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Khalfallah HB, Jelassi M, Rissaoui H, Barchouchi M, Baraille C, Gardes J, Demongeot J. Information Gradient among Nucleotide Sequences of Essential RNAs from an Evolutionary Perspective. Int J Mol Sci 2024; 25:7521. [PMID: 39062761 PMCID: PMC11277137 DOI: 10.3390/ijms25147521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 06/17/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
We hypothesize that the first ancestral "protocell" molecular structures, i.e., the first RNAs and peptides that gradually transformed into real cells once the Earth had cooled sufficiently for organic molecules to appear, have left traces in the RNAs and the genes in present cells. We propose a circular RNA that could have been one of these ancestral structures whose vestigial pentameric subsequences would mark the evolution from this key moment when the protocells began to join with living organisms. In particular, we propose that, in present RNAs (ribosomal or messenger), which play an important role in the metabolism of current cells, we look for traces of the proposed primitive structure in the form of pentamers (or longer fragments) that belong to their nucleotide sequence. The result obtained can be summarized in the existence of a gradient of occurrence of such pentamers, with a high frequency for the most vital functions (protein synthesis, nucleic synthesis, cell respiration, etc.). This gradient is also visible between organisms, from the oldest (Archaea) to the most recent (Eukaryotes) in the evolution of species.
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Affiliation(s)
- Houssem Ben Khalfallah
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, University Grenoble Alpes (UGA), 38700 La Tronche, France; (H.B.K.); (H.R.); (M.B.)
- ENSI—Ecole Nationale des Sciences de l’Informatique, Campus Universitaire de la Manouba, La Manouba 2010, Tunisia
| | - Mariem Jelassi
- ENSI—Ecole Nationale des Sciences de l’Informatique, Campus Universitaire de la Manouba, La Manouba 2010, Tunisia
| | - Hajar Rissaoui
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, University Grenoble Alpes (UGA), 38700 La Tronche, France; (H.B.K.); (H.R.); (M.B.)
| | - Mohtadi Barchouchi
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, University Grenoble Alpes (UGA), 38700 La Tronche, France; (H.B.K.); (H.R.); (M.B.)
| | | | - Joël Gardes
- Orange Laboratorys, 38229 Meylan, France; (C.B.); (J.G.)
| | - Jacques Demongeot
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, University Grenoble Alpes (UGA), 38700 La Tronche, France; (H.B.K.); (H.R.); (M.B.)
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Gehlbach EM, Robinson AO, Engelhart AE, Adamala KP. Sequential gentle hydration increases encapsulation in model protocells. DISCOVER LIFE 2024; 54:2. [PMID: 38765272 PMCID: PMC11099956 DOI: 10.1007/s11084-024-09645-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/17/2024] [Indexed: 05/21/2024]
Abstract
Small, spherical vesicles are a widely used chassis for the formation of model protocells and investigating the beginning of compartmentalized evolution. Various methods exist for their preparation, with one of the most common approaches being gentle hydration, where thin layers of lipids are hydrated with aqueous solutions and gently agitated to form vesicles. An important benefit to gentle hydration is that the method produces vesicles without introducing any organic contaminants, such as mineral oil, into the lipid bilayer. However, compared to other methods of liposome formation, gentle hydration is much less efficient at encapsulating aqueous cargo. Improving the encapsulation efficiency of gentle hydration would be of broad use for medicine, biotechnology, and protocell research. Here, we describe a method of sequentially hydrating lipid thin films to increase encapsulation efficiency. We demonstrate that sequential gentle hydration significantly improves encapsulation of water-soluble cargo compared to the traditional method, and that this improved efficiency is dependent on buffer composition. Similarly, we also demonstrate how this method can be used to increase concentrations of oleic acid, a fatty acid commonly used in origins of life research, to improve the formation of vesicles in aqueous buffer.
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Affiliation(s)
- Emma M. Gehlbach
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN USA
| | - Abbey O. Robinson
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN USA
| | - Aaron E. Engelhart
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN USA
| | - Katarzyna P. Adamala
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN USA
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3
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Todd ZR, Lozano GG, Kufner CL, Ranjan S, Catling DC, Sasselov DD. UV Transmission in Prebiotic Environments on Early Earth. ASTROBIOLOGY 2024; 24:559-569. [PMID: 38768432 DOI: 10.1089/ast.2023.0077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Ultraviolet (UV) light is likely to have played important roles in surficial origins of life scenarios, potentially as a productive source of energy and molecular activation, as a selective means to remove unwanted side products, or as a destructive mechanism resulting in loss of molecules/biomolecules over time. The transmission of UV light through prebiotic waters depends upon the chemical constituents of such waters, but constraints on this transmission are limited. Here, we experimentally measure the molar decadic extinction coefficients for a number of small molecules used in various prebiotic synthetic schemes. We find that many small feedstock molecules absorb most at short (∼200 nm) wavelengths, with decreasing UV absorption at longer wavelengths. For comparison, we also measured the nucleobase adenine and found that adenine absorbs significantly more than the simpler molecules often invoked in prebiotic synthesis. Our results enable the calculation of UV photon penetration under varying chemical scenarios and allow further constraints on plausibility and self-consistency of such scenarios. While the precise path that prebiotic chemistry took remains elusive, improved understanding of the UV environment in prebiotically plausible waters can help constrain both the chemistry and the environmental conditions that may allow such chemistry to occur.
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Affiliation(s)
- Zoe R Todd
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
- Department of Chemistry, Department of Astronomy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Gabriella G Lozano
- Center for Astrophysics, Harvard and Smithsonian, Cambridge, Massachusetts, USA
| | - Corinna L Kufner
- Center for Astrophysics, Harvard and Smithsonian, Cambridge, Massachusetts, USA
| | - Sukrit Ranjan
- Lunar & Planetary Laboratory/Department of Planetary Sciences, University of Arizona, Tucson, Arizona, USA
| | - David C Catling
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
| | - Dimitar D Sasselov
- Center for Astrophysics, Harvard and Smithsonian, Cambridge, Massachusetts, USA
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Lopez A, Vauchez A, Ajram G, Shvetsova A, Leveau G, Fiore M, Strazewski P. From the RNA-Peptide World: Prebiotic Reaction Conditions Compatible with Lipid Membranes for the Formation of Lipophilic Random Peptides in the Presence of Short Oligonucleotides, and More. Life (Basel) 2024; 14:108. [PMID: 38255723 PMCID: PMC10817532 DOI: 10.3390/life14010108] [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: 11/27/2023] [Revised: 12/25/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Deciphering the origins of life on a molecular level includes unravelling the numerous interactions that could occur between the most important biomolecules being the lipids, peptides and nucleotides. They were likely all present on the early Earth and all necessary for the emergence of cellular life. In this study, we intended to explore conditions that were at the same time conducive to chemical reactions critical for the origins of life (peptide-oligonucleotide couplings and templated ligation of oligonucleotides) and compatible with the presence of prebiotic lipid vesicles. For that, random peptides were generated from activated amino acids and analysed using NMR and MS, whereas short oligonucleotides were produced through solid-support synthesis, manually deprotected and purified using HPLC. After chemical activation in prebiotic conditions, the resulting mixtures were analysed using LC-MS. Vesicles could be produced through gentle hydration in similar conditions and observed using epifluorescence microscopy. Despite the absence of coupling or ligation, our results help to pave the way for future investigations on the origins of life that may gather all three types of biomolecules rather than studying them separately, as it is still too often the case.
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Affiliation(s)
- Augustin Lopez
- Laboratoire de Chimie Organique 2 (LCO2), Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS, UMR CNRS 5246), Bâtiment Edgar Lederer, Université Claude Bernard Lyon 1, Université de Lyon, 1 rue Victor Grignard, 69100 Villeurbanne, France (M.F.)
| | - Antoine Vauchez
- Centre Commun de la Spectrométrie de Masse (CCSM), ICBMS, Bâtiment Edgar Lederer, 1 rue Victor Grignard, 69100 Villeurbanne, France;
| | - Ghinwa Ajram
- Laboratoire de Chimie Organique 2 (LCO2), Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS, UMR CNRS 5246), Bâtiment Edgar Lederer, Université Claude Bernard Lyon 1, Université de Lyon, 1 rue Victor Grignard, 69100 Villeurbanne, France (M.F.)
| | - Anastasiia Shvetsova
- Laboratoire de Chimie Organique 2 (LCO2), Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS, UMR CNRS 5246), Bâtiment Edgar Lederer, Université Claude Bernard Lyon 1, Université de Lyon, 1 rue Victor Grignard, 69100 Villeurbanne, France (M.F.)
| | - Gabrielle Leveau
- Laboratoire de Chimie Organique 2 (LCO2), Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS, UMR CNRS 5246), Bâtiment Edgar Lederer, Université Claude Bernard Lyon 1, Université de Lyon, 1 rue Victor Grignard, 69100 Villeurbanne, France (M.F.)
| | - Michele Fiore
- Laboratoire de Chimie Organique 2 (LCO2), Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS, UMR CNRS 5246), Bâtiment Edgar Lederer, Université Claude Bernard Lyon 1, Université de Lyon, 1 rue Victor Grignard, 69100 Villeurbanne, France (M.F.)
| | - Peter Strazewski
- Laboratoire de Chimie Organique 2 (LCO2), Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS, UMR CNRS 5246), Bâtiment Edgar Lederer, Université Claude Bernard Lyon 1, Université de Lyon, 1 rue Victor Grignard, 69100 Villeurbanne, France (M.F.)
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Santos TCB, Futerman AH. The fats of the matter: Lipids in prebiotic chemistry and in origin of life studies. Prog Lipid Res 2023; 92:101253. [PMID: 37659458 DOI: 10.1016/j.plipres.2023.101253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/04/2023]
Abstract
The unique biophysical and biochemical properties of lipids render them crucial in most models of the origin of life (OoL). Many studies have attempted to delineate the prebiotic pathways by which lipids were formed, how micelles and vesicles were generated, and how these micelles and vesicles became selectively permeable towards the chemical precursors required to initiate and support biochemistry and inheritance. Our analysis of a number of such studies highlights the extremely narrow and limited range of conditions by which an experiment is considered to have successfully modeled a role for lipids in an OoL experiment. This is in line with a recent proposal that bias is introduced into OoL studies by the extent and the kind of human intervention. It is self-evident that OoL studies can only be performed by human intervention, and we now discuss the possibility that some assumptions and simplifications inherent in such experimental approaches do not permit determination of mechanistic insight into the roles of lipids in the OoL. With these limitations in mind, we suggest that more nuanced experimental approaches than those currently pursued may be required to elucidate the generation and function of lipids, micelles and vesicles in the OoL.
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Affiliation(s)
- Tania C B Santos
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Anthony H Futerman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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Gehlbach EM, Robinson AO, Engelhart AE, Adamala KP. Sequential gentle hydration increases encapsulation in model protocells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.15.562404. [PMID: 37873423 PMCID: PMC10592796 DOI: 10.1101/2023.10.15.562404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Small, spherical vesicles are a widely used chassis for the formation of model protocells and investigating the beginning of compartmentalized evolution. Various methods exist for their preparation, with one of the most common approaches being gentle hydration, where thin layers of lipids are hydrated with aqueous solutions and gently agitated to form vesicles. An important benefit to gentle hydration is that the method produces vesicles without introducing any organic contaminants, such as mineral oil, into the lipid bilayer. However, compared to other methods of liposome formation, gentle hydration is much less efficient at encapsulating aqueous cargo. Improving the encapsulation efficiency of gentle hydration would be of broad use for medicine, biotechnology, and protocell research. Here, we describe a method of sequentially hydrating lipid thin films to increase encapsulation efficiency. We demonstrate that sequential gentle hydration significantly improves encapsulation of water-soluble cargo compared to the traditional method, and that this improved efficiency is dependent on buffer composition. Similarly, we also demonstrate how this method can be used to increase concentrations of oleic acid, a fatty acid commonly used in origins of life research, to improve the formation of vesicles in aqueous buffer.
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Affiliation(s)
- Emma M. Gehlbach
- University of Minnesota Department of Genetics, Cell Biology and Development, Minneapolis, MN, USA
| | - Abbey O. Robinson
- University of Minnesota Department of Genetics, Cell Biology and Development, Minneapolis, MN, USA
| | - Aaron E. Engelhart
- University of Minnesota Department of Genetics, Cell Biology and Development, Minneapolis, MN, USA
| | - Katarzyna P. Adamala
- University of Minnesota Department of Genetics, Cell Biology and Development, Minneapolis, MN, USA
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Subbotin V, Fiksel G. Aquatic Ferrous Solutions of Prebiotic Mineral Salts as Strong UV Protectants and Possible Loci of Life Origin. ASTROBIOLOGY 2023; 23:741-745. [PMID: 37327365 PMCID: PMC10354304 DOI: 10.1089/ast.2023.0011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/19/2023] [Indexed: 06/18/2023]
Abstract
Liposomes are lipid-bilayer vesicles that spontaneously self-assemble from fatty acids (or other amphiphiles) in water by encapsulating surrounding aqueous media. After British scientist Alec Bangham described this phenomenon in the early 1960s, they became a prominent participant in the hypotheses on life origin, particularly in the Lipid World model. A novel scenario of self-sustained Darwinian liposome evolution is based on ever-present natural phenomena of cyclic day/night solar UV radiation and gravitational submersion of liposomes in the Archean aqueous media. One of the assumptions of the hypothesis is the UV-shielding ability of the Archean waters that could protect the submerged liposomes from the damaging solar UV radiation. To corroborate the idea, we measured UV absorption in aquatic solutions of several ferrous mineral salts assumed to be present in Archean pools. Single-agent solutions of simple salts such as FeCl2-iron dichloride, FeCl3-iron trichoride, Fe(NO3)3-ferric nitride, NH4Fe(SO4)2-ferric ammonium sulfate, and (NH4)5[Fe(C6H4O7)2]-ferric ammonium citrate were tested. These direct measurements of UV light absorption supplement and reinforce the proposed hypothesis.
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Affiliation(s)
- Vladimir Subbotin
- Department of Human Oncology, University of Wisconsin, Madison, Wisconsin, USA
| | - Gennady Fiksel
- Department of Nuclear Engineering and Radiological Sciences, University of Michigan, Ann Arbor, Michigan, USA
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