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Saha R, Poduval P, Baratam K, Nagesh J, Srivastava A. Membrane Catalyzed Formation of Nucleotide Clusters and Their Role in the Origins of Life: Insights from Molecular Simulations and Lattice Modeling. J Phys Chem B 2024; 128:3121-3132. [PMID: 38518175 DOI: 10.1021/acs.jpcb.3c08061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]
Abstract
One of the mysteries in studying the molecular "Origin of Life" is the emergence of RNA and RNA-based life forms, where nonenzymatic polymerization of nucleotides is a crucial hypothesis in formation of large RNA chains. The nonenzymatic polymerization can be mediated by various environmental settings, such as cycles of hydration and dehydration, temperature variations, and proximity to a variety of organizing matrices, such as clay, salt, fatty acids, lipid membrane, and mineral surface. In this work, we explore the influence of different phases of the lipid membrane toward nucleotide organization and polymerization in a simulated prebiotic setting. Our molecular simulations quantify the localization propensity of a mononucleotide, uridine monophosphate (UMP), in distinct membrane settings. We perform all-atom molecular dynamics (MD) simulations to estimate the role of the monophasic and biphasic membranes in modifying the behavior of UMPs localization and their clustering mechanism. Based on the interaction energy of mononucleotides with the membrane and their diffusion profile from our MD calculations, we developed a lattice-based model to explore the thermodynamic limits of the observations made from the MD simulations. The mathematical model substantiates our hypothesis that the lipid layers can act as unique substrates for "catalyzing" polymerization of mononucleotides due to the inherent spatiotemporal heterogeneity and phase change behavior.
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Affiliation(s)
- Rajlaxmi Saha
- Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata 741246, India
| | - Prathyush Poduval
- Department of Physics, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Krishnakanth Baratam
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Jayashree Nagesh
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
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Verma A, Mateo T, Quintero Botero J, Mohankumar N, Fraccia TP. Microfluidics-Based Drying-Wetting Cycles to Investigate Phase Transitions of Small Molecules Solutions. Life (Basel) 2024; 14:472. [PMID: 38672743 PMCID: PMC11050796 DOI: 10.3390/life14040472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/24/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Drying-wetting cycles play a crucial role in the investigation of the origin of life as processes that both concentrate and induce the supramolecular assembly and polymerization of biomolecular building blocks, such as nucleotides and amino acids. Here, we test different microfluidic devices to study the dehydration-hydration cycles of the aqueous solutions of small molecules, and to observe, by optical microscopy, the insurgence of phase transitions driven by self-assembly, exploiting water pervaporation through polydimethylsiloxane (PDMS). As a testbed, we investigate solutions of the chromonic dye Sunset Yellow (SSY), which self-assembles into face-to-face columnar aggregates and produces nematic and columnar liquid crystal (LC) phases as a function of concentration. We show that the LC temperature-concentration phase diagram of SSY can be obtained with a fair agreement with previous reports, that droplet hydration-dehydration can be reversibly controlled and automated, and that the simultaneous incubation of samples with different final water contents, corresponding to different phases, can be implemented. These methods can be further extended to study the assembly of diverse prebiotically relevant small molecules and to characterize their phase transitions.
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Affiliation(s)
- Ajay Verma
- IPGG, CBI UMR 8231—CNRS—ESPCI Paris, PSL Research University, 75005 Paris, France
| | - Tiphaine Mateo
- IPGG, CBI UMR 8231—CNRS—ESPCI Paris, PSL Research University, 75005 Paris, France
| | | | - Nishanth Mohankumar
- IPGG, CBI UMR 8231—CNRS—ESPCI Paris, PSL Research University, 75005 Paris, France
| | - Tommaso P. Fraccia
- IPGG, CBI UMR 8231—CNRS—ESPCI Paris, PSL Research University, 75005 Paris, France
- Department of Pharmacological and Biomolecular Sciences, University of Milan, 20133 Milan, Italy
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Šponer JE, Šponer J, Výravský J, Matyášek R, Kovařík A, Dudziak W, Ślepokura K. Crystallization as a selection force at the polymerization of nucleotides in a prebiotic context. iScience 2023; 26:107600. [PMID: 37664611 PMCID: PMC10470394 DOI: 10.1016/j.isci.2023.107600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/14/2023] [Accepted: 08/08/2023] [Indexed: 09/05/2023] Open
Abstract
Accumulation and selection of nucleotides is one of the most challenging problems surrounding the origin of the first RNA molecules on our planet. In the current work we propose that guanosine 3',5' cyclic monophosphate could selectively crystallize upon evaporation of an acidic prebiotic pool containing various other nucleotides. The conditions of the evaporative crystallization are fully compatible with the subsequent acid catalyzed polymerization of this cyclic nucleotide reported in earlier studies and may be relevant in a broad range of possible prebiotic environments. Albeit cytidine 3',5' cyclic monophosphate has the ability to selectively accumulate under the same conditions, its crystal structure is not likely to support polymer formation.
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Affiliation(s)
- Judit E. Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Jakub Výravský
- TESCAN Brno, s.r.o, Libušina třída 1, 62300 Brno, Czech Republic
- Department of Geological Sciences, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Roman Matyášek
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Aleš Kovařík
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Wojciech Dudziak
- University of Wrocław, Faculty of Chemistry, 14 F. Joliot-Curie, 50-383 Wrocław, Poland
| | - Katarzyna Ślepokura
- University of Wrocław, Faculty of Chemistry, 14 F. Joliot-Curie, 50-383 Wrocław, Poland
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Dagar S, Sarkar S, Rajamani S. Nonenzymatic Template-Directed Primer Extension Using 2'-3' Cyclic Nucleotides Under Wet-Dry Cycles. ORIGINS LIFE EVOL B 2023; 53:43-60. [PMID: 37243884 DOI: 10.1007/s11084-023-09636-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 04/15/2023] [Indexed: 05/29/2023]
Abstract
RNA World Hypothesis is centred around the idea of a period in the early history of life's origin, wherein nonenzymatic oligomerization and replication of RNA resulted in functional ribozymes. Previous studies in this endeavour have demonstrated template-directed primer extension using chemically modified nucleotides and primers. Nonetheless, similar studies that used non-activated nucleotides led to the formation of RNA only with abasic sites. In this study, we report template-directed primer extension with prebiotically relevant cyclic nucleotides, under dehydration-rehydration (DH-RH) cycles occurring at high temperature (90 °C) and alkaline conditions (pH 8). 2'-3' cyclic nucleoside monophosphates (cNMP) resulted in primer extension, while 3'-5' cNMP failed to do so. Intact extension of up to two nucleotide additions was observed with both canonical hydroxy-terminated (OH-primer) and activated amino-terminated (NH2-primer) primers. We demonstrate primer extension reactions using both purine and pyrimidine 2'-3' cNMPs, with higher product yield observed during cAMP additions. Further, the presence of lipid was observed to significantly enhance the extended product in cCMP reactions. In all, our study provides a proof-of-concept for nonenzymatic primer extension of RNA, using intrinsically activated prebiotically relevant cyclic nucleotides as monomers.
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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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Di Liegro CM, Schiera G, Schirò G, Di Liegro I. RNA-Binding Proteins as Epigenetic Regulators of Brain Functions and Their Involvement in Neurodegeneration. Int J Mol Sci 2022; 23:ijms232314622. [PMID: 36498959 PMCID: PMC9739182 DOI: 10.3390/ijms232314622] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/18/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022] Open
Abstract
A central aspect of nervous system development and function is the post-transcriptional regulation of mRNA fate, which implies time- and site-dependent translation, in response to cues originating from cell-to-cell crosstalk. Such events are fundamental for the establishment of brain cell asymmetry, as well as of long-lasting modifications of synapses (long-term potentiation: LTP), responsible for learning, memory, and higher cognitive functions. Post-transcriptional regulation is in turn dependent on RNA-binding proteins that, by recognizing and binding brief RNA sequences, base modifications, or secondary/tertiary structures, are able to control maturation, localization, stability, and translation of the transcripts. Notably, most RBPs contain intrinsically disordered regions (IDRs) that are thought to be involved in the formation of membrane-less structures, probably due to liquid-liquid phase separation (LLPS). Such structures are evidenced as a variety of granules that contain proteins and different classes of RNAs. The other side of the peculiar properties of IDRs is, however, that, under altered cellular conditions, they are also prone to form aggregates, as observed in neurodegeneration. Interestingly, RBPs, as part of both normal and aggregated complexes, are also able to enter extracellular vesicles (EVs), and in doing so, they can also reach cells other than those that produced them.
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Affiliation(s)
- Carlo Maria Di Liegro
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche) (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Gabriella Schiera
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche) (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Giuseppe Schirò
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata) (Bi.N.D.), University of Palermo, 90127 Palermo, Italy
| | - Italia Di Liegro
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata) (Bi.N.D.), University of Palermo, 90127 Palermo, Italy
- Correspondence: ; Tel.: +39-091-238-97 (ext. 415/446)
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The Coevolution of Biomolecules and Prebiotic Information Systems in the Origin of Life: A Visualization Model for Assembling the First Gene. Life (Basel) 2022; 12:life12060834. [PMID: 35743865 PMCID: PMC9225589 DOI: 10.3390/life12060834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/23/2022] [Accepted: 06/01/2022] [Indexed: 11/24/2022] Open
Abstract
Prebiotic information systems exist in three forms: analog, hybrid, and digital. The Analog Information System (AIS), manifested early in abiogenesis, was expressed in the chiral selection, nucleotide formation, self-assembly, polymerization, encapsulation of polymers, and division of protocells. It created noncoding RNAs by polymerizing nucleotides that gave rise to the Hybrid Information System (HIS). The HIS employed different species of noncoding RNAs, such as ribozymes, pre-tRNA and tRNA, ribosomes, and functional enzymes, including bridge peptides, pre-aaRS, and aaRS (aminoacyl-tRNA synthetase). Some of these hybrid components build the translation machinery step-by-step. The HIS ushered in the Digital Information System (DIS), where tRNA molecules become molecular architects for designing mRNAs step-by-step, employing their two distinct genetic codes. First, they created codons of mRNA by the base pair interaction (anticodon–codon mapping). Secondly, each charged tRNA transferred its amino acid information to the corresponding codon (codon–amino acid mapping), facilitated by an aaRS enzyme. With the advent of encoded mRNA molecules, the first genes emerged before DNA. With the genetic memory residing in the digital sequences of mRNA, a mapping mechanism was developed between each codon and its cognate amino acid. As more and more codons ‘remembered’ their respective amino acids, this mapping system developed the genetic code in their memory bank. We compared three kinds of biological information systems with similar types of human-made computer systems.
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The Origin(s) of Cell(s): Pre-Darwinian Evolution from FUCAs to LUCA : To Carl Woese (1928-2012), for his Conceptual Breakthrough of Cellular Evolution. J Mol Evol 2021; 89:427-447. [PMID: 34173011 DOI: 10.1007/s00239-021-10014-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 05/29/2021] [Indexed: 10/21/2022]
Abstract
The coming of the Last Universal Cellular Ancestor (LUCA) was the singular watershed event in the making of the biotic world. If the coming of LUCA marked the crossing of the "Darwinian Threshold", then pre-LUCA evolution must have been Pre-Darwinian and at least partly non-Darwinian. But how did Pre-Darwinian evolution before LUCA actually operate? I broaden our understanding of the central mechanism of biological evolution (i.e., variation-selection-inheritance) and then extend this broadened understanding to its natural starting point: the origin(s) of the First Universal Cellular Ancestors (FUCAs) before LUCA. My hypothesis centers upon vesicles' making-and-remaking as variation and competition as selection. More specifically, I argue that vesicles' acquisition and merger, via breaking-and-repacking, proto-endocytosis, proto-endosymbiosis, and other similar processes had been a central force of both variation and selection in the pre-Darwinian epoch. These new perspectives shed important new light upon the origin of FUCAs and their subsequent evolution into LUCA.
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