1
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Banfalvi G. The Origin of RNA and the Formose-Ribose-RNA Pathway. Int J Mol Sci 2024; 25:6727. [PMID: 38928433 PMCID: PMC11203418 DOI: 10.3390/ijms25126727] [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: 05/10/2024] [Revised: 06/03/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Prebiotic pre-Darwinian reactions continued throughout biochemical or Darwinian evolution. Early chemical processes could have occurred on Earth between 4.5 and 3.6 billion years ago when cellular life was about to come into being. Pre-Darwinian evolution assumes the development of hereditary elements but does not regard them as self-organizing processes. The presence of biochemical self-organization after the pre-Darwinian evolution did not justify distinguishing between different types of evolution. From the many possible solutions, evolution selected from among those stable reactions that led to catalytic networks, and under gradually changing external conditions produced a reproducible, yet constantly evolving and adaptable, living system. Major abiotic factors included sunlight, precipitation, air, minerals, soil and the Earth's atmosphere, hydrosphere and lithosphere. Abiotic sources of chemicals contributed to the formation of prebiotic RNA, the development of genetic RNA, the RNA World and the initial life forms on Earth and the transition of genRNA to the DNA Empire, and eventually to the multitude of life forms today. The transition from the RNA World to the DNA Empire generated new processes such as oxygenic photosynthesis and the hierarchical arrangement of processes involved in the transfer of genetic information. The objective of this work is to unite earlier work dealing with the formose, the origin and synthesis of ribose and RNA reactions that were published as a series of independent reactions. These reactions are now regarded as the first metabolic pathway.
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Affiliation(s)
- Gaspar Banfalvi
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, 4032 Debrecen, Hungary
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2
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Di Giulio M. Theories of the origin of the genetic code: Strong corroboration for the coevolution theory. Biosystems 2024; 239:105217. [PMID: 38663520 DOI: 10.1016/j.biosystems.2024.105217] [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: 03/21/2024] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 04/29/2024]
Abstract
I analyzed all the theories and models of the origin of the genetic code, and over the years, I have considered the main suggestions that could explain this origin. The conclusion of this analysis is that the coevolution theory of the origin of the genetic code is the theory that best captures the majority of observations concerning the organization of the genetic code. In other words, the biosynthetic relationships between amino acids would have heavily influenced the origin of the organization of the genetic code, as supported by the coevolution theory. Instead, the presence in the genetic code of physicochemical properties of amino acids, which have also been linked to the physicochemical properties of anticodons or codons or bases by stereochemical and physicochemical theories, would simply be the result of natural selection. More explicitly, I maintain that these correlations between codons, anticodons or bases and amino acids are in fact the result not of a real correlation between amino acids and codons, for example, but are only the effect of the intervention of natural selection. Specifically, in the genetic code table we expect, for example, that the most similar codons - that is, those that differ by only one base - will have more similar physicochemical properties. Therefore, the 64 codons of the genetic code table ordered in a certain way would also represent an ordering of some of their physicochemical properties. Now, a study aimed at clarifying which physicochemical property of amino acids has influenced the allocation of amino acids in the genetic code has established that the partition energy of amino acids has played a role decisive in this. Indeed, under some conditions, the genetic code was found to be approximately 98% optimized on its columns. In this same work, it was shown that this was most likely the result of the action of natural selection. If natural selection had truly allocated the amino acids in the genetic code in such a way that similar amino acids also have similar codons - this, not through a mechanism of physicochemical interaction between, for example, codons and amino acids - then it might turn out that even different physicochemical properties of codons (or anticodons or bases) show some correlation with the physicochemical properties of amino acids, simply because the partition energy of amino acids is correlated with other physicochemical properties of amino acids. It is very likely that this would inevitably lead to a correlation between codons (or anticodons or bases) and amino acids. In other words, since the codons (anticodons or bases) are ordered in the genetic code, that is to say, some of their physicochemical properties should also be ordered by a similar order, and given that the amino acids would also appear to have been ordered in the genetic code by selection natural, then it should inevitably turn out that there is a correlation between, for example, the hydrophobicity of anticodons and that of amino acids. Instead, the intervention of natural selection in organizing the genetic code would appear to be highly compatible with the main mechanism of structuring the genetic code as supported by the coevolution theory. This would make the coevolution theory the only plausible explanation for the origin of the genetic code.
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Affiliation(s)
- Massimo Di Giulio
- The Ionian School, Early Evolution of Life Department, Genetic Code and tRNA Origin Laboratory, Via Roma 19, 67030, Alfedena, L'Aquila, Italy.
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3
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Matreux T, Aikkila P, Scheu B, Braun D, Mast CB. Heat flows enrich prebiotic building blocks and enhance their reactivity. Nature 2024; 628:110-116. [PMID: 38570715 PMCID: PMC10990939 DOI: 10.1038/s41586-024-07193-7] [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: 09/13/2022] [Accepted: 02/09/2024] [Indexed: 04/05/2024]
Abstract
The emergence of biopolymer building blocks is a crucial step during the origins of life1-6. However, all known formation pathways rely on rare pure feedstocks and demand successive purification and mixing steps to suppress unwanted side reactions and enable high product yields. Here we show that heat flows through thin, crack-like geo-compartments could have provided a widely available yet selective mechanism that separates more than 50 prebiotically relevant building blocks from complex mixtures of amino acids, nucleobases, nucleotides, polyphosphates and 2-aminoazoles. Using measured thermophoretic properties7,8, we numerically model and experimentally prove the advantageous effect of geological networks of interconnected cracks9,10 that purify the previously mixed compounds, boosting their concentration ratios by up to three orders of magnitude. The importance for prebiotic chemistry is shown by the dimerization of glycine11,12, in which the selective purification of trimetaphosphate (TMP)13,14 increased reaction yields by five orders of magnitude. The observed effect is robust under various crack sizes, pH values, solvents and temperatures. Our results demonstrate how geologically driven non-equilibria could have explored highly parallelized reaction conditions to foster prebiotic chemistry.
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Affiliation(s)
- Thomas Matreux
- Systems Biophysics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Paula Aikkila
- Systems Biophysics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Bettina Scheu
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dieter Braun
- Systems Biophysics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Christof B Mast
- Systems Biophysics, Ludwig-Maximilians-Universität München, Munich, Germany.
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4
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Colón-Santos S, Vázquez-Salazar A, Adams A, Campillo-Balderas JA, Hernández-Morales R, Jácome R, Muñoz-Velasco I, Rodriguez LE, Schaible MJ, Schaible GA, Szeinbaum N, Thweatt JL, Trubl G. Chapter 2: What Is Life? ASTROBIOLOGY 2024; 24:S40-S56. [PMID: 38498820 DOI: 10.1089/ast.2021.0116] [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: 03/20/2024]
Abstract
The question "What is life?" has existed since the beginning of recorded history. However, the scientific and philosophical contexts of this question have changed and been refined as advancements in technology have revealed both fine details and broad connections in the network of life on Earth. Understanding the framework of the question "What is life?" is central to formulating other questions such as "Where else could life be?" and "How do we search for life elsewhere?" While many of these questions are addressed throughout the Astrobiology Primer 3.0, this chapter gives historical context for defining life, highlights conceptual characteristics shared by all life on Earth as well as key features used to describe it, discusses why it matters for astrobiology, and explores both challenges and opportunities for finding an informative operational definition.
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Affiliation(s)
- Stephanie Colón-Santos
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Wisconsin, USA
- Department of Botany, University of Wisconsin-Madison, Wisconsin, USA
| | - Alberto Vázquez-Salazar
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, California, USA
| | - Alyssa Adams
- Department of Botany, University of Wisconsin-Madison, Wisconsin, USA
| | | | - Ricardo Hernández-Morales
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rodrigo Jácome
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Israel Muñoz-Velasco
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Laura E Rodriguez
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Lunar and Planetary Institute, Universities Space Research Association, Houston, Texas, USA
| | - Micah J Schaible
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - George A Schaible
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nadia Szeinbaum
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Jennifer L Thweatt
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA. (Former)
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
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5
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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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6
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Welsch F, Kervio E, Tremmel P, Richert C. Prolinyl Nucleotides Drive Enzyme-Free Genetic Copying of RNA. Angew Chem Int Ed Engl 2023; 62:e202307591. [PMID: 37382466 DOI: 10.1002/anie.202307591] [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: 05/30/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 06/30/2023]
Abstract
Proline is one of the proteinogenic amino acids. It is found in all kingdoms of life. It also has remarkable activity as an organocatalyst and is of structural importance in many folded polypeptides. Here, we show that prolinyl nucleotides with a phosphoramidate linkage are active building blocks in enzyme- and ribozyme-free copying of RNA in the presence of monosubstituted imidazoles as organocatalysts. Both dinucleotides and mononucleotides are incorporated at the terminus of RNA primers in aqueous buffer, as instructed by the template sequence, in up to eight consecutive extension steps. Our results show that condensation products of amino acids and ribonucleotides can act like nucleoside triphosphates in media devoid of enzymes or ribozymes. Prolinyl nucleotides are metastable building blocks, readily activated by catalysts, helping to explain why the combination of α-amino acids and nucleic acids was selected in molecular evolution.
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Affiliation(s)
- Franziska Welsch
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Eric Kervio
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Peter Tremmel
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
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7
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Sadihov-Hanoch H, Bandela AK, Chotera-Ouda A, Ben David O, Cohen-Luria R, Lynn DG, Ashkenasy G. Dynamic exchange controls the assembly structure of nucleic-acid-peptide chimeras. SOFT MATTER 2023; 19:3940-3945. [PMID: 37211859 DOI: 10.1039/d2sm01528e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Recent attempts to develop the next generation of functional biomaterials focus on systems chemistry approaches exploiting dynamic networks of hybrid molecules. This task is often found challenging, but we herein present ways for profiting from the multiple interaction interfaces forming Nucleic-acid-Peptide assemblies and tuning their formation. We demonstrate that the formation of well-defined structures by double-stranded DNA-peptide conjugates (dsCon) is restricted to a specific range of environmental conditions and that precise DNA hybridization, satisfying the interaction interfaces, is a crucial factor in this process. We further reveal the impact of external stimuli, such as competing free DNA elements or salt additives, which initiate dynamic interconversions, resulting in hybrid structures exhibiting spherical and fibrillar domains or a mixture of spherical and fibrillar particles. This extensive analysis of the co-assembly systems chemistry offers new insights into prebiotic hybrid assemblies that may now facilitate the design of new functional materials. We discuss the implications of these findings for the emergence of function in synthetic materials and during early chemical evolution.
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Affiliation(s)
- Hava Sadihov-Hanoch
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - Anil Kumar Bandela
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - Agata Chotera-Ouda
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - Oshrat Ben David
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - Rivka Cohen-Luria
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
| | - David G Lynn
- Departments of Chemistry and Biology, Emory University, Atlanta, GA, USA
| | - Gonen Ashkenasy
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
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8
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Guo X, Su M. The Origin of Translation: Bridging the Nucleotides and Peptides. Int J Mol Sci 2022; 24:ijms24010197. [PMID: 36613641 PMCID: PMC9820756 DOI: 10.3390/ijms24010197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/09/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Extant biology uses RNA to record genetic information and proteins to execute biochemical functions. Nucleotides are translated into amino acids via transfer RNA in the central dogma. tRNA is essential in translation as it connects the codon and the cognate amino acid. To reveal how the translation emerged in the prebiotic context, we start with the structure and dissection of tRNA, followed by the theory and hypothesis of tRNA and amino acid recognition. Last, we review how amino acids assemble on the tRNA and further form peptides. Understanding the origin of life will also promote our knowledge of artificial living systems.
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Affiliation(s)
- Xuyuan Guo
- School of Genetics and Microbiology, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, D02 PN40 Dublin, Ireland
| | - Meng Su
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
- Correspondence:
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9
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Kumar Bandela A, Sadihov‐Hanoch H, Cohen‐Luria R, Gordon C, Blake A, Poppitz G, Lynn DG, Ashkenasy G. The Systems Chemistry of Nucleic‐acid‐Peptide Networks. Isr J Chem 2022. [DOI: 10.1002/ijch.202200030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anil Kumar Bandela
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Hava Sadihov‐Hanoch
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Rivka Cohen‐Luria
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Christella Gordon
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Alexis Blake
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - George Poppitz
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - David G. Lynn
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Gonen Ashkenasy
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
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10
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Englert A, Vogel JF, Bergner T, Loske J, von Delius M. A Ribonucleotide ↔ Phosphoramidate Reaction Network Optimized by Computer-Aided Design. J Am Chem Soc 2022; 144:15266-15274. [PMID: 35953065 PMCID: PMC9413217 DOI: 10.1021/jacs.2c05861] [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] [Indexed: 12/02/2022]
Abstract
![]()
A growing number of out-of-equilibrium systems have been
created
and investigated in chemical laboratories over the past decade. One
way to achieve this is to create a reaction cycle, in which the forward
reaction is driven by a chemical fuel and the backward reaction follows
a different pathway. Such dissipative reaction networks are still
relatively rare, however, and most non-enzymatic examples are based
on the carbodiimide-driven generation of carboxylic acid anhydrides.
In this work, we describe a dissipative reaction network that comprises
the chemically fueled formation of phosphoramidates from natural ribonucleotides
(e.g., GMP or AMP) and phosphoramidate hydrolysis as a mild backward
reaction. Because the individual reactions are subject to a multitude
of interconnected parameters, the software-assisted tool “Design
of Experiments” (DoE) was a great asset for optimizing and
understanding the network. One notable insight was the stark effect
of the nucleophilic catalyst 1-ethylimidazole (EtIm) on the hydrolysis
rate, which is reminiscent of the action of the histidine group in
phosphoramidase enzymes (e.g., HINT1). We were also able to use the
reaction cycle to generate transient self-assemblies, which were characterized
by dynamic light scattering (DLS), confocal microscopy (CLSM), and
cryogenic transmission electron microscopy (cryo-TEM). Because these
compartments are based on prebiotically plausible building blocks,
our findings may have relevance for origin-of-life scenarios.
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Affiliation(s)
- Andreas Englert
- Institute of Organic Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Julian F Vogel
- Institute of Organic Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Tim Bergner
- Central Facility for Electron Microscopy, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Jessica Loske
- Institute of Organic Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Max von Delius
- Institute of Organic Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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11
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Bremer J, Richter C, Schwalbe H, Richert C. Synthesis of a Peptidoyl RNA Hairpin via a Combination of Solid-Phase and Template-Directed Chain Assembly. Chembiochem 2022; 23:e202200352. [PMID: 35867587 PMCID: PMC9542650 DOI: 10.1002/cbic.202200352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 07/21/2022] [Indexed: 12/02/2022]
Abstract
Peptidoyl RNAs are the products of ribosome‐free, single‐nucleotide translation. They contain a peptide in the backbone of the oligoribonucleotide and are interesting from a synthetic and a bioorganic point of view. A synthesis of a stabilized version of peptidoyl RNA, with an amide bond between the C‐terminus of a peptide and a 3′‐amino‐2′,3′‐dideoxynucleoside in the RNA chain was developed. The preferred synthetic route used an N‐Teoc‐protected aminonucleoside support and involved a solution‐phase coupling of the amino‐terminal oligonucleotide to a dipeptido dinucleotide. Exploratory UV‐melting and NMR analysis of the hairpin 5′‐UUGGCGAAAGCdC‐LeuLeu‐AA‐3′ indicated that the peptide‐linked RNA segments do not fold in a cooperative fashion. The synthetic access to doubly RNA‐linked peptides on a scale sufficient for structural biology opens the door to the exploration of their structural and biochemical properties.
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Affiliation(s)
- Jennifer Bremer
- University of Stuttgart: Universitat Stuttgart, Chemistry, GERMANY
| | - Christian Richter
- Universität Frankfurt am Main: Goethe-Universitat Frankfurt am Main, Chemistry, GERMANY
| | - Harald Schwalbe
- Universität Frankfurt am Main: Goethe-Universitat Frankfurt am Main, Chemistry, GERMANY
| | - Clemens Richert
- Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, GERMANY
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12
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Bonfio C. A possible path towards encoded protein synthesis on ancient Earth. Nature 2022; 605:231-232. [PMID: 35546187 DOI: 10.1038/d41586-022-01256-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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13
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Abstract
The RNA world concept1 is one of the most fundamental pillars of the origin of life theory2–4. It predicts that life evolved from increasingly complex self-replicating RNA molecules1,2,4. The question of how this RNA world then advanced to the next stage, in which proteins became the catalysts of life and RNA reduced its function predominantly to information storage, is one of the most mysterious chicken-and-egg conundrums in evolution3–5. Here we show that non-canonical RNA bases, which are found today in transfer and ribosomal RNAs6,7, and which are considered to be relics of the RNA world8–12, are able to establish peptide synthesis directly on RNA. The discovered chemistry creates complex peptide-decorated RNA chimeric molecules, which suggests the early existence of an RNA–peptide world13 from which ribosomal peptide synthesis14 may have emerged15,16. The ability to grow peptides on RNA with the help of non-canonical vestige nucleosides offers the possibility of an early co-evolution of covalently connected RNAs and peptides13,17,18, which then could have dissociated at a higher level of sophistication to create the dualistic nucleic acid–protein world that is the hallmark of all life on Earth. Peptide synthesis can take place directly on RNA, which suggests how a nucleic acid–protein world might have originated on early Earth.
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14
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Jash B, Kool ET. Conjugation of RNA via 2'-OH acylation: Mechanisms determining nucleotide reactivity. Chem Commun (Camb) 2022; 58:3693-3696. [PMID: 35226025 PMCID: PMC9211027 DOI: 10.1039/d2cc00660j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The acylation reactivity of RNA 2'-OH groups has proven broadly useful for labeling and mapping RNA. Here we perform kinetics studies to test the mechanisms governing this reaction, and we find strong steric and inductive effects modulating reactivity. The results shed light on new strategies for improved conjugation and mapping.
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Affiliation(s)
- Biswarup Jash
- Department of Chemistry and ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.
| | - Eric T Kool
- Department of Chemistry and ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.
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Doppleb O, Schwarz RJ, Landa M, Richert C. Efficient Oligomerization of Aromatic Amino Acids Induced by Gaps in Four-Helix Bundles of DNA or RNA. Chemistry 2022; 28:e202104104. [PMID: 35050538 PMCID: PMC9303611 DOI: 10.1002/chem.202104104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Indexed: 11/09/2022]
Abstract
The formation of peptides from amino acids is one of the processes associated with life. Because of the dominant role of translation in extant biology, peptide‐forming processes that are RNA induced are of particular interest. We have previously reported the formation of phosphoramidate‐linked peptido RNAs as the products of spontaneous condensation reactions between ribonucleotides and free amino acids in aqueous solution. We now asked whether four‐helix bundle (4HB) DNA or RNA folding motifs with a single‐ or double‐nucleotide gap next to a 5’‐phosphate can act as reaction sites for phosphoramidate formation. For glycine, this was found to be the case, whereas phenylalanine and tryptophan showed accelerated formation of peptides without a covalent link to the nucleic acid. Free peptides with up to 11 tryptophan or phenylalanine residues were found in precipitates forming in the presence of gap‐containing DNA or RNA 4HBs. Control experiments using motifs with just a nick or primer alone did not have the same effect. Because folded structures with a gap in a double helix are likely products of hybridization of strands formed in statistically controlled oligomerization reactions, our results are interesting in the context of prebiotic scenarios. Independent of a putative role in evolution, our findings suggest that for some aromatic amino acids an RNA‐induced pathway for oligomerization exists that does not have a discernable link to translation.
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Affiliation(s)
- Olivia Doppleb
- Institut für Organische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Rainer Joachim Schwarz
- Institut für Organische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Maria Landa
- Institut für Organische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Clemens Richert
- Institut für Organische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
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Jia TZ, Nishikawa S, Fujishima K. Sequencing the Origins of Life. BBA ADVANCES 2022; 2:100049. [PMID: 37082609 PMCID: PMC10074849 DOI: 10.1016/j.bbadva.2022.100049] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 01/10/2023] Open
Abstract
One goal of origins of life research is to understand how primitive informational and catalytic biopolymers emerged and evolved. Recently, a number of sequencing techniques have been applied to analysis of replicating and evolving primitive biopolymer systems, providing a sequence-specific and high-resolution view of primitive chemical processes. Here, we review application of sequencing techniques to analysis of synthetic and primitive nucleic acids and polypeptides. This includes next-generation sequencing of primitive polymerization and evolution processes, followed by discussion of other novel biochemical techniques that could contribute to sequence analysis of primitive biopolymer driven chemical systems. Further application of sequencing to origins of life research, perhaps as a life detection technology, could provide insight into the origin and evolution of informational and catalytic biopolymers on early Earth or elsewhere.
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Affiliation(s)
- Tony Z. Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Blue Marble Space Institute of Science, 600 1st Ave, Floor 1, Seattle, WA 98104, USA
- Corresponding author
| | - Shota Nishikawa
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa-shi, Kanagawa 252-0882, Japan
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Sun J, Vogel J, Chen L, Schleper AL, Bergner T, Kuehne AJC, von Delius M. Carbodiimide-Driven Dimerization and Self-Assembly of Artificial, Ribose-Based Amphiphiles. Chemistry 2022; 28:e202104116. [PMID: 35038189 PMCID: PMC9303926 DOI: 10.1002/chem.202104116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Indexed: 12/20/2022]
Abstract
The aqueous self‐assembly of amphiphiles into aggregates such as micelles and vesicles has been widely investigated over the past decades with applications ranging from materials science to drug delivery. The combination of characteristic properties of nucleic acids and amphiphiles is of substantial interest to mimic biological self‐organization and compartmentalization. Herein, we present ribose‐ and ribonucleotide‐based amphiphiles and investigate their self‐assembly as well as their fundamental reactivity. We found that various types of aggregates are formed, ranging in size from nanometers to micrometers and all amphiphiles exhibit aggregation‐induced emission (AIE) in solution as well as in the solid state. We also observed that the addition of 1‐ethyl‐3‐(3‐dimethylaminopropyl)carbodiimide (EDC) leads to rapid and selective dimerization of the amphiphiles into pyrophosphates, which decreases the critical aggregation concentration (CAC) by a factor of 25 when compared to the monomers. Since the propensity for amphiphile dimerization is correlated with their tendency to self‐assemble, our results may be relevant for the formation of rudimentary compartments under prebiotic conditions.
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Affiliation(s)
- Jing Sun
- Institute of Organic Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Julian Vogel
- Institute of Organic Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Lisa Chen
- Institute of Macromolecular and Organic Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - A Lennart Schleper
- Institute of Macromolecular and Organic Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Tim Bergner
- Central Facility for Electron Microscopy, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Alexander J C Kuehne
- Institute of Macromolecular and Organic Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.,DWI - Leibniz-Institute for Interactive Materials, Forckenbeckstraße 50, 52074, Aachen, Germany
| | - Max von Delius
- Institute of Organic Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
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Nonenzymatic assembly of active chimeric ribozymes from aminoacylated RNA oligonucleotides. Proc Natl Acad Sci U S A 2022; 119:2116840119. [PMID: 35140183 PMCID: PMC8851484 DOI: 10.1073/pnas.2116840119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2022] [Indexed: 02/07/2023] Open
Abstract
The emergence of a primordial ribosome from the RNA world would have required access to aminoacylated RNA substrates. The spontaneous generation of such substrates without enzymes is inefficient, and it remains unclear how they could be selected for in a prebiotic milieu. In our study, we identify a possible role for aminoacylated RNA in ribozyme assembly, a longstanding problem in the origin-of-life research. We show that aminoacylation of short RNAs greatly accelerates their assembly into functional ribozymes by forming amino acid bridges in the phosphodiester backbone. Our work therefore addresses two key challenges within the origin-of-life field: we demonstrate assembly of functional ribozymes, and we identify a potential evolutionary benefit for RNA aminoacylation that is independent of coded peptide translation. Aminoacylated transfer RNAs, which harbor a covalent linkage between amino acids and RNA, are a universally conserved feature of life. Because they are essential substrates for ribosomal translation, aminoacylated oligonucleotides must have been present in the RNA world prior to the evolution of the ribosome. One possibility we are exploring is that the aminoacyl ester linkage served another function before being recruited for ribosomal protein synthesis. The nonenzymatic assembly of ribozymes from short RNA oligomers under realistic conditions remains a key challenge in demonstrating a plausible pathway from prebiotic chemistry to the RNA world. Here, we show that aminoacylated RNAs can undergo template-directed assembly into chimeric amino acid–RNA polymers that are active ribozymes. We demonstrate that such chimeric polymers can retain the enzymatic function of their all-RNA counterparts by generating chimeric hammerhead, RNA ligase, and aminoacyl transferase ribozymes. Amino acids with diverse side chains form linkages that are well tolerated within the RNA backbone and, in the case of an aminoacyl transferase, even in its catalytic center, potentially bringing novel functionalities to ribozyme catalysis. Our work suggests that aminoacylation chemistry may have played a role in primordial ribozyme assembly. Increasing the efficiency of this process provides an evolutionary rationale for the emergence of sequence and amino acid–specific aminoacyl-RNA synthetase ribozymes, which could then have generated the substrates for ribosomal protein synthesis.
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