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Kahana A, Lancet D. Self-reproducing catalytic micelles as nanoscopic protocell precursors. Nat Rev Chem 2021; 5:870-878. [PMID: 37117387 DOI: 10.1038/s41570-021-00329-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2021] [Indexed: 12/31/2022]
Abstract
Protocells at life's origin are often conceived as bilayer-enclosed precursors of life, whose self-reproduction rests on the early advent of replicating catalytic biopolymers. This Perspective describes an alternative scenario, wherein reproducing nanoscopic lipid micelles with catalytic capabilities were forerunners of biopolymer-containing protocells. This postulate gains considerable support from experiments describing micellar catalysis and autocatalytic proliferation, and, more recently, from reports on cross-catalysis in mixed micelles that lead to life-like steady-state dynamics. Such results, along with evidence for micellar prebiotic compatibility, synergize with predictions of our chemically stringent computer-simulated model, illustrating how mutually catalytic lipid networks may enable micellar compositional reproduction that could underlie primal selection and evolution. Finally, we highlight studies on how endogenously catalysed lipid modifications could guide further protocellular complexification, including micelle to vesicle transition and monomer to biopolymer progression. These portrayals substantiate the possibility that protocellular evolution could have been seeded by pre-RNA lipid assemblies.
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Walde P, Umakoshi H, Stano P, Mavelli F. Emergent properties arising from the assembly of amphiphiles. Artificial vesicle membranes as reaction promoters and regulators. Chem Commun (Camb) 2015; 50:10177-97. [PMID: 24921467 DOI: 10.1039/c4cc02812k] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This article deals with artificial vesicles and their membranes as reaction promoters and regulators. Among the various molecular assemblies which can form in an aqueous medium from amphiphilic molecules, vesicle systems are unique. Vesicles compartmentalize the aqueous solution in which they exist, independent on whether the vesicles are biological vesicles (existing in living systems) or whether they are artificial vesicles (formed in vitro from natural or synthetic amphiphiles). After the formation of artificial vesicles, their aqueous interior (the endovesicular volume) may become - or may be made - chemically different from the external medium (the exovesicular solution), depending on how the vesicles are prepared. The existence of differences between endo- and exovesicular composition is one of the features on the basis of which biological vesicles contribute to the complex functioning of living organisms. Furthermore, artificial vesicles can be formed from mixtures of amphiphiles in such a way that the vesicle membranes become molecularly, compositionally and organizationally highly complex, similarly to the lipidic matrix of biological membranes. All the various properties of artificial vesicles as membranous compartment systems emerge from molecular assembly as these properties are not present in the individual molecules the system is composed of. One particular emergent property of vesicle membranes is their possible functioning as promoters and regulators of chemical reactions caused by the localization of reaction components, and possibly catalysts, within or on the surface of the membranes. This specific feature is reviewed and highlighted with a few selected examples which range from the promotion of decarboxylation reactions, the selective binding of DNA or RNA to suitable vesicle membranes, and the reactivation of fragmented enzymes to the regulation of the enzymatic synthesis of polymers. Such type of emergent properties of vesicle membranes may have been important for the prebiological evolution of protocells, the hypothetical compartment systems preceding the first cells in those chemical and physico-chemical processes that led to the origin of life.
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Affiliation(s)
- Peter Walde
- Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, CH-8093 Zürich, Switzerland.
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Attwater J, Wochner A, Holliger P. In-ice evolution of RNA polymerase ribozyme activity. Nat Chem 2013; 5:1011-8. [PMID: 24256864 DOI: 10.1038/nchem.1781] [Citation(s) in RCA: 170] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 09/10/2013] [Indexed: 01/13/2023]
Abstract
Mechanisms of molecular self-replication have the potential to shed light on the origins of life. In particular, self-replication through RNA-catalysed templated RNA synthesis is thought to have supported a primordial 'RNA world'. However, existing polymerase ribozymes lack the capacity to synthesize RNAs approaching their own size. Here, we report the in vitro evolution of such catalysts directly in the RNA-stabilizing medium of water ice, which yielded RNA polymerase ribozymes specifically adapted to sub-zero temperatures and able to synthesize RNA in ices at temperatures as low as -19 °C. The combination of cold-adaptive mutations with a previously described 5' extension operating at ambient temperatures enabled the design of a first polymerase ribozyme capable of catalysing the accurate synthesis of an RNA sequence longer than itself (adding up to 206 nucleotides), an important stepping stone towards RNA self-replication.
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Affiliation(s)
- James Attwater
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
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Attwater J, Tagami S, Kimoto M, Butler K, Kool ET, Wengel J, Herdewijn P, Hirao I, Holliger P. Chemical fidelity of an RNA polymerase ribozyme. Chem Sci 2013. [DOI: 10.1039/c3sc50574j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Stano P, Rampioni G, Carrara P, Damiano L, Leoni L, Luisi PL. Semi-synthetic minimal cells as a tool for biochemical ICT. Biosystems 2012; 109:24-34. [DOI: 10.1016/j.biosystems.2012.01.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2011] [Accepted: 01/04/2012] [Indexed: 11/25/2022]
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Zhao G, Li Y, Wang J, Zhu H. Reversible immobilization of glucoamylase onto magnetic carbon nanotubes functionalized with dendrimer. Appl Microbiol Biotechnol 2011; 91:591-601. [DOI: 10.1007/s00253-011-3299-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2011] [Revised: 03/12/2011] [Accepted: 03/31/2011] [Indexed: 10/18/2022]
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Astrochemistry and the origin of genetic material. RENDICONTI LINCEI-SCIENZE FISICHE E NATURALI 2011. [DOI: 10.1007/s12210-011-0118-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Maurer SE, DeClue MS, Albertsen AN, Dörr M, Kuiper DS, Ziock H, Rasmussen S, Boncella JM, Monnard PA. Interactions between catalysts and amphiphilic structures and their implications for a protocell model. Chemphyschem 2011; 12:828-35. [PMID: 21344602 DOI: 10.1002/cphc.201000843] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Indexed: 11/09/2022]
Abstract
One of the essential elements of any cell, including primitive ancestors, is a structural component that protects and confines the metabolism and genes while allowing access to essential nutrients. For the targeted protocell model, bilayers of decanoic acid, a single-chain fatty acid amphiphile, are used as the container. These bilayers interact with a ruthenium-nucleobase complex, the metabolic complex, to convert amphiphile precursors into more amphiphiles. These interactions are dependent on non-covalent bonding. The initial rate of conversion of an oily precursor molecule into fatty acid was examined as a function of these interactions. It is shown that the precursor molecule associates strongly with decanoic acid structures. This results in a high dependence of conversion rates on the interaction of the catalyst with the self-assembled structures. The observed rate logically increases when a tight interaction between catalyst complex and container exists. A strong association between the metabolic complex and the container was achieved by bonding a sufficiently long hydrocarbon tail to the complex. Surprisingly, the rate enhancement was nearly as strong when the ruthenium and nucleobase elements of the complex were each given their own hydrocarbon tail and existed as separate molecules, as when the two elements were covalently bonded to each other and the resulting molecule was given a hydrocarbon tail. These results provide insights into the possibilities and constraints of such a reaction system in relation to building the ultimate protocell.
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Affiliation(s)
- Sarah E Maurer
- Center for Fundamental Living Technology, University of Southern Denmark, Campusvej 55, 5000 Odense C, Denmark
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Mathew DC, Luthey-Schulten Z. Influence of montmorillonite on nucleotide oligomerization reactions: a molecular dynamics study. ORIGINS LIFE EVOL B 2010; 40:303-17. [PMID: 20213159 DOI: 10.1007/s11084-010-9207-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2009] [Accepted: 12/28/2009] [Indexed: 02/04/2023]
Abstract
We investigate a proposed origins of life scenario involving the clay montmorillonite and its catalytic role in forming oligonucleotides from activated mononucleotides. Clay and mineral surfaces are important for concentrating the reactants and for promoting nucleotide polymerization reactions. Using classical molecular dynamics methods we provide atomic details of reactant conformations prior to polynucleotide formation, lending insight into previously reported experimental observations of this phenomenon. The simulations clarify the catalytic role of metal ions, demonstrate that reactions leading to correct linkages take place primarily in the interlayer, and explain the observed sequence selectivity in the elongation of the chain. The study comparing reaction probabilities involving L- and D-chiral forms of the reactants has found enhancement of homochiral over heterochiral products when catalyzed by montmorillonite.
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Affiliation(s)
- Damien C Mathew
- School of Chemical Sciences, University of Illinois, 600 S Mathews Ave., MC-712, Box 68-6, Urbana, IL 61801, USA.
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Briones C, Stich M, Manrubia SC. The dawn of the RNA World: toward functional complexity through ligation of random RNA oligomers. RNA (NEW YORK, N.Y.) 2009; 15:743-9. [PMID: 19318464 PMCID: PMC2673073 DOI: 10.1261/rna.1488609] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Accepted: 01/31/2009] [Indexed: 05/23/2023]
Abstract
A main unsolved problem in the RNA World scenario for the origin of life is how a template-dependent RNA polymerase ribozyme emerged from short RNA oligomers obtained by random polymerization on mineral surfaces. A number of computational studies have shown that the structural repertoire yielded by that process is dominated by topologically simple structures, notably hairpin-like ones. A fraction of these could display RNA ligase activity and catalyze the assembly of larger, eventually functional RNA molecules retaining their previous modular structure: molecular complexity increases but template replication is absent. This allows us to build up a stepwise model of ligation-based, modular evolution that could pave the way to the emergence of a ribozyme with RNA replicase activity, step at which information-driven Darwinian evolution would be triggered.
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Affiliation(s)
- Carlos Briones
- Centro de Astrobiología (CSIC-INTA), 28850 Torrejón de Ardoz, Madrid, Spain.
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Lee G, Kim J, Lee JH. Development of magnetically separable polyaniline nanofibers for enzyme immobilization and recovery. Enzyme Microb Technol 2008. [DOI: 10.1016/j.enzmictec.2007.12.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Monnard PA, Luptak A, Deamer DW. Models of primitive cellular life: polymerases and templates in liposomes. Philos Trans R Soc Lond B Biol Sci 2007; 362:1741-50. [PMID: 17472931 PMCID: PMC2442390 DOI: 10.1098/rstb.2007.2066] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Nutrient transport, polymerization and expression of genetic information in cellular compartments are hallmarks of all life today, and must have appeared at some point during the origin and early evolution of life. Because the first cellular life lacked membrane transport systems based on highly evolved proteins, they presumably depended on simpler processes of nutrient uptake. Using a system consisting of an RNA polymerase and DNA template entrapped in submicrometre-sized lipid vesicles (liposomes), we found that the liposome membrane could be made sufficiently permeable to allow access of ionized substrate molecules as large as nucleoside triphosphates (NTPs) to the enzyme. The encapsulated polymerase transcribed the template-specific base sequences of the DNA to the RNA that was synthesized. These experiments demonstrate that units of genetic information can be associated with a functional catalyst in a single compartment, and that transcription of gene-sized DNA fragments can be achieved by relying solely on passive diffusion to supply NTPs substrates.
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Affiliation(s)
- Pierre-Alain Monnard
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 94720, USA.
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Monnard PA. Question 5: does the RNA-world still retain its appeal after 40 years of research? ORIGINS LIFE EVOL B 2007; 37:387-90. [PMID: 17611815 DOI: 10.1007/s11084-007-9099-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2007] [Accepted: 05/03/2007] [Indexed: 11/27/2022]
Abstract
Forty years after its formulation, the hypothesis of the RNA-World remains rather controversial even though studies of RNA catalysis in cellular processes (for example, in the ubiquitous ribosomal peptide-bond formation) have clearly lent increased plausibility to the idea that an RNA-World existed at some point in the evolution leading to the emergence of cellular life. Indeed, several issues remain that weaken the concept: the synthesis of the RNA monomers under prebiotic conditions, their subsequent, efficient polymerization to yield ribozymes that specifically catalyze their own replication. This communication summarizes existing studies of the RNA polymerization from monomers. In our opinion, the recent developments show that given time plausible answers to some of the issues facing the RNA-World hypothesis will be found.
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Affiliation(s)
- Pierre-Alain Monnard
- Earth and Environmental Sciences EES-6, Los Alamos National Laboratory, Los Alamos, NM, USA.
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Hanczyc MM, Mansy SS, Szostak JW. Mineral surface directed membrane assembly. ORIGINS LIFE EVOL B 2007; 37:67-82. [PMID: 16909329 DOI: 10.1007/s11084-006-9018-5] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2006] [Accepted: 07/01/2006] [Indexed: 11/25/2022]
Abstract
The transition from non-living to living matter may have resulted from the self-organizing properties of organic molecules and their interactions with a chemically rich inorganic environment. We have shown that a solution containing RNA, fatty acids and clay produces structures that contain a potentially catalytic surface (clay) and a potential informational biopolymer (RNA) encapsulated within a membrane. This highlights the ability of mineral surfaces to bring together and organize key components of primordial life. We have extended our analysis of mineral-mediated vesicle catalysis to include other natural minerals and synthetic surfaces of varying shape, size, and charge density. Our results show that while RNA polymerization on minerals may be restricted to the surface environment provided by montmorillonite, vesicle formation is enhanced in the presence of disparate types of surfaces. A model is presented in which new sheets of amphiphiles form just proximal to a surface. Similar interactions between amphiphiles and minerals on early Earth may have resulted in the encapsulation of a diverse array of mineral particulates with catalytic properties.
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Affiliation(s)
- Martin M Hanczyc
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
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La Clair JJ. Cellular routines in the synthesis of cyclic peptide probes. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.01.113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Vlassov AV, Kazakov SA, Johnston BH, Landweber LF. The RNA World on Ice: A New Scenario for the Emergence of RNA Information. J Mol Evol 2005; 61:264-73. [PMID: 16044244 DOI: 10.1007/s00239-004-0362-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2004] [Accepted: 04/08/2005] [Indexed: 10/25/2022]
Abstract
The RNA world hypothesis refers to a hypothetical era prior to coded peptide synthesis, where RNA was the major structural, genetic, and catalytic agent. Though it is a widely accepted scenario, a number of vexing difficulties remain. In this review we focus on a missing link of the RNA world hypothesis-primitive miniribozymes, in particular ligases, and discuss the role of these molecules in the evolution of RNA size and complexity. We argue that prebiotic conditions associated with freezing, rather than "warm and wet" conditions, could have been of key importance in the early RNA world.
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