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Sarkar S, Das S, Dagar S, Joshi MP, Mungi CV, Sawant AA, Patki GM, Rajamani S. Prebiological Membranes and Their Role in the Emergence of Early Cellular Life. J Membr Biol 2020; 253:589-608. [PMID: 33200235 DOI: 10.1007/s00232-020-00155-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/08/2020] [Indexed: 01/30/2023]
Abstract
Membrane compartmentalization is a fundamental feature of contemporary cellular life. Given this, it is rational to assume that at some stage in the early origins of life, membrane compartments would have potentially emerged to form a dynamic semipermeable barrier in primitive cells (protocells), protecting them from their surrounding environment. It is thought that such prebiological membranes would likely have played a crucial role in the emergence and evolution of life on the early Earth. Extant biological membranes are highly organized and complex, which is a consequence of a protracted evolutionary history. On the other hand, prebiotic membrane assemblies, which are thought to have preceded sophisticated contemporary membranes, are hypothesized to have been relatively simple and composed of single chain amphiphiles. Recent studies indicate that the evolution of prebiotic membranes potentially resulted from interactions between the membrane and its physicochemical environment. These studies have also speculated on the origin, composition, function and influence of environmental conditions on protocellular membranes as the niche parameters would have directly influenced their composition and biophysical properties. Nonetheless, the evolutionary pathways involved in the transition from prebiological membranes to contemporary membranes are largely unknown. This review critically evaluates existing research on prebiotic membranes in terms of their probable origin, composition, energetics, function and evolution. Notably, we outline new approaches that can further our understanding about how prebiotic membranes might have evolved in response to relevant physicochemical parameters that would have acted as pertinent selection pressures on the early Earth.
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Affiliation(s)
- Susovan Sarkar
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Souradeep Das
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Shikha Dagar
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Manesh Prakash Joshi
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Chaitanya V Mungi
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Anupam A Sawant
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Gauri M Patki
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Sudha Rajamani
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India.
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Fairén AG, Gómez-Elvira J, Briones C, Prieto-Ballesteros O, Rodríguez-Manfredi JA, López Heredero R, Belenguer T, Moral AG, Moreno-Paz M, Parro V. The Complex Molecules Detector (CMOLD): A Fluidic-Based Instrument Suite to Search for (Bio)chemical Complexity on Mars and Icy Moons. ASTROBIOLOGY 2020; 20:1076-1096. [PMID: 32856927 PMCID: PMC7116096 DOI: 10.1089/ast.2019.2167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 06/01/2020] [Indexed: 06/11/2023]
Abstract
Organic chemistry is ubiquitous in the Solar System, and both Mars and a number of icy satellites of the outer Solar System show substantial promise for having hosted or hosting life. Here, we propose a novel astrobiologically focused instrument suite that could be included as scientific payload in future missions to Mars or the icy moons: the Complex Molecules Detector, or CMOLD. CMOLD is devoted to determining different levels of prebiotic/biotic chemical and structural targets following a chemically general approach (i.e., valid for both terrestrial and nonterrestrial life), as well as their compatibility with terrestrial life. CMOLD is based on a microfluidic block that distributes a liquid suspension sample to three instruments by using complementary technologies: (1) novel microscopic techniques for identifying ultrastructures and cell-like morphologies, (2) Raman spectroscopy for detecting universal intramolecular complexity that leads to biochemical functionality, and (3) bioaffinity-based systems (including antibodies and aptamers as capture probes) for finding life-related and nonlife-related molecular structures. We highlight our current developments to make this type of instruments flight-ready for upcoming Mars missions: the Raman spectrometer included in the science payload of the ESAs Rosalind Franklin rover (Raman Laser Spectrometer instrument) to be launched in 2022, and the biomarker detector that was included as payload in the NASA Icebreaker lander mission proposal (SOLID instrument). CMOLD is a robust solution that builds on the combination of three complementary, existing techniques to cover a wide spectrum of targets in the search for (bio)chemical complexity in the Solar System.
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Affiliation(s)
- Alberto G. Fairén
- Centro de Astrobiología (CSIC-INTA), Madrid, Spain
- Department of Astronomy, Cornell University, Ithaca New York, USA
| | - Javier Gómez-Elvira
- Payload & Space Science Department, Instituto Nacional de Técnica Aeroespacial (INTA), Madrid, Spain
| | | | | | | | - Raquel López Heredero
- Payload & Space Science Department, Instituto Nacional de Técnica Aeroespacial (INTA), Madrid, Spain
| | - Tomás Belenguer
- Payload & Space Science Department, Instituto Nacional de Técnica Aeroespacial (INTA), Madrid, Spain
| | - Andoni G. Moral
- Payload & Space Science Department, Instituto Nacional de Técnica Aeroespacial (INTA), Madrid, Spain
| | | | - Víctor Parro
- Centro de Astrobiología (CSIC-INTA), Madrid, Spain
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53
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Guevara R, Mateos DM, Pérez Velázquez JL. Consciousness as an Emergent Phenomenon: A Tale of Different Levels of Description. ENTROPY (BASEL, SWITZERLAND) 2020; 22:E921. [PMID: 33286690 PMCID: PMC7597170 DOI: 10.3390/e22090921] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 08/15/2020] [Accepted: 08/19/2020] [Indexed: 01/17/2023]
Abstract
One of the biggest queries in cognitive sciences is the emergence of consciousness from matter. Modern neurobiological theories of consciousness propose that conscious experience is the result of interactions between large-scale neuronal networks in the brain, traditionally described within the realm of classical physics. Here, we propose a generalized connectionist framework in which the emergence of "conscious networks" is not exclusive of large brain areas, but can be identified in subcellular networks exhibiting nontrivial quantum phenomena. The essential feature of such networks is the existence of strong correlations in the system (classical or quantum coherence) and the presence of an optimal point at which the system's complexity and energy dissipation are maximized, whereas free-energy is minimized. This is expressed either by maximization of the information content in large scale functional networks or by achieving optimal efficiency through the quantum Goldilock effect.
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Affiliation(s)
- Ramón Guevara
- Integrative Neuroscience and Cognition Centre (INCC UMR8002), University of Paris and CNRS, 75270 Paris, France
- Department of Physics and Astronomy, University of Padova, 35131 Padova, Italy
| | - Diego M. Mateos
- Department of Science and Technology, Universidad Autónoma de Entre Ríos, Paraná 3100, Argentina;
- Instituto de Matemática Aplicada del Litoral (IMAL-CONICET-UNL), Santa Fe 3000, Argentina
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54
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From self-replication to replicator systems en route to de novo life. Nat Rev Chem 2020; 4:386-403. [PMID: 37127968 DOI: 10.1038/s41570-020-0196-x] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2020] [Indexed: 01/01/2023]
Abstract
The process by which chemistry can give rise to biology remains one of the biggest mysteries in contemporary science. The de novo synthesis and origin of life both require the functional integration of three key characteristics - replication, metabolism and compartmentalization - into a system that is maintained out of equilibrium and is capable of open-ended Darwinian evolution. This Review takes systems of self-replicating molecules as starting points and describes the steps necessary to integrate additional characteristics of life. We analyse how far experimental self-replicators have come in terms of Darwinian evolution. We also cover models of replicator communities that attempt to solve Eigen's paradox, whereby accurate replication needs complex machinery yet obtaining such complex self-replicators through evolution requires accurate replication. Successful models rely on a collective metabolism and a way of (transient) compartmentalization, suggesting that the invention and integration of these two characteristics is driven by evolution. Despite our growing knowledge, there remain numerous key challenges that may be addressed by a combined theoretical and experimental approach.
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55
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Dagar S, Sarkar S, Rajamani S. Geochemical influences on nonenzymatic oligomerization of prebiotically relevant cyclic nucleotides. RNA (NEW YORK, N.Y.) 2020; 26:756-769. [PMID: 32205323 PMCID: PMC7266160 DOI: 10.1261/rna.074302.119] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/19/2020] [Indexed: 06/01/2023]
Abstract
The spontaneous emergence of long RNA molecules on the early Earth, a phenomenon central to the RNA World hypothesis, continues to remain an enigma in the field of origins of life. Few studies have looked at the nonenzymatic oligomerization of cyclic mononucleotides under neutral to alkaline conditions, albeit in fully dehydrated state. In this study, we systematically investigated the oligomerization of cyclic nucleotides under prebiotically relevant conditions, wherein starting reactants were subjected to repeated dehydration-rehydration (DH-RH) regimes. DH-RH conditions, a recurring geological theme that was prevalent on prebiotic Earth, are driven by naturally occurring processes including diurnal cycles and tidal pool activity. These conditions have been shown to facilitate uphill oligomerization reactions. The polymerization of 2'-3' and 3'-5' cyclic nucleotides of a purine (adenosine) and a pyrimidine (cytidine) was investigated. Additionally, the effect of amphiphiles was also evaluated. Furthermore, to discern the effect of "realistic" conditions on this process, the reactions were also performed using a hot spring water sample from a candidate early Earth environment. Our study showed that the oligomerization of cyclic nucleotides under DH-RH conditions resulted in intact informational oligomers. Amphiphiles increased the stability of both the starting monomers and the resultant oligomers in selected reactions. In the hot spring reactions, both the oligomerization of nucleotides and the back hydrolysis of the resultant oligomers were pronounced. Altogether, this study demonstrates how nonenzymatic oligomerization of cyclic nucleotides, under both laboratory-simulated prebiotic conditions and in a candidate early Earth environment, could have resulted in RNA oligomers of a putative RNA World.
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Affiliation(s)
- Shikha Dagar
- Department of Biology, Indian Institute of Science Education and Research, Pune 411008, India
| | - Susovan Sarkar
- Department of Biology, Indian Institute of Science Education and Research, Pune 411008, India
| | - Sudha Rajamani
- Department of Biology, Indian Institute of Science Education and Research, Pune 411008, India
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56
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Sarkar S, Dagar S, Verma A, Rajamani S. Compositional heterogeneity confers selective advantage to model protocellular membranes during the origins of cellular life. Sci Rep 2020; 10:4483. [PMID: 32161377 PMCID: PMC7066133 DOI: 10.1038/s41598-020-61372-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 02/24/2020] [Indexed: 12/21/2022] Open
Abstract
Protocellular membranes are thought to be composed of mixtures of single chain amphiphiles, such as fatty acids and their derivatives, moieties that would have been part of the complex prebiotic chemical landscape. The composition and physico-chemical properties of these prebiological membranes would have been significantly affected and regulated by their environment. In this study, pertinent properties were systematically characterized, under early Earth conditions. Two different fatty acids were mixed with their respective alcohol and/or glycerol monoester derivatives to generate combinations of binary and tertiary membrane systems. Their properties were then evaluated as a function of multiple factors including their stability under varying pH, varying Mg2+ ion concentrations, dilution regimes, and their permeability to calcein. Our results demonstrate how environmental constraints would have acted as important prebiotic selection pressures to shape the evolution of prebiological membranes. The study also illustrates that compositionally diverse membrane systems are more stable and robust to multiple selection pressures, thereby making them more suitable for supporting protocellular life.
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Affiliation(s)
- Susovan Sarkar
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Shikha Dagar
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Ajay Verma
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Sudha Rajamani
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India.
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57
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On the emergence of cognition: from catalytic closure to neuroglial closure. J Biol Phys 2020; 46:95-119. [PMID: 32130568 DOI: 10.1007/s10867-020-09543-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 02/12/2020] [Indexed: 10/24/2022] Open
Abstract
In an analogous manner as occurred during the development of a connected metabolism that at some point reached characteristics associated with what is called "life"-due mainly to a catalytic closure phenomenon when chemicals started to autocatalyze themselves forming a closed web of chemical reactions-it is here proposed that cognition and consciousness (or features associated with them) arose as a consequence of another type of closure within the nervous system, the brain especially. Proper brain function requires an efficient web of connections and once certain complexity is attained due to the number and coordinated activities of the brain cell networks, the emergent properties of cognition and consciousness take place. Seeking to identify main features of the nervous system organization for optimal function, it is here proposed that while catalytic closure yielded life, neuroglial closure produced cognition/consciousness.
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58
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Preiner M, Asche S, Becker S, Betts HC, Boniface A, Camprubi E, Chandru K, Erastova V, Garg SG, Khawaja N, Kostyrka G, Machné R, Moggioli G, Muchowska KB, Neukirchen S, Peter B, Pichlhöfer E, Radványi Á, Rossetto D, Salditt A, Schmelling NM, Sousa FL, Tria FDK, Vörös D, Xavier JC. The Future of Origin of Life Research: Bridging Decades-Old Divisions. Life (Basel) 2020; 10:E20. [PMID: 32110893 PMCID: PMC7151616 DOI: 10.3390/life10030020] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/19/2020] [Accepted: 02/21/2020] [Indexed: 12/12/2022] Open
Abstract
Research on the origin of life is highly heterogeneous. After a peculiar historical development, it still includes strongly opposed views which potentially hinder progress. In the 1st Interdisciplinary Origin of Life Meeting, early-career researchers gathered to explore the commonalities between theories and approaches, critical divergence points, and expectations for the future. We find that even though classical approaches and theories-e.g. bottom-up and top-down, RNA world vs. metabolism-first-have been prevalent in origin of life research, they are ceasing to be mutually exclusive and they can and should feed integrating approaches. Here we focus on pressing questions and recent developments that bridge the classical disciplines and approaches, and highlight expectations for future endeavours in origin of life research.
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Affiliation(s)
- Martina Preiner
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany; (S.G.G.); (F.D.K.T.)
| | - Silke Asche
- School of Chemistry, University of Glasgow, Glasgow G128QQ, UK;
| | - Sidney Becker
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK;
| | - Holly C. Betts
- School of Earth Sciences, University of Bristol, Bristol BS8 1RL, UK;
| | - Adrien Boniface
- Environmental Microbial Genomics, Laboratoire Ampère, Ecole Centrale de Lyon, Université de Lyon, 69130 Ecully, France;
| | - Eloi Camprubi
- Origins Center, Department of Earth Sciences, Utrecht University, 3584 CB Utrecht, The Netherlands;
| | - Kuhan Chandru
- Space Science Center (ANGKASA), Institute of Climate Change, Level 3, Research Complex, National University of Malaysia, UKM Bangi 43600, Selangor, Malaysia;
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technicka 5, 16628 Prague 6–Dejvice, Czech Republic
| | - Valentina Erastova
- UK Centre for Astrobiology, School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, UK;
| | - Sriram G. Garg
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany; (S.G.G.); (F.D.K.T.)
| | - Nozair Khawaja
- Institut für Geologische Wissenschaften, Freie Universität Berlin, 12249 Berlin, Germany;
| | | | - Rainer Machné
- Institute of Synthetic Microbiology, University of Düsseldorf, 40225 Düsseldorf, Germany; (R.M.); (N.M.S.)
- Quantitative and Theoretical Biology, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Giacomo Moggioli
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4DQ, UK;
| | - Kamila B. Muchowska
- Université de Strasbourg, CNRS, ISIS, 8 allée Gaspard Monge, 67000 Strasbourg, France;
| | - Sinje Neukirchen
- Archaea Biology and Ecogenomics Division, University of Vienna, 1090 Vienna, Austria; (S.N.); (E.P.); (F.L.S.)
| | - Benedikt Peter
- Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;
| | - Edith Pichlhöfer
- Archaea Biology and Ecogenomics Division, University of Vienna, 1090 Vienna, Austria; (S.N.); (E.P.); (F.L.S.)
| | - Ádám Radványi
- Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary (D.V.)
- Institute of Evolution, MTA Centre for Ecological Research, Klebelsberg Kuno u. 3., H-8237 Tihany, Hungary
| | - Daniele Rossetto
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy;
| | - Annalena Salditt
- Systems Biophysics, Physics Department, Ludwig-Maximilians-Universität München, 80799 Munich, Germany;
| | - Nicolas M. Schmelling
- Institute of Synthetic Microbiology, University of Düsseldorf, 40225 Düsseldorf, Germany; (R.M.); (N.M.S.)
- Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674 Cologne, Germany
| | - Filipa L. Sousa
- Archaea Biology and Ecogenomics Division, University of Vienna, 1090 Vienna, Austria; (S.N.); (E.P.); (F.L.S.)
| | - Fernando D. K. Tria
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany; (S.G.G.); (F.D.K.T.)
| | - Dániel Vörös
- Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary (D.V.)
- Institute of Evolution, MTA Centre for Ecological Research, Klebelsberg Kuno u. 3., H-8237 Tihany, Hungary
| | - Joana C. Xavier
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany; (S.G.G.); (F.D.K.T.)
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59
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Lin Y, Jing H, Liu Z, Chen J, Liang D. Dynamic Behavior of Complex Coacervates with Internal Lipid Vesicles under Nonequilibrium Conditions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:1709-1717. [PMID: 32004005 DOI: 10.1021/acs.langmuir.9b03561] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
During the evolution of life on earth, the emergence of lipid membrane-bounded compartments is one of the most enigmatic events. Endosymbiosis has been hypothesized as one of the solutions. In this work, using a coacervate droplet formed by single-stranded oligonucleotides (ss-oligo) and poly(l-lysine) (PLL) as the protocell model, we monitored the uptake of liposomes of different types and studied the dynamic behavior of the resulting composite droplet under the electric field. The coacervate droplet exhibits affinity for the liposomes of varying charges. However, the permeation of liposome is also controlled by electrostatic interactions. Dominated by electrostatic attraction, the positively charged liposome is retained inside the droplet as growing fibrous structures, while the negatively charged liposome is mainly coated on the droplet surface. Permeation and even distribution occur when the liposome and the droplet carry the same charges, or at least one of them is neutral. As an electric field is applied to trigger repetitive cycles of vacuolization in the ss-oligo/PLL droplet, the fibrous structure formed by the positively charged liposome is basically intact, while a new phase is generated together with uneven mass transport as the negatively charged liposome is internalized. Interestingly, the release of daughter droplets with similar components occurs on the droplet containing neutral liposomes. Our work not only provides a step toward creating protocells with hierarchical structures and biofunctions using a biogenetic material via simple mixing but also sheds light on the possible origin of the lipid structure inside a living organism.
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Affiliation(s)
- Ya'nan Lin
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China
| | - Hairong Jing
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China
| | - Zhijun Liu
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China
| | - Jiaxin Chen
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China
| | - Dehai Liang
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China
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60
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A protocell with fusion and division. Biochem Soc Trans 2019; 47:1909-1919. [PMID: 31819942 DOI: 10.1042/bst20190576] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/12/2019] [Accepted: 11/25/2019] [Indexed: 11/17/2022]
Abstract
A protocell is a synthetic form of cellular life that is constructed from phospholipid vesicles and used to understand the emergence of life from a nonliving chemical network. To be considered 'living', a protocell should be capable of self-proliferation, which includes successive growth and division processes. The growth of protocells can be achieved via vesicle fusion approaches. In this review, we provide a brief overview of recent research on the formation of a protocell, fusion and division processes of the protocell, and encapsulation of a defined chemical network such as the genetic material. We also provide some perspectives on the challenges and future developments of synthetic protocell research.
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61
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Saha B, Chatterjee A, Reja A, Das D. Condensates of short peptides and ATP for the temporal regulation of cytochrome c activity. Chem Commun (Camb) 2019; 55:14194-14197. [PMID: 31702760 DOI: 10.1039/c9cc07358b] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Herein, we report the generation of simple condensates of short peptides with ATP, which are spatiotemporally formed under dissipative conditions created in presence of ATP-ase. These coacervates could imbibe cytochrome c and temporally modulate a redox reaction catalyzed by the entrapped protein, thus mimicking the advanced functional machinery of transient intercellular membraneless condensates of large proteins and RNA.
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Affiliation(s)
- Baishakhi Saha
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Ayan Chatterjee
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Antara Reja
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Dibyendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
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62
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Campbell TD, Febrian R, McCarthy JT, Kleinschmidt HE, Forsythe JG, Bracher PJ. Prebiotic condensation through wet-dry cycling regulated by deliquescence. Nat Commun 2019; 10:4508. [PMID: 31586058 PMCID: PMC6778215 DOI: 10.1038/s41467-019-11834-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/26/2019] [Indexed: 12/16/2022] Open
Abstract
Wet-dry cycling is widely regarded as a means of driving condensation reactions under prebiotic conditions to generate mixtures of prospective biopolymers. A criticism of this model is its reliance on unpredictable rehydration events, like rainstorms. Here, we report the ability of deliquescent minerals to mediate the oligomerization of glycine during iterative wet-dry cycles. The reaction mixtures evaporate to dryness at high temperatures and spontaneously reacquire water vapor to form aqueous solutions at low temperatures. Deliquescent mixtures can foster yields of oligomerization over ten-fold higher than non-deliquescent controls. The deliquescent mixtures tightly regulate their moisture content, which is crucial, as too little water precludes dissolution of the reactants while too much water favors hydrolysis over condensation. The model also suggests a potential reason why life evolved to favor the enrichment of potassium: so living systems could acquire and retain sufficient water to serve as a solvent for biochemical reactions.
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Affiliation(s)
- Thomas D Campbell
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri, 63103, USA
| | - Rio Febrian
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri, 63103, USA
| | - Jack T McCarthy
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri, 63103, USA
| | - Holly E Kleinschmidt
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri, 63103, USA
| | - Jay G Forsythe
- Department of Chemistry and Biochemistry, College of Charleston, 66 George Street, Charleston, South Carolina, 29424, USA
| | - Paul J Bracher
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, St. Louis, Missouri, 63103, USA.
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64
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Köksal ES, Liese S, Kantarci I, Olsson R, Carlson A, Gözen I. Nanotube-Mediated Path to Protocell Formation. ACS NANO 2019; 13:6867-6878. [PMID: 31177769 DOI: 10.1021/acsnano.9b01646] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cellular compartments are membrane-enclosed, spatially distinct microenvironments that confine and protect biochemical reactions in the biological cell. On the early Earth, the autonomous formation of compartments is thought to have led to the encapsulation of nucleotides, thereby satisfying a starting condition for the emergence of life. Recently, surfaces have come into focus as potential platforms for the self-assembly of prebiotic compartments, as significantly enhanced vesicle formation was reported in the presence of solid interfaces. The detailed mechanism of such formation at the mesoscale is still under discussion. We report here on the spontaneous transformation of solid-surface-adhered lipid deposits to unilamellar membrane compartments through a straightforward sequence of topological changes, proceeding via a network of interconnected lipid nanotubes. We show that this transformation is entirely driven by surface-free energy minimization and does not require hydrolysis of organic molecules or external stimuli such as electrical currents or mechanical agitation. The vesicular structures take up and encapsulate their external environment during formation and can subsequently separate and migrate upon exposure to hydrodynamic flow. This may link the self-directed transition from weakly organized bioamphiphile assemblies on solid surfaces to protocells with secluded internal contents.
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Affiliation(s)
- Elif S Köksal
- Centre for Molecular Medicine Norway, Faculty of Medicine , University of Oslo , 0318 Oslo , Norway
| | - Susanne Liese
- Department of Chemistry, Faculty of Mathematics and Natural Sciences , University of Oslo , 0315 Oslo , Norway
| | - Ilayda Kantarci
- Centre for Molecular Medicine Norway, Faculty of Medicine , University of Oslo , 0318 Oslo , Norway
| | - Ragni Olsson
- Centre for Molecular Medicine Norway, Faculty of Medicine , University of Oslo , 0318 Oslo , Norway
| | - Andreas Carlson
- Department of Chemistry, Faculty of Mathematics and Natural Sciences , University of Oslo , 0315 Oslo , Norway
| | - Irep Gözen
- Centre for Molecular Medicine Norway, Faculty of Medicine , University of Oslo , 0318 Oslo , Norway
- Department of Mathematics, Faculty of Mathematics and Natural Sciences , University of Oslo , 0315 Oslo , Norway
- Department of Chemistry and Chemical Engineering , Chalmers University of Technology , SE-412 96 Göteborg , Sweden
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65
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Chemical Basis of Biological Homochirality during the Abiotic Evolution Stages on Earth. Symmetry (Basel) 2019. [DOI: 10.3390/sym11060814] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Spontaneous mirror symmetry breaking (SMSB), a phenomenon leading to non-equilibrium stationary states (NESS) that exhibits biases away from the racemic composition is discussed here in the framework of dissipative reaction networks. Such networks may lead to a metastable racemic non-equilibrium stationary state that transforms into one of two degenerate but stable enantiomeric NESSs. In such a bifurcation scenario, the type of the reaction network, as well the boundary conditions, are similar to those characterizing the currently accepted stages of emergence of replicators and autocatalytic systems. Simple asymmetric inductions by physical chiral forces during previous stages of chemical evolution, for example in astrophysical scenarios, must involve unavoidable racemization processes during the time scales associated with the different stages of chemical evolution. However, residual enantiomeric excesses of such asymmetric inductions suffice to drive the SMSB stochastic distribution of chiral signs into a deterministic distribution. According to these features, we propose that a basic model of the chiral machinery of proto-life would emerge during the formation of proto-cell systems by the convergence of the former enantioselective scenarios.
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66
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Maraldi NM. In search of a primitive signaling code. Biosystems 2019; 183:103984. [PMID: 31201829 DOI: 10.1016/j.biosystems.2019.103984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/11/2019] [Accepted: 06/12/2019] [Indexed: 10/26/2022]
Abstract
Cells must have preceded by simpler chemical systems (protocells) that had the capacity of a spontaneous self-assembly process and the ability to confine chemical reaction networks together with a form of information. The presence of lipid molecules in the early Earth conditions is sufficient to ensure the occurrence of spontaneous self-assembly processes, not defined by genetic information, but related to their chemical amphiphilic nature. Ribozymes are plausible molecules for early life, being the first small polynucleotides made up of random oligomers or formed by non-enzymatic template copying. Compartmentalization represents a strategy for the evolution of ribozymes; the attachment of ribozymes to surfaces, such as formed by lipid micellar aggregates may be particular relevant if the surface itself catalyzes RNA polymerization.It is conceivable that the transition from pre-biotic molecular aggregates to cellular life required the coevolution of the RNA world, capable of synthesizing specific, instead of statistical proteins, and of the Lipid world, with a transition from micellar aggregates to semipermeable vesicles. Small molecules available in the prebiotic inventory might promote RNA stability and the evolution of hydrophobic micellar aggregates into membrane-delimited vesicles. The transition from ribozymes catalyzing the assembly of statistical polypeptides to the synthesis of proteins, required the appearance of the genetic code; the transition from hydrophobic platforms favoring the stability of ribozymes and of nascent polypeptides to the selective transport of reagents through a membrane, required the appearance of the signal transduction code.A further integration between the RNA and Lipid worlds can be advanced, taking into account the emerging roles of phospholipid aggregates not only in ensuring stability to ribozymes by compartmentalization, but also in a crucial step of evolution through natural selection mechanisms, based on signal transduction pathways that convert environmental changes into biochemical responses that could vary according to the context. Here I present evidences on the presence of traces of the evolution of a signal transduction system in extant cells, which utilize a phosphoinositide signaling system located both at nucleoplasmic level as well as at the plasma membrane, based on the very same molecules but responding to different rules. The model herewith proposed is based on the following assumptions on the biomolecules of extant organisms: i) amphiphils can be converted into structured aggregates by hydrophobic forces thus giving rise to functional platforms for the interaction of other biomolecules and to their compartmentalization; ii) fundamental biochemical pathways, including protein synthesis, can be sustained by natural ribozymes of ancient origin; iii) ribozymes and nucleotide-derived coenzymes could have existed long before protein enzymes emerged; iv) signaling molecules, both derived from phospholipids and from RNAs could have guided the evolution of complex metabolic processes before the emergence of proteins.
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Affiliation(s)
- Nadir M Maraldi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy
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67
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Lopez A, Fiore M. Investigating Prebiotic Protocells for A Comprehensive Understanding of the Origins of Life: A Prebiotic Systems Chemistry Perspective. Life (Basel) 2019; 9:E49. [PMID: 31181679 PMCID: PMC6616946 DOI: 10.3390/life9020049] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/21/2019] [Accepted: 06/06/2019] [Indexed: 01/06/2023] Open
Abstract
Protocells are supramolecular systems commonly used for numerous applications, such as the formation of self-evolvable systems, in systems chemistry and synthetic biology. Certain types of protocells imitate plausible prebiotic compartments, such as giant vesicles, that are formed with the hydration of thin films of amphiphiles. These constructs can be studied to address the emergence of life from a non-living chemical network. They are useful tools since they offer the possibility to understand the mechanisms underlying any living cellular system: Its formation, its metabolism, its replication and its evolution. Protocells allow the investigation of the synergies occurring in a web of chemical compounds. This cooperation can explain the transition between chemical (inanimate) and biological systems (living) due to the discoveries of emerging properties. The aim of this review is to provide an overview of relevant concept in prebiotic protocell research.
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Affiliation(s)
- Augustin Lopez
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Université de Lyon, Claude Bernard Lyon 1, 1 Rue Victor Grignard, Bâtiment Lederer, 69622 Villeurbanne CEDEX, France.
- Master de Biologie, École Normale Supérieure de Lyon, Université Claude Bernard Lyon I, Université de Lyon, 69342 Lyon CEDEX 07, France.
| | - Michele Fiore
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Université de Lyon, Claude Bernard Lyon 1, 1 Rue Victor Grignard, Bâtiment Lederer, 69622 Villeurbanne CEDEX, France.
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68
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Sweatman MB, Lue L. The Giant SALR Cluster Fluid: A Review. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201900025] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Martin B. Sweatman
- School of EngineeringUniversity of EdinburghMayfield Road Edinburgh EH9 3JL UK
| | - Leo Lue
- Department of Chemical and Process EngineeringUniversity of StrathclydeJames Weir Building, 75 Montrose Street Glasgow G1 1XJ UK
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69
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Jing H, Lin Y, Chang H, Bai Q, Liang D. Mass Transport in Coacervate-Based Protocell Coated with Fatty Acid under Nonequilibrium Conditions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:5587-5593. [PMID: 30942596 DOI: 10.1021/acs.langmuir.9b00470] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Construction of protocell models from prebiotically plausible components to mimic the basic features or functions of living cells is still a challenge. In this work, we prepare a hybrid protocell model by coating sodium oleate on the coacervate droplet constituted by poly(l-lysine) and oligonucleotide and investigate the transport of different molecules under electric field. Results show that sodium oleate forms a layered viscoelastic membrane on the droplet surface, which is selectively permeable to small, polar molecules, such as oligolysine. As the droplet is stimulated at 10 V cm-1, the oleate membrane slips along the direction of electric field while maintaining its integrity. Most of the molecules are still excluded under such conditions. As repetitive cycles of vacuolization occur at 20 V cm-1, all molecules are internalized and sequestrated in the droplet through their specific pathways except enzyme, which anchors in the oleate membrane and is immune to electric field. Cascade enzymatic reactions are then carried out, and the product generated from the membrane exhibits a time-dependent concentration gradient across the droplet. Our work makes a step toward the nonequilibrium functionalization of synthetic protocells capable of biomimetic operations.
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Affiliation(s)
- Hairong Jing
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Polymer Chemistry and Physics, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China
| | - Ya'nan Lin
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Polymer Chemistry and Physics, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China
| | - Haojing Chang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Polymer Chemistry and Physics, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China
| | - Qingwen Bai
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Polymer Chemistry and Physics, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China
| | - Dehai Liang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Polymer Chemistry and Physics, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China
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70
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Paleos CM. Organization and Compartmentalization by Lipid Membranes Promote Reactions Related to the Origin of Cellular Life. ASTROBIOLOGY 2019; 19:547-552. [PMID: 30431329 DOI: 10.1089/ast.2018.1832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Liquid crystals have certain physical properties that promote chemical reactions which cannot occur in bulk phase media. These properties are displayed, among other molecules, by amphiphilic compounds which assemble into membrane structures then concentrate and organize biologically relevant monomers within their confined spaces. When mixtures of lipids and nucleotides are cycled multiple times between hydrated and anhydrous conditions, the monomers polymerize in the dry phase into oligonucleotides. Upon rehydration, mixtures of the polymers are encapsulated in lipid-bounded compartments called protocells. Reactions in liquid crystalline organizing matrices represent a promising approach for future research on how primitive cells could emerge on the early Earth and other habitable planets.
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71
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Otrin L, Kleineberg C, Caire da Silva L, Landfester K, Ivanov I, Wang M, Bednarz C, Sundmacher K, Vidaković-Koch T. Artificial Organelles for Energy Regeneration. ACTA ACUST UNITED AC 2019; 3:e1800323. [PMID: 32648709 DOI: 10.1002/adbi.201800323] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 02/11/2019] [Indexed: 01/03/2023]
Abstract
One of the critical steps in sustaining life-mimicking processes in synthetic cells is energy, i.e., adenosine triphosphate (ATP) regeneration. Previous studies have shown that the simple addition of ATP or ATP regeneration systems, which do not regenerate ATP directly from ADP and Pi , have no or only limited success due to accumulation of ATP hydrolysis products. In general, ATP regeneration can be achieved by converting light or chemical energy into ATP, which may also involve redox transformations of cofactors. The present contribution provides an overview of the existing ATP regeneration strategies and the related nicotinamide adenine dinucleotide (NAD+ ) redox cycling, with a focus on compartmentalized systems. Special attention is being paid to those approaches where so-called artificial organelles are developed. They comprise a semipermeable membrane functionalized by biological or man-made components and employ external energy in the form of light or nutrients in order to generate a transmembrane proton gradient, which is further utilized for ATP synthesis.
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Affiliation(s)
- Lado Otrin
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany
| | - Christin Kleineberg
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany
| | - Lucas Caire da Silva
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Katharina Landfester
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Ivan Ivanov
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany
| | - Minhui Wang
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany
| | - Claudia Bednarz
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany
| | - Kai Sundmacher
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany
| | - Tanja Vidaković-Koch
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany
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Cebecauer M, Amaro M, Jurkiewicz P, Sarmento MJ, Šachl R, Cwiklik L, Hof M. Membrane Lipid Nanodomains. Chem Rev 2018; 118:11259-11297. [PMID: 30362705 DOI: 10.1021/acs.chemrev.8b00322] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Lipid membranes can spontaneously organize their components into domains of different sizes and properties. The organization of membrane lipids into nanodomains might potentially play a role in vital functions of cells and organisms. Model membranes represent attractive systems to study lipid nanodomains, which cannot be directly addressed in living cells with the currently available methods. This review summarizes the knowledge on lipid nanodomains in model membranes and exposes how their specific character contrasts with large-scale phase separation. The overview on lipid nanodomains in membranes composed of diverse lipids (e.g., zwitterionic and anionic glycerophospholipids, ceramides, glycosphingolipids) and cholesterol aims to evidence the impact of chemical, electrostatic, and geometric properties of lipids on nanodomain formation. Furthermore, the effects of curvature, asymmetry, and ions on membrane nanodomains are shown to be highly relevant aspects that may also modulate lipid nanodomains in cellular membranes. Potential mechanisms responsible for the formation and dynamics of nanodomains are discussed with support from available theories and computational studies. A brief description of current fluorescence techniques and analytical tools that enabled progress in lipid nanodomain studies is also included. Further directions are proposed to successfully extend this research to cells.
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Affiliation(s)
- Marek Cebecauer
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Dolejškova 3 , 18223 Prague 8 , Czech Republic
| | - Mariana Amaro
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Dolejškova 3 , 18223 Prague 8 , Czech Republic
| | - Piotr Jurkiewicz
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Dolejškova 3 , 18223 Prague 8 , Czech Republic
| | - Maria João Sarmento
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Dolejškova 3 , 18223 Prague 8 , Czech Republic
| | - Radek Šachl
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Dolejškova 3 , 18223 Prague 8 , Czech Republic
| | - Lukasz Cwiklik
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Dolejškova 3 , 18223 Prague 8 , Czech Republic
| | - Martin Hof
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences , Dolejškova 3 , 18223 Prague 8 , Czech Republic
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73
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Serrano-Luginbühl S, Ruiz-Mirazo K, Ostaszewski R, Gallou F, Walde P. Soft and dispersed interface-rich aqueous systems that promote and guide chemical reactions. Nat Rev Chem 2018. [DOI: 10.1038/s41570-018-0042-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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74
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Abstract
Background This essay highlights critical aspects of the plausibility of pre-Darwinian evolution. It is based on a critical review of some better-known open, far-from-equilibrium system-based scenarios supposed to explain processes that took place before Darwinian evolution had emerged and that resulted in the origin of the first systems capable of Darwinian evolution. The researchers’ responses to eight crucial questions are reviewed. The majority of the researchers claim that there would have been an evolutionary continuity between chemistry and “biology”. A key question is how did this evolution begin before Darwinian evolution had begun? In other words the question is whether pre-Darwinian evolution is plausible. Results Strengths and weaknesses of the reviewed scenarios are presented. They are distinguished between metabolism-first, replicator-first and combined metabolism-replicator models. The metabolism-first scenarios show major issues, the worst concerns heredity and chirality. Although the replicator-first scenarios answer the heredity question they have their own problems, notably chirality. Among the reviewed combined metabolism-replicator models, one shows the fewest issues. In particular, it seems to answer the chiral question, and eventually implies Darwinian evolution from the very beginning. Its main hypothesis needs to be validated with experimental data. Conclusion From this critical review it is that the concept of “pre-Darwinian evolution” appears questionable, in particular because it is unlikely if not impossible that any evolution in complexity over time may work without multiplication and heritability allowing the emergence of genetically and ecologically diverse lineages on which natural selection may operate. Only Darwinian evolution could have led to such an evolution. Thus, Pre-Darwinian evolution is not plausible according to the author. Surely, the answer to the question posed in the title is a prerequisite to the understanding of the origin of Darwinian evolution. Reviewers This article was reviewed by Purificacion Lopez-Garcia, Anthony Poole, Doron Lancet, and Thomas Dandekar.
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75
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Mizuuchi R, Ichihashi N. Sustainable replication and coevolution of cooperative RNAs in an artificial cell-like system. Nat Ecol Evol 2018; 2:1654-1660. [PMID: 30150742 DOI: 10.1038/s41559-018-0650-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 07/04/2018] [Indexed: 11/09/2022]
Abstract
Cooperation among independently replicating molecules is a key phenomenon that allowed the development of complexity during the early evolution of life. Generally, this process is vulnerable to parasitic or selfish entities, which can easily appear and destroy such cooperation. It remains unclear how this fragile cooperation process appeared and has been sustained through evolution. Theoretical studies have indicated that spatial structures, such as compartments, allow sustainable replication and the evolution of cooperative replication, although this has yet to be confirmed experimentally. In this study, we constructed a molecular cooperative replication system, in which two types of RNA, encoding replication or metabolic enzymes, cooperate for their replication in compartments, and we performed long-term replication experiments to examine the sustainability and evolution of the RNAs. We demonstrate that the cooperative relationship of the two RNAs could be sustained at a certain range of RNA concentrations, even when parasitic RNA appeared in the system. We also found that more efficient cooperative RNA replication evolved during long-term replication through seemingly selfish evolution of each RNA. Our results provide experimental evidence supporting the sustainability and robustness of molecular cooperation on an evolutionary timescale.
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Affiliation(s)
- Ryo Mizuuchi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Norikazu Ichihashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan. .,Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
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76
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Komáromy D, Tezcan M, Schaeffer G, Marić I, Otto S. Effector-Triggered Self-Replication in Coupled Subsystems. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707191] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Dávid Komáromy
- Centre for Systems Chemistry; Stratingh Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Meniz Tezcan
- Centre for Systems Chemistry; Stratingh Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Gaël Schaeffer
- Centre for Systems Chemistry; Stratingh Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Ivana Marić
- Centre for Systems Chemistry; Stratingh Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry; Stratingh Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
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77
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Komáromy D, Tezcan M, Schaeffer G, Marić I, Otto S. Effector-Triggered Self-Replication in Coupled Subsystems. Angew Chem Int Ed Engl 2017; 56:14658-14662. [DOI: 10.1002/anie.201707191] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Dávid Komáromy
- Centre for Systems Chemistry; Stratingh Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Meniz Tezcan
- Centre for Systems Chemistry; Stratingh Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Gaël Schaeffer
- Centre for Systems Chemistry; Stratingh Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Ivana Marić
- Centre for Systems Chemistry; Stratingh Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry; Stratingh Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
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78
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Hanczyc MM, Monnard PA. Primordial membranes: more than simple container boundaries. Curr Opin Chem Biol 2017; 40:78-86. [DOI: 10.1016/j.cbpa.2017.07.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 06/19/2017] [Accepted: 07/20/2017] [Indexed: 01/14/2023]
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79
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Kee TP, Monnard PA. Chemical systems, chemical contiguity and the emergence of life. Beilstein J Org Chem 2017; 13:1551-1563. [PMID: 28904604 PMCID: PMC5564265 DOI: 10.3762/bjoc.13.155] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 07/11/2017] [Indexed: 12/17/2022] Open
Abstract
Charting the emergence of living cells from inanimate matter remains an intensely challenging scientific problem. The complexity of the biochemical machinery of cells with its exquisite intricacies hints at cells being the product of a long evolutionary process. Research on the emergence of life has long been focusing on specific, well-defined problems related to one aspect of cellular make-up, such as the formation of membranes or the build-up of information/catalytic apparatus. This approach is being gradually replaced by a more "systemic" approach that privileges processes inherent to complex chemical systems over specific isolated functional apparatuses. We will summarize the recent advances in system chemistry and show that chemical systems in the geochemical context imply a form of chemical contiguity in the syntheses of the various molecules that precede modern biomolecules.
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Affiliation(s)
- Terrence P Kee
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | - Pierre-Alain Monnard
- Institute of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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80
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Rapf RJ, Perkins RJ, Yang H, Miyake GM, Carpenter BK, Vaida V. Photochemical Synthesis of Oligomeric Amphiphiles from Alkyl Oxoacids in Aqueous Environments. J Am Chem Soc 2017; 139:6946-6959. [PMID: 28481114 PMCID: PMC5518611 DOI: 10.1021/jacs.7b01707] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The aqueous phase photochemistry of a series of amphiphilic α-keto acids with differing linear alkyl chain lengths was investigated, demonstrating the ability of sunlight-initiated reactions to build molecular complexity under environmentally relevant conditions. We show that the photochemical reaction mechanisms for α-keto acids in aqueous solution are robust and generalizable across alkyl chain lengths. The organic radicals generated during photolysis are indiscriminate, leading to a large mixture of photoproducts that are observed using high-resolution electrospray ionization mass spectrometry, but these products are identifiable following literature photochemical mechanisms. The alkyl oxoacids under study here can undergo a Norrish Type II reaction to generate pyruvic acid, increasing the diversity of observed photoproducts. The major products of this photochemistry are covalently bonded dimers and trimers of the starting oxoacids, many of which are multi-tailed lipids. The properties of these oligomers are discussed, including their spontaneous self-assembly into aggregates.
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Affiliation(s)
- Rebecca J. Rapf
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Russell J. Perkins
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Haishen Yang
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Garret M. Miyake
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
- Materials Science and Engineering Program, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Barry K. Carpenter
- School of Chemistry and the Physical Organic Chemistry Centre, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Veronica Vaida
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
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81
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Luginbühl S, Iwasaki F, Chirackal Varkey E, Umakoshi H, Walde P. A Novel Role of Vesicles as Templates for the Oxidation and Oligomerization of p-Aminodiphenylamine by Cytochrome c. Helv Chim Acta 2017. [DOI: 10.1002/hlca.201700027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sandra Luginbühl
- Polymer Chemistry Group; Department of Materials (D-MATL); ETH Zürich; Vladimir Prelog-Weg 5 CH-8093 Zürich
| | - Fumihiko Iwasaki
- Polymer Chemistry Group; Department of Materials (D-MATL); ETH Zürich; Vladimir Prelog-Weg 5 CH-8093 Zürich
- Bio-Inspired Chemical Engineering Lab; Division of Chemical Engineering; Graduate School of Engineering Science; Osaka University; 1-3 Machikaneyamacho Toyonaka Osaka 560-8531 Japan
| | - Elizabeth Chirackal Varkey
- Polymer Chemistry Group; Department of Materials (D-MATL); ETH Zürich; Vladimir Prelog-Weg 5 CH-8093 Zürich
| | - Hiroshi Umakoshi
- Bio-Inspired Chemical Engineering Lab; Division of Chemical Engineering; Graduate School of Engineering Science; Osaka University; 1-3 Machikaneyamacho Toyonaka Osaka 560-8531 Japan
| | - Peter Walde
- Polymer Chemistry Group; Department of Materials (D-MATL); ETH Zürich; Vladimir Prelog-Weg 5 CH-8093 Zürich
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82
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Deamer D. The Role of Lipid Membranes in Life's Origin. Life (Basel) 2017; 7:life7010005. [PMID: 28106741 PMCID: PMC5370405 DOI: 10.3390/life7010005] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 01/06/2017] [Accepted: 01/09/2017] [Indexed: 01/23/2023] Open
Abstract
At some point in early evolution, life became cellular. Assuming that this step was required for the origin of life, there would necessarily be a pre-existing source of amphihilic compounds capable of assembling into membranous compartments. It is possible to make informed guesses about the properties of such compounds and the conditions most conducive to their self-assembly into boundary structures. The membranes were likely to incorporate mixtures of hydrocarbon derivatives between 10 and 20 carbons in length with carboxylate or hydroxyl head groups. Such compounds can be synthesized by chemical reactions and small amounts were almost certainly present in the prebiotic environment. Membrane assembly occurs most readily in low ionic strength solutions with minimal content of salt and divalent cations, which suggests that cellular life began in fresh water pools associated with volcanic islands rather than submarine hydrothermal vents.
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Affiliation(s)
- David Deamer
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95060, USA.
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83
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Abstract
A series of exciting phenomena that can occur in supramolecular systems away from equilibrium are reviewed.
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Affiliation(s)
- Gonen Ashkenasy
- Department of Chemistry
- Ben-Gurion University of the Negev
- Beer Sheva
- Israel
| | | | - Sijbren Otto
- Centre for Systems Chemistry
- Stratingh Institute
- University of Groningen
- 9747 AG Groningen
- The Netherlands
| | - Annette F. Taylor
- Chemical and Biological Engineering
- University of Sheffield
- Sheffield S1 3JD
- UK
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84
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Deamer D. Membranes and the Origin of Life: A Century of Conjecture. J Mol Evol 2016; 83:159-168. [PMID: 27913841 DOI: 10.1007/s00239-016-9770-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 11/19/2016] [Indexed: 11/29/2022]
Abstract
Cells are the units of all life today, and are defined by their membranous boundaries. The membranes have multiple functions; the most obvious being that, in the absence of a boundary, the systems of functional macromolecular components of the cytosol would spill into the environment and disperse. Membranes also contain the pigments essential for photosynthesis, electron transport enzymes that pump and maintain proton gradients, the ATP synthase that uses proton gradients to produce energy for the cell, and enzymes that use ATP to maintain ion gradients essential for life. But what about the function of membranes in the first forms of cellular life? Could life have begun in the absence of membranous boundaries? In order to answer that question, this review presents a history of the key research observations that began over a century ago.
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Affiliation(s)
- David Deamer
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA.
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85
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Vieregg JR, Tang TYD. Polynucleotides in cellular mimics: Coacervates and lipid vesicles. Curr Opin Colloid Interface Sci 2016. [DOI: 10.1016/j.cocis.2016.09.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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86
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Taming Prebiotic Chemistry: The Role of Heterogeneous and Interfacial Catalysis in the Emergence of a Prebiotic Catalytic/Information Polymer System. Life (Basel) 2016; 6:life6040040. [PMID: 27827919 PMCID: PMC5198075 DOI: 10.3390/life6040040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/31/2016] [Accepted: 11/01/2016] [Indexed: 01/10/2023] Open
Abstract
Cellular life is based on interacting polymer networks that serve as catalysts, genetic information and structural molecules. The complexity of the DNA, RNA and protein biochemistry suggests that it must have been preceded by simpler systems. The RNA world hypothesis proposes RNA as the prime candidate for such a primal system. Even though this proposition has gained currency, its investigations have highlighted several challenges with respect to bulk aqueous media: (1) the synthesis of RNA monomers is difficult; (2) efficient pathways for monomer polymerization into functional RNAs and their subsequent, sequence-specific replication remain elusive; and (3) the evolution of the RNA function towards cellular metabolism in isolation is questionable in view of the chemical mixtures expected on the early Earth. This review will address the question of the possible roles of heterogeneous media and catalysis as drivers for the emergence of RNA-based polymer networks. We will show that this approach to non-enzymatic polymerizations of RNA from monomers and RNA evolution cannot only solve some issues encountered during reactions in bulk aqueous solutions, but may also explain the co-emergence of the various polymers indispensable for life in complex mixtures and their organization into primitive networks.
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87
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Blocher WC, Perry SL. Complex coacervate-based materials for biomedicine. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2016; 9. [DOI: 10.1002/wnan.1442] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/10/2016] [Accepted: 10/02/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Whitney C. Blocher
- Department of Chemical Engineering; University of Massachusetts Amherst; Amherst MA USA
| | - Sarah L. Perry
- Department of Chemical Engineering; University of Massachusetts Amherst; Amherst MA USA
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88
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Solé R. Synthetic transitions: towards a new synthesis. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150438. [PMID: 27431516 PMCID: PMC4958932 DOI: 10.1098/rstb.2015.0438] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2016] [Indexed: 12/17/2022] Open
Abstract
The evolution of life in our biosphere has been marked by several major innovations. Such major complexity shifts include the origin of cells, genetic codes or multicellularity to the emergence of non-genetic information, language or even consciousness. Understanding the nature and conditions for their rise and success is a major challenge for evolutionary biology. Along with data analysis, phylogenetic studies and dedicated experimental work, theoretical and computational studies are an essential part of this exploration. With the rise of synthetic biology, evolutionary robotics, artificial life and advanced simulations, novel perspectives to these problems have led to a rather interesting scenario, where not only the major transitions can be studied or even reproduced, but even new ones might be potentially identified. In both cases, transitions can be understood in terms of phase transitions, as defined in physics. Such mapping (if correct) would help in defining a general framework to establish a theory of major transitions, both natural and artificial. Here, we review some advances made at the crossroads between statistical physics, artificial life, synthetic biology and evolutionary robotics.This article is part of the themed issue 'The major synthetic evolutionary transitions'.
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Affiliation(s)
- Ricard Solé
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain Institut de Biologia Evolutiva, CSIC-UPF, Pg Maritim de la Barceloneta 37, 08003 Barcelona, Spain Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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89
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Black RA, Blosser MC. A Self-Assembled Aggregate Composed of a Fatty Acid Membrane and the Building Blocks of Biological Polymers Provides a First Step in the Emergence of Protocells. Life (Basel) 2016; 6:E33. [PMID: 27529283 PMCID: PMC5041009 DOI: 10.3390/life6030033] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/02/2016] [Accepted: 08/09/2016] [Indexed: 02/01/2023] Open
Abstract
We propose that the first step in the origin of cellular life on Earth was the self-assembly of fatty acids with the building blocks of RNA and protein, resulting in a stable aggregate. This scheme provides explanations for the selection and concentration of the prebiotic components of cells; the stabilization and growth of early membranes; the catalysis of biopolymer synthesis; and the co-localization of membranes, RNA and protein. In this article, we review the evidence and rationale for the formation of the proposed aggregate: (i) the well-established phenomenon of self-assembly of fatty acids to form vesicles; (ii) our published evidence that nucleobases and sugars bind to and stabilize such vesicles; and (iii) the reasons why amino acids likely do so as well. We then explain how the conformational constraints and altered chemical environment due to binding of the components to the membrane could facilitate the formation of nucleosides, oligonucleotides and peptides. We conclude by discussing how the resulting oligomers, even if short and random, could have increased vesicle stability and growth more than their building blocks did, and how competition among these vesicles could have led to longer polymers with complex functions.
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Affiliation(s)
- Roy A Black
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
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90
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Ichihashi N, Yomo T. Constructive Approaches for Understanding the Origin of Self-Replication and Evolution. Life (Basel) 2016; 6:life6030026. [PMID: 27420098 PMCID: PMC5041002 DOI: 10.3390/life6030026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/07/2016] [Accepted: 07/07/2016] [Indexed: 11/16/2022] Open
Abstract
The mystery of the origin of life can be divided into two parts. The first part is the origin of biomolecules: under what physicochemical conditions did biomolecules such as amino acids, nucleotides, and their polymers arise? The second part of the mystery is the origin of life-specific functions such as the replication of genetic information, the reproduction of cellular structures, metabolism, and evolution. These functions require the coordination of many different kinds of biological molecules. A direct strategy to approach the second part of the mystery is the constructive approach, in which life-specific functions are recreated in a test tube from specific biological molecules. Using this approach, we are able to employ design principles to reproduce life-specific functions, and the knowledge gained through the reproduction process provides clues as to their origins. In this mini-review, we introduce recent insights gained using this approach, and propose important future directions for advancing our understanding of the origins of life.
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Affiliation(s)
- Norikazu Ichihashi
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Tetsuya Yomo
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
- Graduate School of Frontier Biosciences, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
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91
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Frankel EA, Bevilacqua PC, Keating CD. Polyamine/Nucleotide Coacervates Provide Strong Compartmentalization of Mg²⁺, Nucleotides, and RNA. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:2041-9. [PMID: 26844692 DOI: 10.1021/acs.langmuir.5b04462] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Phase separation of aqueous solutions containing polyelectrolytes can lead to formation of dense, solute-rich liquid droplets referred to as coacervates, surrounded by a dilute continuous phase of much larger volume. This type of liquid-liquid phase separation is thought to help explain the appearance of polyelectrolyte-rich intracellular droplets in the cytoplasm and nucleoplasm of extant biological cells and may be relevant to protocellular compartmentalization of nucleic acids on the early Earth. Here we describe complex coacervates formed upon mixing the polycation poly(allylamine) (PAH, 15 kDa) with the anionic nucleotides adenosine 5'-mono-, di-, and triphosphate (AMP, ADP, and ATP). Droplet formation was observed over a wide range of pH and MgCl2 concentrations. The nucleotides themselves as well as Mg(2+) and RNA oligonucleotides were all extremely concentrated within the coacervates. Nucleotides present at just 2.5 mM in bulk solution had concentrations greater than 1 M inside the coacervate droplets. A solution with a total Mg(2+) concentration of 10 mM had 1-5 M Mg(2+) in the coacervates, and RNA random sequence (N54) partitioned ∼10,000-fold into the coacervates. Coacervate droplets are thus rich in nucleotides, Mg(2+), and RNA, providing a medium favorable for generating functional RNAs. Compartmentalization of nucleotides at high concentrations could have facilitated their polymerization to form oligonucleotides, which preferentially accumulate in the droplets. Locally high Mg(2+) concentrations could have aided folding and catalysis in an RNA world, making coacervate droplets an appealing platform for exploring protocellular environments.
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Affiliation(s)
- Erica A Frankel
- Department of Chemistry, ‡Center for RNA Molecular Biology, and §Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Philip C Bevilacqua
- Department of Chemistry, ‡Center for RNA Molecular Biology, and §Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Christine D Keating
- Department of Chemistry, ‡Center for RNA Molecular Biology, and §Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
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92
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Yin Y, Niu L, Zhu X, Zhao M, Zhang Z, Mann S, Liang D. Non-equilibrium behaviour in coacervate-based protocells under electric-field-induced excitation. Nat Commun 2016; 7:10658. [PMID: 26876162 PMCID: PMC4756681 DOI: 10.1038/ncomms10658] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 01/11/2016] [Indexed: 12/17/2022] Open
Abstract
Although numerous strategies are now available to generate rudimentary forms of synthetic cell-like entities, minimal progress has been made in the sustained excitation of artificial protocells under non-equilibrium conditions. Here we demonstrate that the electric field energization of coacervate microdroplets comprising polylysine and short single strands of DNA generates membrane-free protocells with complex, dynamical behaviours. By confining the droplets within a microfluidic channel and applying a range of electric field strengths, we produce protocells that exhibit repetitive cycles of vacuolarization, dynamical fluctuations in size and shape, chaotic growth and fusion, spontaneous ejection and sequestration of matter, directional capture of solute molecules, and pulsed enhancement of enzyme cascade reactions. Our results highlight new opportunities for the study of non-equilibrium phenomena in synthetic protocells, provide a strategy for inducing complex behaviour in electrostatically assembled soft matter microsystems and illustrate how dynamical properties can be activated and sustained in microcompartmentalized media.
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Affiliation(s)
- Yudan Yin
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Polymer Chemistry and Physics, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Lin Niu
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Polymer Chemistry and Physics, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiaocui Zhu
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zexin Zhang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
| | - Stephen Mann
- Centre for Protolife Research, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - Dehai Liang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Polymer Chemistry and Physics, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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93
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Giorgio G, Colafemmina G, Mavelli F, Murgia S, Palazzo G. The impact of alkanes on the structure of Triton X100 micelles. RSC Adv 2016. [DOI: 10.1039/c5ra21691e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Here we investigate the structural evolution of TX100 micelles upon loading with several linear and cyclic alkanes by DLS, PGSE-NMR, 2D NOESY NMR, viscosity measurements, and molecular dynamic simulations.
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Affiliation(s)
- G. Giorgio
- Department of Chemistry
- University of Bari “Aldo Moro”
- 70126 Bari
- Italy
| | - G. Colafemmina
- Department of Chemistry
- University of Bari “Aldo Moro”
- 70126 Bari
- Italy
- Consorzio Interuniversitario Sistemi a Grande Interfase
| | - F. Mavelli
- Department of Chemistry
- University of Bari “Aldo Moro”
- 70126 Bari
- Italy
- Consorzio Interuniversitario Sistemi a Grande Interfase
| | - S. Murgia
- Department of Chemical & Geological Sciences
- University of Cagliari
- I-09042 Monserrato
- Italy
- Consorzio Interuniversitario Sistemi a Grande Interfase
| | - G. Palazzo
- Department of Chemistry
- University of Bari “Aldo Moro”
- 70126 Bari
- Italy
- Consorzio Interuniversitario Sistemi a Grande Interfase
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