes in major evolutionary transitions. Biosystems 2024; 237:105133. [PMID: 38336225 DOI: 10.1016/j.biosystems.2024.105133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/26/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024]
Abstract
Life codes increase in both number and variety with biological complexity. Although our knowledge of codes is constantly expanding, the evolutionary progression of organic, neural, and cultural codes in response to selection pressure remains poorly understood. Greater clarification of the selective mechanisms is achieved by investigating how major evolutionary transitions reduce spatiotemporal and energetic constraints on transmitting heritable code to offspring. Evolution toward less constrained flows is integral to enduring flow architecture everywhere, in both engineered and natural flow systems. Beginning approximately 4 billion years ago, the most basic level for transmitting genetic material to offspring was initiated by protocell division. Evidence from ribosomes suggests that protocells transmitted comma-free or circular codes, preceding the evolution of standard genetic code. This rudimentary information flow within protocells is likely to have first emerged within the geo-energetic and geospatial constraints of hydrothermal vents. A broad-gauged hypothesis is that major evolutionary transitions overcame such constraints with tri-flow adaptations. The interconnected triple flows incorporated energy-converting, spatiotemporal, and code-based informational dynamics. Such tri-flow adaptations stacked sequence splicing code on top of protein-DNA recognition code in eukaryotes, prefiguring the transition to sexual reproduction. Sex overcame the spatiotemporal-energetic constraints of binary fission with further code stacking. Examples are tubulin code and transcription initiation code in vertebrates. In a later evolutionary transition, language reduced metabolic-spatiotemporal constraints on inheritance by stacking phonetic, phonological, and orthographic codes. In organisms that reproduce sexually, each major evolutionary transition is shown to be a tri-flow adaptation that adds new levels of code-based informational exchange. Evolving biological complexity is also shown to increase the nongenetic transmissibility of code.
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Affiliation(s)
- Chris Girard
- Department of Global and Sociocultural Studies, Florida International University, Miami, FL 33199, United States.
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10
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Hazra B, Prasad M, Das S, Mandal R, Sardar A, Dewangan N, Tarafdar PK. Phosphate-Based Amphiphile and Lipidated Lysine Assemble into Superior Protocellular Membranes over Carboxylate and Sulfate-Based Systems: A Potential Missing Link between Prebiotic and the Modern Era? LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:17031-17042. [PMID: 37984966 DOI: 10.1021/acs.langmuir.3c01617] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Amphiphiles are among the most extensively studied building blocks that self-assemble into cell-like compartments. Most literature suggested that the building blocks/amphiphiles of early Earth (fatty acid-based membrane) were much simpler than today's phospholipids. To establish the bridge between the prebiotic fatty acid era and the modern phospholipid era, the investigation and characterization of alternate building blocks that form protocellular membranes are necessary. Herein, we report the potential prebiotic synthesis of alkyl phosphate, alkyl carboxylate, and alkyl sulfate amphiphiles (anionic) using dry-down reactions and demonstrate a more general role of cationic amino acid-based amphiphiles to recruit the anionic amphiphiles via ion-pair, hydrogen bonding, and hydrophobic interactions. The formation and self-assembly of the catanionic (mixed) amphiphilic system to vesicular morphology were characterized by turbidimetric, dynamic light scattering, transmission electron microscopy, fluorescence lifetime imaging microscopy, and glucose encapsulation experiments. Further experiments suggest that the phosphate-based vesicles were more stable than the alkyl sulfate and alkyl carboxylate-based systems. Moreover, the alkyl phosphate system can form vesicles at prebiotically relevant acidic pH (5.0), while alkyl carboxylate mainly forms cluster-type aggregates. An extended supramolecular polymer-type network formation via H-bonding and ion-pair interactions might order the membrane interface and stabilize the phosphate-based vesicles. The results suggest that phosphate-based amphiphiles might be a superior successor to fatty acids as early compartment building blocks. The work highlights the importance of previously unexplored building blocks that participate in protocellular membrane formation to encapsulate important precursors required for the functions of early life.
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Affiliation(s)
- Bibhas Hazra
- Indian Institute of Science Education and Research Kolkata, Nadia, Mohanpur 741246, West Bengal, India
| | - Mahesh Prasad
- Indian Institute of Science Education and Research Kolkata, Nadia, Mohanpur 741246, West Bengal, India
| | - Subrata Das
- Indian Institute of Science Education and Research Kolkata, Nadia, Mohanpur 741246, West Bengal, India
| | - Raki Mandal
- Indian Institute of Science Education and Research Kolkata, Nadia, Mohanpur 741246, West Bengal, India
| | - Avijit Sardar
- Indian Institute of Science Education and Research Kolkata, Nadia, Mohanpur 741246, West Bengal, India
| | - Nikesh Dewangan
- Indian Institute of Science Education and Research Kolkata, Nadia, Mohanpur 741246, West Bengal, India
| | - Pradip K Tarafdar
- Indian Institute of Science Education and Research Kolkata, Nadia, Mohanpur 741246, West Bengal, India
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11
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Douliez JP. Double Emulsion Droplets as a Plausible Step to Fatty Acid Protocells. SMALL METHODS 2023; 7:e2300530. [PMID: 37574259 DOI: 10.1002/smtd.202300530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/07/2023] [Indexed: 08/15/2023]
Abstract
It is assumed that life originated on the Earth from vesicles made of fatty acids. These amphiphiles are the simplest chemicals, which can be present in the prebiotic soup, capable of self-assembling into compartments mimicking modern cells. Production of fatty acid vesicles is widely studied, as their growing and division. However, how prebiotic chemicals require to further yield living cells encapsulated within protocells remains unclear. Here, one suggests a scenario based on recent studies, which shows that phospholipid vesicles can form from double emulsions affording facile encapsulation of cargos. In these works, water-in-oil-in-water droplets are produced by microfluidics, having dispersed lipids in the oil. Dewetting of the oil droplet leaves the internal aqueous droplet covered by a lipid bilayer, entrapping cargos. In this review, formation of fatty acid protocells is briefly reviewed, together with the procedure for preparing double emulsions and vesicles from double emulsion and finally, it is proposed that double emulsion droplets formed in the deep ocean where undersea volcano expulsed materials, with fatty acids (under their carboxylic form) and alkanols as the oily phase, entrapping hydrosoluble prebiotic chemicals in a double emulsion droplet core. Once formed, double emulsion droplets can move up to the surface, where an increase of pH, variation of pressure and/or temperature may have allowed dewetting of the oily droplet, leaving a fatty acid vesicular protocell with encapsulated prebiotic materials.
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Affiliation(s)
- Jean-Paul Douliez
- Biologie du Fruit et Pathologie, UMR 1332, Institut National de Recherche Agronomique (INRAE), Université De Bordeaux, Villenave d'Ornon, F-33140, France
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12
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Nogal N, Sanz-Sánchez M, Vela-Gallego S, Ruiz-Mirazo K, de la Escosura A. The protometabolic nature of prebiotic chemistry. Chem Soc Rev 2023; 52:7359-7388. [PMID: 37855729 PMCID: PMC10614573 DOI: 10.1039/d3cs00594a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Indexed: 10/20/2023]
Abstract
The field of prebiotic chemistry has been dedicated over decades to finding abiotic routes towards the molecular components of life. There is nowadays a handful of prebiotically plausible scenarios that enable the laboratory synthesis of most amino acids, fatty acids, simple sugars, nucleotides and core metabolites of extant living organisms. The major bottleneck then seems to be the self-organization of those building blocks into systems that can self-sustain. The purpose of this tutorial review is having a close look, guided by experimental research, into the main synthetic pathways of prebiotic chemistry, suggesting how they could be wired through common intermediates and catalytic cycles, as well as how recursively changing conditions could help them engage in self-organized and dissipative networks/assemblies (i.e., systems that consume chemical or physical energy from their environment to maintain their internal organization in a dynamic steady state out of equilibrium). In the article we also pay attention to the implications of this view for the emergence of homochirality. The revealed connectivity between those prebiotic routes should constitute the basis for a robust research program towards the bottom-up implementation of protometabolic systems, taken as a central part of the origins-of-life problem. In addition, this approach should foster further exploration of control mechanisms to tame the combinatorial explosion that typically occurs in mixtures of various reactive precursors, thus regulating the functional integration of their respective chemistries into self-sustaining protocellular assemblies.
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Affiliation(s)
- Noemí Nogal
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Marcos Sanz-Sánchez
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Sonia Vela-Gallego
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Kepa Ruiz-Mirazo
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain
- Department of Philosophy, University of the Basque Country, Leioa, Spain
| | - Andrés de la Escosura
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
- Institute for Advanced Research in Chemistry (IAdChem), Campus de Cantoblanco, 28049, Madrid, Spain
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13
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Lauber N, Tichacek O, Narayanankutty K, De Martino D, Ruiz-Mirazo K. Collective catalysis under spatial constraints: Phase separation and size-scaling effects on mass action kinetics. Phys Rev E 2023; 108:044410. [PMID: 37978605 DOI: 10.1103/physreve.108.044410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 09/07/2023] [Indexed: 11/19/2023]
Abstract
Chemical reactions are usually studied under the assumption that both substrates and catalysts are well-mixed (WM) throughout the system. Although this is often applicable to test-tube experimental conditions, it is not realistic in cellular environments, where biomolecules can undergo liquid-liquid phase separation (LLPS) and form condensates, leading to important functional outcomes, including the modulation of catalytic action. Similar processes may also play a role in protocellular systems, like primitive coacervates, or in membrane-assisted prebiotic pathways. Here we explore whether the demixing of catalysts could lead to the formation of microenvironments that influence the kinetics of a linear (multistep) reaction pathway, as compared to a WM system. We implemented a general lattice model to simulate LLPS of a collection of different catalysts and extended it to include diffusion and a sequence of reactions of small substrates. We carried out a quantitative analysis of how the phase separation of the catalysts affects reaction times depending on the affinity between substrates and catalysts, the length of the reaction pathway, the system size, and the degree of homogeneity of the condensate. A key aspect underlying the differences reported between the two scenarios is that the scale invariance observed in the WM system is broken by condensation processes. The main theoretical implications of our results for mean-field chemistry are drawn, extending the mass action kinetics scheme to include substrate initial "hitting times" to reach the catalysts condensate. We finally test this approach by considering open nonlinear conditions, where we successfully predict, through microscopic simulations, that phase separation inhibits chemical oscillatory behavior, providing a possible explanation for the marginal role that this complex dynamic behavior plays in real metabolisms.
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Affiliation(s)
- Nino Lauber
- Biofisika Institute (CSIC, UPV/EHU), 48940 Leioa, Spain
- Donostia International Physics Center, 20018 Donostia-San Sebastian, Spain
- Department of Philosophy, University of the Basque Country, 20018 Donostia-San Sebastian, Spain
| | - Ondrej Tichacek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague, Czech Republic
| | - Krishnadev Narayanankutty
- Biofisika Institute (CSIC, UPV/EHU), 48940 Leioa, Spain
- Department of Molecular Biology and Biochemistry, University of the Basque Country, 48940 Leioa, Spain
| | - Daniele De Martino
- Biofisika Institute (CSIC, UPV/EHU), 48940 Leioa, Spain
- Ikerbasque Foundation, 48009 Bilbao, Spain
| | - Kepa Ruiz-Mirazo
- Biofisika Institute (CSIC, UPV/EHU), 48940 Leioa, Spain
- Department of Philosophy, University of the Basque Country, 20018 Donostia-San Sebastian, Spain
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14
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Geisberger T, Diederich P, Kaiser CJO, Vogele K, Ruf A, Seitz C, Simmel F, Eisenreich W, Schmitt-Kopplin P, Huber C. Formation of vesicular structures from fatty acids formed under simulated volcanic hydrothermal conditions. Sci Rep 2023; 13:15227. [PMID: 37710028 PMCID: PMC10502091 DOI: 10.1038/s41598-023-42552-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 09/12/2023] [Indexed: 09/16/2023] Open
Abstract
Microscopic compartmentalization is beneficial in synthetic chemistry and indispensable for the evolution of life to separate a reactive "inside" from a hydrolyzing "outside". Here, we show compartmentalization in aqueous solution containing mixtures of fatty acids up to 19 carbon atoms which were synthesized by one-pot reactions of acetylene and carbon monoxide in contact with nickel sulfide at 105 °C, reaction requirements which are compatible to Hadean Early Earth conditions. Based on confocal, dynamic light scattering (DLS) and transmission electron microscopy (TEM) measurements, vesicle-like structures with diameters of 10-150 nm are formed after solvent extraction and resolubilisation. Moreover fluorescent dye was encapsulated into the structures proving their vesicular properties. This self-assembly could also have occurred on Early Earth as a crucial step in establishing simple membranes of proto-cells as a prerequisite in the evolution of metabolism and life.
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Affiliation(s)
- Thomas Geisberger
- Structural Membrane Biochemistry, Technical University of Munich, BNMRZ, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Philippe Diederich
- Research Unit Analytical BioGeoChemistry, Helmholtz Center Munich, 85764, Neuherberg, Germany
| | - Christoph J O Kaiser
- Division for Electron Microscopy, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Kilian Vogele
- Physics of Synthetic Biological Systems, Physics Department E14, Technical University of Munich, Am Coulombwall 4a, 85748, Garching, Germany
| | - Alexander Ruf
- Faculty of Physics, LMU Munich, Schellingstraße 4, 80799, Munich, Germany
- Excellence Cluster ORIGINS, Boltzmannstraße 2, 85748, Garching, Germany
| | - Christian Seitz
- Structural Membrane Biochemistry, Technical University of Munich, BNMRZ, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Friedrich Simmel
- Physics of Synthetic Biological Systems, Physics Department E14, Technical University of Munich, Am Coulombwall 4a, 85748, Garching, Germany
| | - Wolfgang Eisenreich
- Structural Membrane Biochemistry, Technical University of Munich, BNMRZ, Lichtenbergstr. 4, 85748, Garching, Germany
| | | | - Claudia Huber
- Structural Membrane Biochemistry, Technical University of Munich, BNMRZ, Lichtenbergstr. 4, 85748, Garching, Germany.
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15
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Dávila MJ, Mayer C. Structural Phenomena in a Vesicle Membrane Obtained through an Evolution Experiment: A Study Based on MD Simulations. Life (Basel) 2023; 13:1735. [PMID: 37629592 PMCID: PMC10455627 DOI: 10.3390/life13081735] [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: 07/19/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
The chemical evolution of biomolecules was clearly affected by the overall extreme environmental conditions found on Early Earth. Periodic temperature changes inside the Earth's crust may have played a role in the emergence and survival of functional peptides embedded in vesicular compartments. In this study, all-atom molecular dynamic (MD) simulations were used to elucidate the effect of temperature on the properties of functionalized vesicle membranes. A plausible prebiotic system was selected, constituted by a model membrane bilayer from an equimolar mixture of long-chain fatty acids and fatty amines, and an octapeptide, KSPFPFAA, previously identified as an optimized functional peptide in an evolution experiment. This peptide tends to form the largest spontaneous aggregates at higher temperatures, thereby enhancing the pore-formation process and the eventual transfer of essential molecules in a prebiotic scenario. The analyses also suggest that peptide-amphiphile interactions affect the structural properties of the membrane, with a significant increase in the degree of interdigitation at the lowest temperatures under study.
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Affiliation(s)
- María J. Dávila
- Institute of Physical Chemistry, CENIDE, University of Duisburg-Essen, 45141 Essen, Germany;
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16
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Dommer A, Wauer NA, Angle KJ, Davasam A, Rubio P, Luo M, Morris CK, Prather KA, Grassian VH, Amaro RE. Revealing the Impacts of Chemical Complexity on Submicrometer Sea Spray Aerosol Morphology. ACS CENTRAL SCIENCE 2023; 9:1088-1103. [PMID: 37396863 PMCID: PMC10311664 DOI: 10.1021/acscentsci.3c00184] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Indexed: 07/04/2023]
Abstract
Sea spray aerosol (SSA) ejected through bursting bubbles at the ocean surface is a complex mixture of salts and organic species. Submicrometer SSA particles have long atmospheric lifetimes and play a critical role in the climate system. Composition impacts their ability to form marine clouds, yet their cloud-forming potential is difficult to study due to their small size. Here, we use large-scale molecular dynamics (MD) simulations as a "computational microscope" to provide never-before-seen views of 40 nm model aerosol particles and their molecular morphologies. We investigate how increasing chemical complexity impacts the distribution of organic material throughout individual particles for a range of organic constituents with varying chemical properties. Our simulations show that common organic marine surfactants readily partition between both the surface and interior of the aerosol, indicating that nascent SSA may be more heterogeneous than traditional morphological models suggest. We support our computational observations of SSA surface heterogeneity with Brewster angle microscopy on model interfaces. These observations indicate that increased chemical complexity in submicrometer SSA leads to a reduced surface coverage by marine organics, which may facilitate water uptake in the atmosphere. Our work thus establishes large-scale MD simulations as a novel technique for interrogating aerosols at the single-particle level.
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17
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Sepulveda RV, Sbarbaro C, Opazo MC, Duarte Y, González-Nilo F, Aguayo D. Insights into Early Steps of Decanoic Acid Self-Assemblies under Prebiotic Temperatures Using Molecular Dynamics Simulations. MEMBRANES 2023; 13:membranes13050469. [PMID: 37233530 DOI: 10.3390/membranes13050469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/18/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023]
Abstract
The origin of life possibly required processes in confined systems that facilitated simple chemical reactions and other more complex reactions impossible to achieve under the condition of infinite dilution. In this context, the self-assembly of micelles or vesicles derived from prebiotic amphiphilic molecules is a cornerstone in the chemical evolution pathway. A prime example of these building blocks is decanoic acid, a short-chain fatty acid capable of self-assembling under ambient conditions. This study explored a simplified system made of decanoic acids under temperatures ranging from 0 °C to 110 °C to replicate prebiotic conditions. The study revealed the first point of aggregation of decanoic acid into vesicles and examined the insertion of a prebiotic-like peptide in a primitive bilayer. The information gathered from this research provides critical insights into molecule interactions with primitive membranes, allowing us to understand the first nanometric compartments needed to trigger further reactions that were essential for the origin of life.
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Affiliation(s)
- Romina V Sepulveda
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Av. República 330, Santiago 8370146, Chile
| | - Christopher Sbarbaro
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Av. República 330, Santiago 8370146, Chile
| | - Ma Cecilia Opazo
- Instituto de Ciencias Naturales, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Manuel Montt 948, Providencia 7500000, Chile
| | - Yorley Duarte
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Av. República 330, Santiago 8370146, Chile
| | - Fernando González-Nilo
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Av. República 330, Santiago 8370146, Chile
| | - Daniel Aguayo
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Av. República 330, Santiago 8370146, Chile
- Agricultura Digital, Servicio Agrícola, Salinas y Fabres S.A., Ruta 5 Sur, Parcela 165, Hijuela Larga, Paine 9540000, Chile
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18
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Jing X, Zhang Y, Li M, Zuo X, Fan C, Zheng J. Surface engineering of colloidal nanoparticles. MATERIALS HORIZONS 2023; 10:1185-1209. [PMID: 36748345 DOI: 10.1039/d2mh01512a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Synthesis of engineered colloidal nanoparticles (NPs) with delicate surface characteristics leads to well-defined physicochemical properties and contributes to multifunctional applications. Surface engineering of colloidal NPs can improve their stability in diverse solvents by inhibiting the interparticle attractive forces, thus providing a prerequisite for further particle manipulation, fabrication of the following materials and biological applications. During the last decades, surface engineering methods for colloidal NPs have been well-developed by numerous researchers. However, accurate control of surface properties is still an important topic. The emerging DNA/protein nanotechnology offers additional possibility of surface modification of NPs and programmable particle self-assembly. Here, we first briefly review the recent progress in surface engineering of colloidal NPs, focusing on the improved stability by grafting suitable small molecules, polymers or biological macromolecules. We then present the practical strategies for nucleic acid surface encoding of NPs and subsequent programmable assembly. Various exciting applications of these unique materials are summarized with a specific focus on the cellular uptake, bio-toxicity, imaging and diagnosis of colloidal NPs in vivo. With the growing interest in colloidal NPs in nano-biological research, we expect that this review can play an instructive role in engineering the surface properties for desired applications.
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Affiliation(s)
- Xinxin Jing
- Department of Urology, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Yueyue Zhang
- Department of Urology, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Min Li
- Department of Urology, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Xiaolei Zuo
- Department of Urology, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
- School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Junhua Zheng
- Department of Urology, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
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19
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Fonseca J, Meng L, Imaz I, Maspoch D. Self-assembly of colloidal metal-organic framework (MOF) particles. Chem Soc Rev 2023; 52:2528-2543. [PMID: 36930224 DOI: 10.1039/d2cs00858k] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Self-assembly of colloidal particles into ordered superstructures enables the development of novel advanced materials for diverse applications such as photonics, electronics, sensing, energy conversion, energy storage, diagnosis, drug or gene delivery, and catalysis. Recently, polyhedral metal-organic framework (MOF) particles have been proposed as promising colloidal particles to form ordered superstructures, based on their colloidal stability, size-tunability, rich polyhedral shapes, porosity and multifunctionality. In this review, we present a comprehensive overview of strategies for the self-assembly of colloidal MOF particles into ordered superstructures of different dimensionalities, highlighting some of their properties and applications, and sharing thoughts on the self-assembly of MOF particles.
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Affiliation(s)
- Javier Fonseca
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, Campus UAB, Bellaterra, 08193, Barcelona, Spain. .,Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Lingxin Meng
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, Campus UAB, Bellaterra, 08193, Barcelona, Spain. .,Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Inhar Imaz
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, Campus UAB, Bellaterra, 08193, Barcelona, Spain. .,Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Daniel Maspoch
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, Campus UAB, Bellaterra, 08193, Barcelona, Spain. .,Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.,ICREA, Pg. Lluıs Companys 23, 08010, Barcelona, Spain
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20
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Lowe LA, Wang A. Preparation of Giant Vesicles with Mixed Single-Tailed and Double-Tailed Lipids. Methods Mol Biol 2023; 2622:71-85. [PMID: 36781751 DOI: 10.1007/978-1-0716-2954-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Giant vesicles are model membrane systems that can be characterized with microscopy. Whereas most giant synthetic vesicles are created with a single phospholipid species, vesicles with mixed membrane compositions, including single-tailed and double-tailed lipids, serve as more accurate models of biological membranes and also have applications in the origins of life and drug delivery fields. Here we describe several approaches that can be used to create giant vesicles with mixed lipid compositions.
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Affiliation(s)
- Lauren A Lowe
- School of Chemistry, UNSW Sydney, Sydney, NSW, Australia.,Australian Centre for Astrobiology, UNSW Sydney, Sydney, NSW, Australia
| | - Anna Wang
- School of Chemistry, UNSW Sydney, Sydney, NSW, Australia. .,Australian Centre for Astrobiology, UNSW Sydney, Sydney, NSW, Australia.
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21
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Cheng X, Huang J, Wang R, Xu Y, Wu N, Zhou J, Liu X, Wang H, Chen H. Inorganic-organic coprecipitation: spontaneous formation of enclosed and porous silica compartments with enriched biopolymers. NANOSCALE 2023; 15:2394-2401. [PMID: 36651126 DOI: 10.1039/d2nr05320a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
We show that it is possible to spontaneously form all-enclosed compartments with microporous shells and enriched biopolymers via simple coprecipitation of silica and biopolymers. The reaction involves mild conditions and tolerates the random mixing of multiple reagents. Such a synthetic advance points to a new direction for resolving the chicken-egg dilemma of how the early life forms were hosted: without a physical barrier it would be difficult to maintain organized reactions, but without organized reactions, it would be difficult to create a cell membrane. In our synthesis, the divalent cation Ca2+ plays a critical role in the co-precipitation and in creating hollow compartments after simple dilution with water. The precursor of silica, poly(silicic acid), is a negatively charged, cross-linked polymer. It could be co-precipitated with negatively charged biopolymers such as DNA and proteins, whereas the remaining silica precursor forms a conformal and microporous shell on the surface of the initial precipitate. After etching, the biopolymers are retained inside the hollow compartments. The fact that multiple favorable conditions are easily brought together in enclosed compartments opens new possibilities in theorizing the host of early life forms.
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Affiliation(s)
- Xuejun Cheng
- Department of Chemistry, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.
- Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Jie Huang
- Institute of Advanced Synthesis (IAS) and School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Centre for Advanced Materials, Nanjing Tech University, Nanjing 211816, China.
| | - Ruoxu Wang
- Department of Chemistry, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.
- Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Yue Xu
- Institute of Advanced Synthesis (IAS) and School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Centre for Advanced Materials, Nanjing Tech University, Nanjing 211816, China.
| | - Nan Wu
- State Key Laboratory of Materials Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China.
| | - Jie Zhou
- State Key Laboratory of Materials Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China.
| | - Xueyang Liu
- Institute of Advanced Synthesis (IAS) and School of Chemistry and Molecular Engineering, Jiangsu National Synergetic Innovation Centre for Advanced Materials, Nanjing Tech University, Nanjing 211816, China.
| | - Hong Wang
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China.
| | - Hongyu Chen
- Department of Chemistry, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.
- Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
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22
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Cohen ZR, Todd ZR, Wogan N, Black RA, Keller SL, Catling DC. Plausible Sources of Membrane-Forming Fatty Acids on the Early Earth: A Review of the Literature and an Estimation of Amounts. ACS EARTH & SPACE CHEMISTRY 2023; 7:11-27. [PMID: 36704178 PMCID: PMC9869395 DOI: 10.1021/acsearthspacechem.2c00168%20] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
The first cells were plausibly bounded by membranes assembled from fatty acids with at least 8 carbons. Although the presence of fatty acids on the early Earth is widely assumed within the astrobiology community, there is no consensus regarding their origin and abundance. In this Review, we highlight three possible sources of fatty acids: (1) delivery by carbonaceous meteorites, (2) synthesis on metals delivered by impactors, and (3) electrochemical synthesis by spark discharges. We also discuss fatty acid synthesis by UV or particle irradiation, gas-phase ion-molecule reactions, and aqueous redox reactions. We compare estimates for the total mass of fatty acids supplied to Earth by each source during the Hadean eon after an extremely massive asteroid impact that would have reset Earth's fatty acid inventory. We find that synthesis on iron-rich surfaces derived from the massive impactor in contact with an impact-generated reducing atmosphere could have contributed ∼102 times more total mass of fatty acids than subsequent delivery by either carbonaceous meteorites or electrochemical synthesis. Additionally, we estimate that a single carbonaceous meteorite would not deliver a high enough concentration of fatty acids (∼15 mM for decanoic acid) into an existing body of water on the Earth's surface to spontaneously form membranes unless the fatty acids were further concentrated by another mechanism, such as subsequent evaporation of the water. Our estimates rely heavily on various assumptions, leading to significant uncertainties; nevertheless, these estimates provide rough order-of-magnitude comparisons of various sources of fatty acids on the early Earth. We also suggest specific experiments to improve future estimates. Our calculations support the view that fatty acids would have been available on the early Earth. Further investigation is needed to assess the mechanisms by which fatty acids could have been concentrated sufficiently to assemble into membranes during the origin of life.
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Affiliation(s)
- Zachary R. Cohen
- Department
of Chemistry, Department of Earth and Space Sciences, and Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
| | - Zoe R. Todd
- Department
of Chemistry, Department of Earth and Space Sciences, and Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
| | - Nicholas Wogan
- Department
of Chemistry, Department of Earth and Space Sciences, and Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
| | - Roy A. Black
- Department
of Chemistry, Department of Earth and Space Sciences, and Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
| | - Sarah L. Keller
- Department
of Chemistry, Department of Earth and Space Sciences, and Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
| | - David C. Catling
- Department
of Chemistry, Department of Earth and Space Sciences, and Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
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23
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Cohen ZR, Todd ZR, Wogan N, Black RA, Keller SL, Catling DC. Plausible Sources of Membrane-Forming Fatty Acids on the Early Earth: A Review of the Literature and an Estimation of Amounts. ACS EARTH & SPACE CHEMISTRY 2023; 7:11-27. [PMID: 36704178 PMCID: PMC9869395 DOI: 10.1021/acsearthspacechem.2c00168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 06/18/2023]
Abstract
The first cells were plausibly bounded by membranes assembled from fatty acids with at least 8 carbons. Although the presence of fatty acids on the early Earth is widely assumed within the astrobiology community, there is no consensus regarding their origin and abundance. In this Review, we highlight three possible sources of fatty acids: (1) delivery by carbonaceous meteorites, (2) synthesis on metals delivered by impactors, and (3) electrochemical synthesis by spark discharges. We also discuss fatty acid synthesis by UV or particle irradiation, gas-phase ion-molecule reactions, and aqueous redox reactions. We compare estimates for the total mass of fatty acids supplied to Earth by each source during the Hadean eon after an extremely massive asteroid impact that would have reset Earth's fatty acid inventory. We find that synthesis on iron-rich surfaces derived from the massive impactor in contact with an impact-generated reducing atmosphere could have contributed ∼102 times more total mass of fatty acids than subsequent delivery by either carbonaceous meteorites or electrochemical synthesis. Additionally, we estimate that a single carbonaceous meteorite would not deliver a high enough concentration of fatty acids (∼15 mM for decanoic acid) into an existing body of water on the Earth's surface to spontaneously form membranes unless the fatty acids were further concentrated by another mechanism, such as subsequent evaporation of the water. Our estimates rely heavily on various assumptions, leading to significant uncertainties; nevertheless, these estimates provide rough order-of-magnitude comparisons of various sources of fatty acids on the early Earth. We also suggest specific experiments to improve future estimates. Our calculations support the view that fatty acids would have been available on the early Earth. Further investigation is needed to assess the mechanisms by which fatty acids could have been concentrated sufficiently to assemble into membranes during the origin of life.
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Affiliation(s)
- Zachary R. Cohen
- Department
of Chemistry, Department of Earth and Space Sciences, and Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
| | - Zoe R. Todd
- Department
of Chemistry, Department of Earth and Space Sciences, and Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
| | - Nicholas Wogan
- Department
of Chemistry, Department of Earth and Space Sciences, and Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
| | - Roy A. Black
- Department
of Chemistry, Department of Earth and Space Sciences, and Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
| | - Sarah L. Keller
- Department
of Chemistry, Department of Earth and Space Sciences, and Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
| | - David C. Catling
- Department
of Chemistry, Department of Earth and Space Sciences, and Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
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24
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Abstract
Ferric heme b (= ferric protoporphyrin IX = hemin) is an important prosthetic group of different types of enzymes, including the intensively investigated and widely applied horseradish peroxidase (HRP). In HRP, hemin is present in monomeric form in a hydrophobic pocket containing among other amino acid side chains the two imidazoyl groups of His170 and His42. Both amino acids are important for the peroxidase activity of HRP as an axial ligand of hemin (proximal His170) and as an acid/base catalyst (distal His42). A key feature of the peroxidase mechanism of HRP is the initial formation of compound I under heterolytic cleavage of added hydrogen peroxide as a terminal oxidant. Investigations of free hemin dispersed in aqueous solution showed that different types of hemin dimers can form, depending on the experimental conditions, possibly resulting in hemin crystallization. Although it has been recognized already in the 1970s that hemin aggregation can be prevented in aqueous solution by using micelle-forming amphiphiles, it remains a challenge to prepare hemin-containing micellar and vesicular systems with peroxidase-like activities. Such systems are of interest as cheap HRP-mimicking catalysts for analytical and synthetic applications. Some of the key concepts on which research in this fascinating and interdisciplinary field is based are summarized, along with major accomplishments and possible directions for further improvement. A systematic analysis of the physico-chemical properties of hemin in aqueous micellar solutions and vesicular dispersions must be combined with a reliable evaluation of its catalytic activity. Future studies should show how well the molecular complexity around hemin in HRP can be mimicked by using micelles or vesicles. Because of the importance of heme b in virtually all biological systems and the fact that porphyrins and hemes can be obtained under potentially prebiotic conditions, ideas exist about the possible role of heme-containing micellar and vesicular systems in prebiotic times.
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Lerin-Morales KM, Olguín LF, Mateo-Martí E, Colín-García M. Prebiotic Chemistry Experiments Using Microfluidic Devices. Life (Basel) 2022; 12:life12101665. [PMID: 36295100 PMCID: PMC9605377 DOI: 10.3390/life12101665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/15/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
Microfluidic devices are small tools mostly consisting of one or more channels, with dimensions between one and hundreds of microns, where small volumes of fluids are manipulated. They have extensive use in the biomedical and chemical fields; however, in prebiotic chemistry, they only have been employed recently. In prebiotic chemistry, just three types of microfluidic devices have been used: the first ones are Y-form devices with laminar co-flow, used to study the precipitation of minerals in hydrothermal vents systems; the second ones are microdroplet devices that can form small droplets capable of mimic cellular compartmentalization; and the last ones are devices with microchambers that recreate the microenvironment inside rock pores under hydrothermal conditions. In this review, we summarized the experiments in the field of prebiotic chemistry that employed microfluidic devices. The main idea is to incentivize their use and discuss their potential to perform novel experiments that could contribute to unraveling some prebiotic chemistry questions.
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Affiliation(s)
- Karen Melissa Lerin-Morales
- Posgrado en Ciencias de la Tierra, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico
- Correspondence: (K.M.L.-M.); (M.C.-G.); Tel.: +52-(55)-5622-4300 (ext. 164) (M.C.-G.)
| | - Luis F. Olguín
- Laboratorio de Biofisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico
| | - Eva Mateo-Martí
- Centro de Astrobiología (CAB), CSIC-INTA, Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - María Colín-García
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico
- Correspondence: (K.M.L.-M.); (M.C.-G.); Tel.: +52-(55)-5622-4300 (ext. 164) (M.C.-G.)
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Coutant M, Lepot K, Fadel A, Addad A, Richard E, Troadec D, Ventalon S, Sugitani K, Javaux EJ. Distinguishing cellular from abiotic spheroidal microstructures in the ca. 3.4 Ga Strelley Pool Formation. GEOBIOLOGY 2022; 20:599-622. [PMID: 35712885 DOI: 10.1111/gbi.12506] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 05/04/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
The morphogenesis of most carbonaceous microstructures that resemble microfossils in Archean (4-2.5 Ga old) rocks remains debated. The associated carbonaceous matter may even-in some cases-derive from abiotic organic molecules. Mineral growths associated with organic matter migration may mimic microbial cells, some anatomical features, and known microfossils-in particular those with simple spheroid shapes. Here, spheroid microstructures from a chert of the ca. 3.4 Ga Strelley Pool Formation (SPF) of the Pilbara Craton (Western Australia) were imaged and analyzed with a combination of high-resolution in situ techniques. This provides new insights into carbonaceous matter distributions and their relationships with the crystallographic textures of associated quartz. Thus, we describe five new types of spheroids and discuss their morphogenesis. In at least three types of microstructures, wall coalescence argues for migration of carbonaceous matter onto abiotic siliceous spherulites or diffusion in poorly crystalline silica. The nanoparticulate walls of these coalescent structures often cut across multiple quartz crystals, consistent with migration in/on silica prior to quartz recrystallization. Sub-continuous walls lying at quartz boundaries occur in some coalescent vesicles. This weakens the "continuous carbonaceous wall" criterion proposed to support cellular inferences. In contrast, some clustered spheroids display wrinkled sub-continuous double walls, and a large sphere shows a thick sub-continuous wall with pustules and depressions. These features appear consistent with post-mortem cell alteration, although abiotic morphogenesis remains difficult to rule out. We compared these siliceous and carbonaceous microstructures to coalescent pyritic spheroids from the same sample, which likely formed as "colloidal" structures in hydrothermal context. The pyrites display a smaller size and only limited carbonaceous coatings, arguing that they could not have acted as precursors to siliceous spheroids. This study revealed new textural features arguing for abiotic morphogenesis of some Archean spheroids. The absence of these features in distinct types of spheroids leaves open the microfossil hypothesis in the same rock. Distinction of such characteristics could help addressing further the origin of other candidate microfossils. This study calls for similar investigations of metamorphosed microfossiliferous rocks and of the products of in vitro growth of cell-mimicking structures in presence of organics and silica.
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Affiliation(s)
- Maxime Coutant
- Univ. Lille, CNRS, Univ. Littoral Côte d'Opale, UMR 8187, LOG - Laboratoire d'Océanologie et de Géosciences, Lille, France
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium
| | - Kevin Lepot
- Univ. Lille, CNRS, Univ. Littoral Côte d'Opale, UMR 8187, LOG - Laboratoire d'Océanologie et de Géosciences, Lille, France
- Institut Universitaire de France (IUF), France
| | - Alexandre Fadel
- UMR 8207 - UMET - Unité Matériaux et Transformations, Univ. Lille, CNRS, INRAE, Centrale Lille, Lille, France
| | - Ahmed Addad
- UMR 8207 - UMET - Unité Matériaux et Transformations, Univ. Lille, CNRS, INRAE, Centrale Lille, Lille, France
| | - Elodie Richard
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, Lille, France
| | - David Troadec
- Univ. Lille, CNRS, Centrale Lille, Junia, Univ. Polytechnique Hauts-de-France, UMR 8520 - IEMN - Institut d'Electronique de Microélectronique et de Nanotechnologie, Lille, France
| | - Sandra Ventalon
- Univ. Lille, CNRS, Univ. Littoral Côte d'Opale, UMR 8187, LOG - Laboratoire d'Océanologie et de Géosciences, Lille, France
| | - Kenichiro Sugitani
- Graduate School of Environmental Studies, Nagoya University, Nagoya, Japan
| | - Emmanuelle J Javaux
- Early Life Traces & Evolution-Astrobiology, UR Astrobiology, University of Liège, Liège, Belgium
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27
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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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28
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Lowe LA, Kindt JT, Cranfield C, Cornell B, Macmillan A, Wang A. Subtle changes in pH affect the packing and robustness of fatty acid bilayers. SOFT MATTER 2022; 18:3498-3504. [PMID: 35474126 DOI: 10.1039/d2sm00272h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Connecting molecular interactions to emergent properties is a goal of physical chemistry, self-assembly, and soft matter science. We show that for fatty acid bilayers, vesicle rupture tension, and permeability to water and ions are coupled to pH via alterations to lipid packing. A change in pH of one, for example, can halve the rupture tension of oleic acid membranes, an effect that is comparable to increasing lipid unsaturation in phospholipid systems. We use both experiments and molecular dynamics simulations to reveal that a subtle increase in pH can lead to increased water penetration, ion permeability, pore formation rates, and membrane disorder. For changes in membrane water content, oleic acid membranes appear to be more than a million times more sensitive to protons than to sodium ions. The work has implications for systems in which fatty acids are likely to be found, for example in the primitive cells on early Earth, biological membranes especially during digestion, and other biomaterials.
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Affiliation(s)
- Lauren A Lowe
- School of Chemistry, UNSW Sydney, NSW 2052, Australia.
- Australian Centre for Astrobiology, UNSW Sydney, NSW 2052, Australia
| | - James T Kindt
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
| | - Charles Cranfield
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Bruce Cornell
- SDx Tethered Membranes Pty. Ltd., Unit 6, 30-32 Barcoo Street, Roseville, NSW 2069, Australia
| | | | - Anna Wang
- School of Chemistry, UNSW Sydney, NSW 2052, Australia.
- Australian Centre for Astrobiology, UNSW Sydney, NSW 2052, Australia
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29
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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: 30] [Impact Index Per Article: 15.0] [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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30
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Smokers IBA, van Haren MHI, Lu T, Spruijt E. Complex coacervation and compartmentalized conversion of prebiotically relevant metabolites. CHEMSYSTEMSCHEM 2022. [DOI: 10.1002/syst.202200004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Iris B. A. Smokers
- Radboud University Nijmegen: Radboud Universiteit Institute for Molecules and Materials NETHERLANDS
| | | | - Tiemei Lu
- Radboud University Nijmegen: Radboud Universiteit Institute for Molecules and Materials NETHERLANDS
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31
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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: 2] [Impact Index Per Article: 1.0] [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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32
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Gohrbandt M, Lipski A, Grimshaw JW, Buttress JA, Baig Z, Herkenhoff B, Walter S, Kurre R, Deckers‐Hebestreit G, Strahl H. Low membrane fluidity triggers lipid phase separation and protein segregation in living bacteria. EMBO J 2022; 41:e109800. [PMID: 35037270 PMCID: PMC8886542 DOI: 10.15252/embj.2021109800] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/19/2021] [Accepted: 12/21/2021] [Indexed: 11/09/2022] Open
Abstract
All living organisms adapt their membrane lipid composition in response to changes in their environment or diet. These conserved membrane-adaptive processes have been studied extensively. However, key concepts of membrane biology linked to regulation of lipid composition including homeoviscous adaptation maintaining stable levels of membrane fluidity, and gel-fluid phase separation resulting in domain formation, heavily rely upon in vitro studies with model membranes or lipid extracts. Using the bacterial model organisms Escherichia coli and Bacillus subtilis, we now show that inadequate in vivo membrane fluidity interferes with essential complex cellular processes including cytokinesis, envelope expansion, chromosome replication/segregation and maintenance of membrane potential. Furthermore, we demonstrate that very low membrane fluidity is indeed capable of triggering large-scale lipid phase separation and protein segregation in intact, protein-crowded membranes of living cells; a process that coincides with the minimal level of fluidity capable of supporting growth. Importantly, the in vivo lipid phase separation is not associated with a breakdown of the membrane diffusion barrier function, thus explaining why the phase separation process induced by low fluidity is biologically reversible.
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Affiliation(s)
- Marvin Gohrbandt
- Mikrobiologie, Fachbereich Biologie/ChemieUniversität OsnabrückOsnabrückGermany
| | - André Lipski
- Lebensmittelmikrobiologie und ‐hygieneInstitut für Ernährungs‐ und LebensmittelwissenschaftenRheinische Friedrich‐Wilhelms‐Universität BonnBonnGermany
| | - James W Grimshaw
- Centre for Bacterial Cell BiologyBiosciences InstituteFaculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Jessica A Buttress
- Centre for Bacterial Cell BiologyBiosciences InstituteFaculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Zunera Baig
- Centre for Bacterial Cell BiologyBiosciences InstituteFaculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Brigitte Herkenhoff
- Mikrobiologie, Fachbereich Biologie/ChemieUniversität OsnabrückOsnabrückGermany
| | - Stefan Walter
- Mikrobiologie, Fachbereich Biologie/ChemieUniversität OsnabrückOsnabrückGermany
| | - Rainer Kurre
- Center of Cellular NanoanalyticsIntegrated Bioimaging FacilityUniversität OsnabrückOsnabrückGermany
| | | | - Henrik Strahl
- Centre for Bacterial Cell BiologyBiosciences InstituteFaculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
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33
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Köksal ES, Põldsalu I, Friis H, Mojzsis SJ, Bizzarro M, Gözen I. Spontaneous Formation of Prebiotic Compartment Colonies on Hadean Earth and Pre‐Noachian Mars**. CHEMSYSTEMSCHEM 2022. [DOI: 10.1002/syst.202100040] [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)
- Elif S. Köksal
- Centre for Molecular Medicine Norway Faculty of Medicine University of Oslo 0318 Oslo Norway
| | - Inga Põldsalu
- Centre for Molecular Medicine Norway Faculty of Medicine University of Oslo 0318 Oslo Norway
| | - Henrik Friis
- Natural History Museum University of Oslo Postboks 1172 Blindern 0318 Oslo Norway
| | - Stephen J. Mojzsis
- Research Centre for Astronomy and Earth Sciences 15–17 Konkoly Thege Miklós Road Budapest 1121 Hungary
- Department of Lithospheric Research University of Vienna UZA 2, Althanstraße 14 1090 Vienna Austria
- Department of Geological Sciences University of Colorado UCB 399, 2200 Colorado Avenue Boulder CO 80309-0399 USA
| | - Martin Bizzarro
- Centre for Star and Planet Formation GLOBE Institute University of Copenhagen 1350 Copenhagen K Denmark
| | - Irep 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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34
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Razavi M, Saberi Fathi SM, Tuszynski JA. The Effect of the Protein Synthesis Entropy Reduction on the Cell Size Regulation and Division Size of Unicellular Organisms. ENTROPY 2022; 24:e24010094. [PMID: 35052120 PMCID: PMC8775074 DOI: 10.3390/e24010094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/04/2021] [Accepted: 12/28/2021] [Indexed: 12/14/2022]
Abstract
The underlying mechanism determining the size of a particular cell is one of the fundamental unknowns in cell biology. Here, using a new approach that could be used for most of unicellular species, we show that the protein synthesis and cell size are interconnected biophysically and that protein synthesis may be the chief mechanism in establishing size limitations of unicellular organisms. This result is obtained based on the free energy balance equation of protein synthesis and the second law of thermodynamics. Our calculations show that protein synthesis involves a considerable amount of entropy reduction due to polymerization of amino acids depending on the cytoplasmic volume of the cell. The amount of entropy reduction will increase with cell growth and eventually makes the free energy variations of the protein synthesis positive (that is, forbidden thermodynamically). Within the limits of the second law of thermodynamics we propose a framework to estimate the optimal cell size at division.
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Affiliation(s)
- Mohammad Razavi
- Department of Physics, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran;
| | - Seyed Majid Saberi Fathi
- Department of Physics, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran;
- Correspondence:
| | - Jack Adam Tuszynski
- Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada;
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, 10129 Torino, Italy
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35
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Wortelboer K, Bakker GJ, Winkelmeijer M, van Riel N, Levin E, Nieuwdorp M, Herrema H, Davids M. Fecal microbiota transplantation as tool to study the interrelation between microbiota composition and miRNA expression. Microbiol Res 2022; 257:126972. [DOI: 10.1016/j.micres.2022.126972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 02/07/2023]
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36
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Tesovnik T, Jenko Bizjan B, Šket R, Debeljak M, Battelino T, Kovač J. Technological Approaches in the Analysis of Extracellular Vesicle Nucleotide Sequences. Front Bioeng Biotechnol 2021; 9:787551. [PMID: 35004647 PMCID: PMC8733665 DOI: 10.3389/fbioe.2021.787551] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/11/2021] [Indexed: 12/12/2022] Open
Abstract
Together with metabolites, proteins, and lipid components, the EV cargo consists of DNA and RNA nucleotide sequence species, which are part of the intracellular communication network regulating specific cellular processes and provoking distinct target cell responses. The extracellular vesicle (EV) nucleotide sequence cargo molecules are often investigated in association with a particular pathology and may provide an insight into the physiological and pathological processes in hard-to-access organs and tissues. The diversity and biological function of EV nucleotide sequences are distinct regarding EV subgroups and differ in tissue- and cell-released EVs. EV DNA is present mainly in apoptotic bodies, while there are different species of EV RNAs in all subgroups of EVs. A limited sample volume of unique human liquid biopsy provides a small amount of EVs with limited isolated DNA and RNA, which can be a challenging factor for EV nucleotide sequence analysis, while the additional difficulty is technical variability of molecular nucleotide detection. Every EV study is challenged with its first step of the EV isolation procedure, which determines the EV's purity, yield, and diameter range and has an impact on the EV's downstream analysis with a significant impact on the final result. The gold standard EV isolation procedure with ultracentrifugation provides a low output and not highly pure isolated EVs, while modern techniques increase EV's yield and purity. Different EV DNA and RNA detection techniques include the PCR procedure for nucleotide sequence replication of the molecules of interest, which can undergo a small-input EV DNA or RNA material. The nucleotide sequence detection approaches with their advantages and disadvantages should be considered to appropriately address the study problem and to extract specific EV nucleotide sequence information with the detection using qPCR or next-generation sequencing. Advanced next-generation sequencing techniques allow the detection of total EV genomic or transcriptomic data even at the single-molecule resolution and thus, offering a sensitive and accurate EV DNA or RNA biomarker detection. Additionally, with the processes where the EV genomic or transcriptomic data profiles are compared to identify characteristic EV differences in specific conditions, novel biomarkers could be discovered. Therefore, a suitable differential expression analysis is crucial to define the EV DNA or RNA differences between conditions under investigation. Further bioinformatics analysis can predict molecular cell targets and identify targeted and affected cellular pathways. The prediction target tools with functional studies are essential to help specify the role of the investigated EV-targeted nucleotide sequences in health and disease and support further development of EV-related therapeutics. This review will discuss the biological diversity of human liquid biopsy-obtained EV nucleotide sequences DNA and RNA species reported as potential biomarkers in health and disease and methodological principles of their detection, from human liquid biopsy EV isolation, EV nucleotide sequence extraction, techniques for their detection, and their cell target prediction.
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Affiliation(s)
- Tine Tesovnik
- Institute for Special Laboratory Diagnostics, University Medical Centre Ljubljana, University Children’s Hospital, Ljubljana, Slovenia
| | - Barbara Jenko Bizjan
- Institute for Special Laboratory Diagnostics, University Medical Centre Ljubljana, University Children’s Hospital, Ljubljana, Slovenia
| | - Robert Šket
- Institute for Special Laboratory Diagnostics, University Medical Centre Ljubljana, University Children’s Hospital, Ljubljana, Slovenia
| | - Maruša Debeljak
- Institute for Special Laboratory Diagnostics, University Medical Centre Ljubljana, University Children’s Hospital, Ljubljana, Slovenia
| | - Tadej Battelino
- Department of Pediatric Endocrinology, Diabetes and Metabolic Diseases, University Medical Centre Ljubljana, University Children’s Hospital, Ljubljana, Slovenia
- Faculty of Medicine, Chair of Paediatrics, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Kovač
- Institute for Special Laboratory Diagnostics, University Medical Centre Ljubljana, University Children’s Hospital, Ljubljana, Slovenia
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Jia TZ, Kuruma Y. Increasing complexity of primitive compartments. Biophys Physicobiol 2021; 18:269-273. [PMID: 34909364 PMCID: PMC8639197 DOI: 10.2142/biophysico.bppb-v18.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 11/15/2021] [Indexed: 12/01/2022] Open
Affiliation(s)
- Tony Z Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan.,Blue Marble Space Institute of Science, Seattle, Washington 98154, USA
| | - Yutetsu Kuruma
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan.,Extra-cutting-edge Science and Technology Avant-garde Research Program, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa 237-0061, Japan.,Japan Science and Technology Agency, PRESTO, Kawaguchi, Saitama 332-0012, Japan
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38
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Thoma J, Burmann BM. Architects of their own environment: How membrane proteins shape the Gram-negative cell envelope. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:1-34. [PMID: 35034716 DOI: 10.1016/bs.apcsb.2021.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Gram-negative bacteria are surrounded by a complex multilayered cell envelope, consisting of an inner and an outer membrane, and separated by the aqueous periplasm, which contains a thin peptidoglycan cell wall. These bacteria employ an arsenal of highly specialized membrane protein machineries to ensure the correct assembly and maintenance of the membranes forming the cell envelope. Here, we review the diverse protein systems, which perform these functions in Escherichia coli, such as the folding and insertion of membrane proteins, the transport of lipoproteins and lipopolysaccharide within the cell envelope, the targeting of phospholipids, and the regulation of mistargeted envelope components. Some of these protein machineries have been known for a long time, yet still hold surprises. Others have only recently been described and some are still missing pieces or yet remain to be discovered.
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Affiliation(s)
- Johannes Thoma
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Göteborg, Sweden; Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden.
| | - Björn M Burmann
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Göteborg, Sweden; Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
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39
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Urakami N, Sakuma Y, Chiba T, Imai M. Vesicle deformation and division induced by flip-flops of lipid molecules. SOFT MATTER 2021; 17:8434-8445. [PMID: 34473188 DOI: 10.1039/d1sm00847a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We investigated the deformation of small unilamellar vesicles (SUVs) induced by flip-flops of lipids using coarse-grained molecular dynamics simulations. In the case of single-component SUVs composed of zero spontaneous curvature lipids (ZLs), the flip-flop of ZLs deformed stomatocyte-shaped SUVs into an oblate shape, whereas pear-shaped SUVs were deformed into a prolate shape. These two equilibrium shapes comply with the local minima of elastic energy. In the case of binary vesicles composed of ZLs and negative spontaneous curvature lipids (NLs), the vesicle deformation pathway depended on the initial NL distribution in the bilayer. If the initial difference in the NL concentration between the outer and inner leaflets was small, the flip-flop of ZLs and NLs rapidly deformed pear-shaped SUVs into an equilibrium prolate shape. On the other hand, when NLs were localised in the inner leaflet, the flip-flop of ZLs and NLs deformed pear-shaped SUVs into a limiting shape and then induced vesicle division. Because the flip-flop rate of NLs is much faster than that of ZLs, the total free energy was first relaxed by the flip-flop of NLs and then by that of ZLs. This kinetic effect is responsible for the observed vesicle division induced by flip-flops.
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Affiliation(s)
- Naohito Urakami
- Department of Physics and Informatics, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8512, Japan.
| | - Yuka Sakuma
- Department of Physics, Tohoku University, Aoba, Sendai 980-8578, Japan
| | - Toshikaze Chiba
- Department of Physics, Tohoku University, Aoba, Sendai 980-8578, Japan
| | - Masayuki Imai
- Department of Physics, Tohoku University, Aoba, Sendai 980-8578, Japan
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41
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Stotz HU, Brotherton D, Inal J. Communication is key: Extracellular vesicles as mediators of infection and defence during host-microbe interactions in animals and plants. FEMS Microbiol Rev 2021; 46:6358524. [PMID: 34448857 PMCID: PMC8767456 DOI: 10.1093/femsre/fuab044] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 08/23/2021] [Indexed: 12/12/2022] Open
Abstract
Extracellular vesicles (EVs) are now understood to be ubiquitous mediators of cellular communication. In this review, we suggest that EVs have evolved into a highly regulated system of communication with complex functions including export of wastes, toxins and nutrients, targeted delivery of immune effectors and vectors of RNA silencing. Eukaryotic EVs come in different shapes and sizes and have been classified according to their biogenesis and size distributions. Small EVs (or exosomes) are released through fusion of endosome-derived multivesicular bodies with the plasma membrane. Medium EVs (or microvesicles) bud off the plasma membrane as a form of exocytosis. Finally, large EVs (or apoptotic bodies) are produced as a result of the apoptotic process. This review considers EV secretion and uptake in four eukaryotic kingdoms, three of which produce cell walls. The impacts cell walls have on EVs in plants and fungi are discussed, as are roles of fungal EVs in virulence. Contributions of plant EVs to development and innate immunity are presented. Compelling cases are sporophytic self-incompatibility and cellular invasion by haustorium-forming filamentous pathogens. The involvement of EVs in all of these eukaryotic processes is reconciled considering their evolutionary history.
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Affiliation(s)
- Henrik U Stotz
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK
| | - Dominik Brotherton
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK
| | - Jameel Inal
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK.,School of Human Sciences, London Metropolitan University, London, N7 8DB, UK
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42
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Hierarchical self-assembly of polydisperse colloidal bananas into a two-dimensional vortex phase. Proc Natl Acad Sci U S A 2021; 118:2107241118. [PMID: 34389681 PMCID: PMC8379995 DOI: 10.1073/pnas.2107241118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hierarchically self-assembled materials—structures with order at multiple length scales—can be found everywhere. Examples range from collagen structures in human bones to engineered photonic materials. These structures usually assemble from monodisperse microscopic building blocks that interact via complex directional interactions. In this work, we show that hierarchical materials can, in fact, also be assembled from polydisperse building blocks and by entropic interactions alone. Our simple yet powerful assembly mechanism opens up avenues toward rationally exploiting the often undesired polydispersity of colloidal building blocks for programming entropy-driven self-assembly of hierarchical materials. Self-assembly of microscopic building blocks into highly ordered and functional structures is ubiquitous in nature and found at all length scales. Hierarchical structures formed by colloidal building blocks are typically assembled from monodisperse particles interacting via engineered directional interactions. Here, we show that polydisperse colloidal bananas self-assemble into a complex and hierarchical quasi–two-dimensional structure, called the vortex phase, only due to excluded volume interactions and polydispersity in the particle curvature. Using confocal microscopy, we uncover the remarkable formation mechanism of the vortex phase and characterize its exotic structure and dynamics at the single-particle level. These results demonstrate that hierarchical self-assembly of complex materials can be solely driven by entropy and shape polydispersity of the constituting particles.
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43
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44
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Xue M, Black RA, Cohen ZR, Roehrich A, Drobny GP, Keller SL. Binding of Dipeptides to Fatty Acid Membranes Explains Their Colocalization in Protocells but Does Not Select for Them Relative to Unjoined Amino Acids. J Phys Chem B 2021; 125:7933-7939. [PMID: 34283913 DOI: 10.1021/acs.jpcb.1c01485] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dipeptides, which consist of two amino acids joined by a peptide bond, have been shown to have catalytic functions. This observation leads to fundamental questions relevant to the origin of life. How could peptides have become colocalized with the first protocells? Which structural features would have determined the association of amino acids and peptides with membranes? Could the association of dipeptides with protocell membranes have driven molecular evolution, favoring dipeptides over individual amino acids? Using pulsed-field gradient nuclear magnetic resonance, we find that several prebiotic amino acids and dipeptides bind to prebiotic membranes. For amino acids, the side chains and carboxylate contribute to the interaction. For dipeptides, the extent of binding is generally less than that of the constituent amino acids, implying that other mechanisms would be necessary to drive molecular evolution. Nevertheless, our results are consistent with a scheme in which the building blocks of the biological polymers colocalized with protocells prior to the emergence of RNA and proteins.
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Affiliation(s)
- Mengjun Xue
- Department of Chemistry, University of Washington, Seattle, Washington 98195 United States
| | - Roy A Black
- Department of Chemistry, University of Washington, Seattle, Washington 98195 United States
| | - Zachary R Cohen
- Department of Chemistry, University of Washington, Seattle, Washington 98195 United States
| | - Adrienne Roehrich
- Department of Chemistry, University of Washington, Seattle, Washington 98195 United States
| | - Gary P Drobny
- Department of Chemistry, University of Washington, Seattle, Washington 98195 United States
| | - Sarah L Keller
- Department of Chemistry, University of Washington, Seattle, Washington 98195 United States
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45
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Gaylor MO, Miro P, Vlaisavljevich B, Kondage AAS, Barge LM, Omran A, Videau P, Swenson VA, Leinen LJ, Fitch NW, Cole KL, Stone C, Drummond SM, Rageth K, Dewitt LR, González Henao S, Karanauskus V. Plausible Emergence and Self Assembly of a Primitive Phospholipid from Reduced Phosphorus on the Primordial Earth. ORIGINS LIFE EVOL B 2021; 51:185-213. [PMID: 34279769 DOI: 10.1007/s11084-021-09613-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 06/19/2021] [Indexed: 11/28/2022]
Abstract
How life arose on the primitive Earth is one of the biggest questions in science. Biomolecular emergence scenarios have proliferated in the literature but accounting for the ubiquity of oxidized (+ 5) phosphate (PO43-) in extant biochemistries has been challenging due to the dearth of phosphate and molecular oxygen on the primordial Earth. A compelling body of work suggests that exogenous schreibersite ((Fe,Ni)3P) was delivered to Earth via meteorite impacts during the Heavy Bombardment (ca. 4.1-3.8 Gya) and there converted to reduced P oxyanions (e.g., phosphite (HPO32-) and hypophosphite (H2PO2-)) and phosphonates. Inspired by this idea, we review the relevant literature to deduce a plausible reduced phospholipid analog of modern phosphatidylcholines that could have emerged in a primordial hydrothermal setting. A shallow alkaline lacustrine basin underlain by active hydrothermal fissures and meteoritic schreibersite-, clay-, and metal-enriched sediments is envisioned. The water column is laden with known and putative primordial hydrothermal reagents. Small system dimensions and thermal- and UV-driven evaporation further concentrate chemical precursors. We hypothesize that a reduced phospholipid arises from Fischer-Tropsch-type (FTT) production of a C8 alkanoic acid, which condenses with an organophosphinate (derived from schreibersite corrosion to hypophosphite with subsequent methylation/oxidation), to yield a reduced protophospholipid. This then condenses with an α-amino nitrile (derived from Strecker-type reactions) to form the polar head. Preliminary modeling results indicate that reduced phospholipids do not aggregate rapidly; however, single layer micelles are stable up to aggregates with approximately 100 molecules.
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Affiliation(s)
- Michael O Gaylor
- Department of Chemistry, Dakota State University, Madison, SD, 57042, USA.
| | - Pere Miro
- Department of Chemistry, University of South Dakota, Vermillion, SD, 57069, USA
| | - Bess Vlaisavljevich
- Department of Chemistry, University of South Dakota, Vermillion, SD, 57069, USA
| | | | - Laura M Barge
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, 91109, USA
| | - Arthur Omran
- School of Geosciences, University of South Florida, Tampa, FL, 33620, USA.,Department of Chemistry, University of North Florida, Jacksonville, FL, 32224, USA
| | - Patrick Videau
- Department of Biology, Southern Oregon University, Ashland, OR, 97520, USA.,Bayer Crop Science, Chesterfield, MO, 63017, USA
| | - Vaille A Swenson
- Department of Chemistry, Dakota State University, Madison, SD, 57042, USA.,Department of Molecular Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Lucas J Leinen
- Department of Chemistry, Dakota State University, Madison, SD, 57042, USA
| | - Nathaniel W Fitch
- Department of Chemistry, Dakota State University, Madison, SD, 57042, USA
| | - Krista L Cole
- Department of Chemistry, Dakota State University, Madison, SD, 57042, USA
| | - Chris Stone
- Department of Biology, Southern Oregon University, Ashland, OR, 97520, USA
| | - Samuel M Drummond
- Department of Chemistry, Dakota State University, Madison, SD, 57042, USA
| | - Kayli Rageth
- Department of Chemistry, Dakota State University, Madison, SD, 57042, USA
| | - Lillian R Dewitt
- Department of Chemistry, Dakota State University, Madison, SD, 57042, USA
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46
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'Whole Organism', Systems Biology, and Top-Down Criteria for Evaluating Scenarios for the Origin of Life. Life (Basel) 2021; 11:life11070690. [PMID: 34357062 PMCID: PMC8306273 DOI: 10.3390/life11070690] [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: 06/07/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 12/22/2022] Open
Abstract
While most advances in the study of the origin of life on Earth (OoLoE) are piecemeal, tested against the laws of chemistry and physics, ultimately the goal is to develop an overall scenario for life's origin(s). However, the dimensionality of non-equilibrium chemical systems, from the range of possible boundary conditions and chemical interactions, renders the application of chemical and physical laws difficult. Here we outline a set of simple criteria for evaluating OoLoE scenarios. These include the need for containment, steady energy and material flows, and structured spatial heterogeneity from the outset. The Principle of Continuity, the fact that all life today was derived from first life, suggests favoring scenarios with fewer non-analog (not seen in life today) to analog (seen in life today) transitions in the inferred first biochemical pathways. Top-down data also indicate that a complex metabolism predated ribozymes and enzymes, and that full cellular autonomy and motility occurred post-LUCA. Using these criteria, we find the alkaline hydrothermal vent microchamber complex scenario with a late evolving exploitation of the natural occurring pH (or Na+ gradient) by ATP synthase the most compelling. However, there are as yet so many unknowns, we also advocate for the continued development of as many plausible scenarios as possible.
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47
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Green DW, Watson JA, Ben-Nissan B, Watson GS, Stamboulis A. Synthetic tissue engineering with smart, cytomimetic protocells. Biomaterials 2021; 276:120941. [PMID: 34298445 DOI: 10.1016/j.biomaterials.2021.120941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 05/25/2021] [Accepted: 05/29/2021] [Indexed: 12/24/2022]
Abstract
Synthetic protocells are rudimentary origin-of-life versions of natural cell counterparts. Protocells are widely engineered to advance efforts and useful accepted outcomes in synthetic biology, soft matter chemistry and bioinspired materials chemistry. Protocells in collective symbiosis generate synthetic proto-tissues that display unprecedented autonomy and yield advanced materials with desirable life-like features for smart multi-drug delivery, micro bioreactors, renewable fuel production, environmental clean-up, and medicine. Current levels of protocell and proto-tissue functionality and adaptivity are just sufficient to apply them in tissue engineering and regenerative medicine, where they animate biomaterials and increase therapeutic cell productivity. As of now, structural biomaterials for tissue engineering lack the properties of living biomaterials such as self-repair, stochasticity, cell synergy and the sequencing of molecular and cellular events. Future protocell-based biomaterials provide these core properties of living organisms, but excluding evolution. Most importantly, protocells are programmable for a broad array of cell functions and behaviors and collectively in consortia are tunable for multivariate functions. Inspired by upcoming designs of smart protocells, we review their developmental background and cover the most recently reported developments in this promising field of synthetic proto-biology. Our emphasis is on manufacturing proto-tissues for tissue engineering of organoids, stem cell niches and reprogramming and tissue formation through stages of embryonic development. We also highlight the exciting reported developments arising from fusing living cells and tissues, in a valuable hybrid symbiosis, with synthetic counterparts to bring about novel functions, and living tissue products for a new synthetic tissue engineering discipline.
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Affiliation(s)
- David William Green
- School of Metallurgy and Materials, Biomaterials Research Group, Proto-cellular Biomaterials Unit, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - Jolanta Anna Watson
- School of Science and Engineering, University of the Sunshine Coast, Fraser Coast Campus, Hervey Bay, QLD 4655, Australia
| | - Besim Ben-Nissan
- Faculty of Science, University of Technology, PO BOX 123, Broadway, NSW 2007, Sydney, Australia
| | - Gregory Shaun Watson
- School of Science and Engineering, University of the Sunshine Coast, Fraser Coast Campus, Hervey Bay, QLD 4655, Australia
| | - Artemis Stamboulis
- School of Metallurgy and Materials, Biomaterials Research Group, Proto-cellular Biomaterials Unit, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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48
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The Origin(s) of Cell(s): Pre-Darwinian Evolution from FUCAs to LUCA : To Carl Woese (1928-2012), for his Conceptual Breakthrough of Cellular Evolution. J Mol Evol 2021; 89:427-447. [PMID: 34173011 DOI: 10.1007/s00239-021-10014-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 05/29/2021] [Indexed: 10/21/2022]
Abstract
The coming of the Last Universal Cellular Ancestor (LUCA) was the singular watershed event in the making of the biotic world. If the coming of LUCA marked the crossing of the "Darwinian Threshold", then pre-LUCA evolution must have been Pre-Darwinian and at least partly non-Darwinian. But how did Pre-Darwinian evolution before LUCA actually operate? I broaden our understanding of the central mechanism of biological evolution (i.e., variation-selection-inheritance) and then extend this broadened understanding to its natural starting point: the origin(s) of the First Universal Cellular Ancestors (FUCAs) before LUCA. My hypothesis centers upon vesicles' making-and-remaking as variation and competition as selection. More specifically, I argue that vesicles' acquisition and merger, via breaking-and-repacking, proto-endocytosis, proto-endosymbiosis, and other similar processes had been a central force of both variation and selection in the pre-Darwinian epoch. These new perspectives shed important new light upon the origin of FUCAs and their subsequent evolution into LUCA.
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49
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Qiu H, Li F, Du Y, Li R, Hyun JY, Lee SY, Choi JH. Programmable Aggregation of Artificial Cells with DNA Signals. ACS Synth Biol 2021; 10:1268-1276. [PMID: 34006093 DOI: 10.1021/acssynbio.0c00550] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cell aggregation is a complex behavior that is closely related to the viability, differentiation, and migration of cells. An effort to create synthetic analogs could lead to considerable advances in cell physiology and biophysics. Rendering and modulating such a dynamic artificial cell system require mechanisms for receiving, transducing, and transmitting intercellular signals, yet effective tools are limited at present. Here we construct synthetic cells from engineered lipids and show their programmable aggregation behaviors using DNA oligonucleotides as signaling molecules. The artificial cells have transmembrane channels made of DNA origami that are used to recognize and process intercellular signals. We demonstrate that multiple small vesicles aggregate onto a giant vesicle after a transduction of external DNA signals by an intracellular enzyme and that the small vesicles dissociate when receiving "release" signals. This work provides new possibilities for building synthetic protocells capable of chemical communication and coordination.
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Affiliation(s)
- Hengming Qiu
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Feiran Li
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yancheng Du
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ruixin Li
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ji Yeon Hyun
- Department of Biomedical Engineering, Yonsei University, Wonju, Gangwon 26427, Republic of Korea
| | - Sei Young Lee
- Department of Biomedical Engineering, Yonsei University, Wonju, Gangwon 26427, Republic of Korea
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
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50
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Lai YC, Liu Z, Chen IA. Encapsulation of ribozymes inside model protocells leads to faster evolutionary adaptation. Proc Natl Acad Sci U S A 2021; 118:e2025054118. [PMID: 34001592 PMCID: PMC8166191 DOI: 10.1073/pnas.2025054118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Functional biomolecules, such as RNA, encapsulated inside a protocellular membrane are believed to have comprised a very early, critical stage in the evolution of life, since membrane vesicles allow selective permeability and create a unit of selection enabling cooperative phenotypes. The biophysical environment inside a protocell would differ fundamentally from bulk solution due to the microscopic confinement. However, the effect of the encapsulated environment on ribozyme evolution has not been previously studied experimentally. Here, we examine the effect of encapsulation inside model protocells on the self-aminoacylation activity of tens of thousands of RNA sequences using a high-throughput sequencing assay. We find that encapsulation of these ribozymes generally increases their activity, giving encapsulated sequences an advantage over nonencapsulated sequences in an amphiphile-rich environment. In addition, highly active ribozymes benefit disproportionately more from encapsulation. The asymmetry in fitness gain broadens the distribution of fitness in the system. Consistent with Fisher's fundamental theorem of natural selection, encapsulation therefore leads to faster adaptation when the RNAs are encapsulated inside a protocell during in vitro selection. Thus, protocells would not only provide a compartmentalization function but also promote activity and evolutionary adaptation during the origin of life.
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Affiliation(s)
- Yei-Chen Lai
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Ziwei Liu
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Irene A Chen
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095;
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
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