1
|
Song X, Simonis P, Deamer D, Zare RN. Wet-dry cycles cause nucleic acid monomers to polymerize into long chains. Proc Natl Acad Sci U S A 2024; 121:e2412784121. [PMID: 39585974 PMCID: PMC11626162 DOI: 10.1073/pnas.2412784121] [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: 06/25/2024] [Accepted: 10/23/2024] [Indexed: 11/27/2024] Open
Abstract
The key first step in the oligomerization of monomers is to find an initiator, which is usually done by thermolysis or photolysis. We present a markedly different approach that initiates acid-catalyzed polymerization at the surface of water films or water droplets, which is the reactive phase during a wet-dry cycle in freshwater hot springs associated with subaerial volcanic landmasses. We apply this method to the oligomerization of different nucleic acids, a topic relevant to how it might be possible to go from simple nucleic acid monomers to long-chain polymers, a key step in forming the building blocks of life. It has long been known that dehydration at elevated temperatures can drive the synthesis of ester and peptide bonds, but this reaction has typically been carried out by incubating dry monomers at elevated temperatures. We report that single or multiple cycles of wetting and drying link mononucleotides by forming phosphodiester bonds. Mass spectrometric analysis reveals uridine monophosphate oligomers up to 53 nucleotides, with an abundance of 35 and 43 nt in length. Long-chain oligomers are also observed for thymidine monophosphate, adenosine monophosphate, and deoxyadenosine monophosphate after exposure to a few wet-dry cycles. Nanopore sequencing confirms that long linear chains are formed. Enzyme digestion shows that the linkage is the phosphodiester bond, which is further confirmed by 31P NMR and Fourier transform infrared spectroscopy. This suggests that nucleic acid oligomers were likely to be present on early Earth in a steady state of synthesis and hydrolysis.
Collapse
Affiliation(s)
- Xiaowei Song
- Department of Chemistry, Stanford University, Stanford, CA94305
| | - Povilas Simonis
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA95064
- Institute of Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, VilniusLT-01513, Lithuania
- State Research Institute Center for Physical Sciences and Technology, VilniusLT-02300, Lithuania
| | - David Deamer
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA95064
| | - Richard N. Zare
- Department of Chemistry, Stanford University, Stanford, CA94305
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Namani T, Ruf RJ, Arsano I, Hu R, Wesdemiotis C, Sahai N. Novel Chimeric Amino Acid-Fatty Alcohol Ester Amphiphiles Self-Assemble into Stable Primitive Membranes in Diverse Geological Settings. ASTROBIOLOGY 2023; 23:327-343. [PMID: 36724479 DOI: 10.1089/ast.2022.0056] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Primitive cells are believed to have been self-assembled vesicular structures with minimal metabolic components, that were capable of self-maintenance and self-propagation in early Earth geological settings. The coevolution and self-assembly of biomolecules, such as amphiphiles, peptides, and nucleic acids, or their precursors, were essential for protocell emergence. Here, we present a novel class of amphiphiles-amino acid-fatty alcohol esters-that self-assemble into stable primitive membrane compartments under a wide range of geochemical conditions. Glycine n-octyl ester (GOE) and isoleucine n-octyl ester (IOE), the condensation ester products of glycine or isoleucine with octanol (OcOH), are expected to form at a mild temperature by wet-dry cycles. The GOE forms micelles in acidic aqueous solutions (pH 2-7) and vesicles at intermediate pH (pH 7.3-8.2). When mixed with cosurfactants (octanoic acid [OcA]; OcOH, or decanol) in different mole fractions [XCosurfactant = 0.1-0.5], the vesicle stability range expands significantly to span the extremely acidic to mildly alkaline (pH 2-8) and extremely alkaline (pH 10-11) regions. Only a small mole fraction of cosurfactant [XCosurfactant = 0.1] is needed to make stable vesicular structures. Notably, these GOE-based vesicles are also stable in the presence of high concentrations of divalent cations, even at low pHs and in simulated Hadean seawater composition (without sulfate). To better understand the self-assembly behavior of GOE-based systems, we devised complementary molecular dynamics computer simulations for a series of mixed GOE/OcA systems under simulated acidic pHs. The resulting calculated critical packing parameter values and self-assembly behavior were consistent with our experimental findings. The IOE is expected to show similar self-assembly behavior. Thus, amino acid-fatty alcohol esters, a novel chimeric amphiphile class composed of an amino acid head group and a fatty alcohol tail, may have aided in building protocell membranes, which were stable in a wide variety of geochemical circumstances and were conducive to supporting replication and self-maintenance. The present work contributes to our body of work supporting our hypothesis for synergism and coevolution of (proto)biomolecules on early Earth.
Collapse
Affiliation(s)
- Trishool Namani
- School of Polymer Science and Polymer Engineering, University of Akron, Akron, Ohio, USA
| | - Reghan J Ruf
- School of Polymer Science and Polymer Engineering, University of Akron, Akron, Ohio, USA
- Integrated Biosciences Program, University of Akron, Akron, Ohio, USA
| | - Iskinder Arsano
- School of Polymer Science and Polymer Engineering, University of Akron, Akron, Ohio, USA
| | - Ruibo Hu
- School of Polymer Science and Polymer Engineering, University of Akron, Akron, Ohio, USA
| | - Chrys Wesdemiotis
- School of Polymer Science and Polymer Engineering, University of Akron, Akron, Ohio, USA
- Department of Chemistry, University of Akron, Akron, Ohio, USA
| | - Nita Sahai
- School of Polymer Science and Polymer Engineering, University of Akron, Akron, Ohio, USA
- Integrated Biosciences Program, University of Akron, Akron, Ohio, USA
- Department of Geosciences, and University of Akron, Akron, Ohio, USA
- Department of Biology, University of Akron, Akron, Ohio, USA
| |
Collapse
|
4
|
Hansma HG. Potassium at the Origins of Life: Did Biology Emerge from Biotite in Micaceous Clay? Life (Basel) 2022; 12:301. [PMID: 35207588 PMCID: PMC8880093 DOI: 10.3390/life12020301] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/31/2022] [Accepted: 01/31/2022] [Indexed: 12/15/2022] Open
Abstract
Intracellular potassium concentrations, [K+], are high in all types of living cells, but the origins of this K+ are unknown. The simplest hypothesis is that life emerged in an environment that was high in K+. One such environment is the spaces between the sheets of the clay mineral mica. The best mica for life's origins is the black mica, biotite, because it has a high content of Mg++ and because it has iron in various oxidation states. Life also has many of the characteristics of the environment between mica sheets, giving further support for the possibility that mica was the substrate on and within which life emerged. Here, a scenario for life's origins is presented, in which the necessary processes and components for life arise in niches between mica sheets; vesicle membranes encapsulate these processes and components; the resulting vesicles fuse, forming protocells; and eventually, all of the necessary components and processes are encapsulated within individual cells, some of which survive to seed the early Earth with life. This paper presents three new foci for the hypothesis of life's origins between mica sheets: (1) that potassium is essential for life's origins on Earth; (2) that biotite mica has advantages over muscovite mica; and (3) that micaceous clay is a better environment than isolated mica for life's origins.
Collapse
|
5
|
Namani T, Snyder S, Eagan JM, Bevilacqua PC, Wesdemiotis C, Sahai N. Amino Acid Specific Nonenzymatic Montmorillonite‐Promoted RNA Polymerization. CHEMSYSTEMSCHEM 2021. [DOI: 10.1002/syst.202000060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Trishool Namani
- School of Polymer Science and Polymer Engineering The University of Akron Akron OH 44325 USA
| | - Savannah Snyder
- Department of Chemistry The University of Akron Akron OH 44325 USA
| | - James M. Eagan
- School of Polymer Science and Polymer Engineering The University of Akron Akron OH 44325 USA
| | - Philip C. Bevilacqua
- Department of Chemistry and Biochemistry Department of Microbiology and Molecular Biology Center for RNA Molecular Biology Pennsylvania State University University Park Pennsylvania PA 16802 USA
| | | | - Nita Sahai
- School of Polymer Science and Polymer Engineering The University of Akron Akron OH 44325 USA
| |
Collapse
|
6
|
Lyu Y, Peng R, Liu H, Kuai H, Mo L, Han D, Li J, Tan W. Protocells programmed through artificial reaction networks. Chem Sci 2019; 11:631-642. [PMID: 34123035 PMCID: PMC8145531 DOI: 10.1039/c9sc05043d] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
As the smallest unit of life, cells attract interest due to their structural complexity and functional reliability. Protocells assembled by inanimate components are created as an artificial entity to mimic the structure and some essential properties of a natural cell, and artificial reaction networks are used to program the functions of protocells. Although the bottom-up construction of a protocell that can be considered truly ‘alive’ is still an ambitious goal, these man-made constructs with a certain degree of ‘liveness’ can offer effective tools to understand fundamental processes of cellular life, and have paved the new way for bionic applications. In this review, we highlight both the milestones and recent progress of protocells programmed by artificial reaction networks, including genetic circuits, enzyme-assisted non-genetic circuits, prebiotic mimicking reaction networks, and DNA dynamic circuits. Challenges and opportunities have also been discussed. In this review, the milestones and recent progress of protocells programmed by various types of artificial reaction networks are highlighted.![]()
Collapse
Affiliation(s)
- Yifan Lyu
- Institute of Molecular Medicine (IMM), State Key Laboratory of Oncogenes and Related Genes Renji Hospital, Shanghai Jiao Tong University School of Medicine, College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai 200240 China.,Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha Hunan 410082 China
| | - Ruizi Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha Hunan 410082 China
| | - Hui Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha Hunan 410082 China
| | - Hailan Kuai
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha Hunan 410082 China
| | - Liuting Mo
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha Hunan 410082 China
| | - Da Han
- Institute of Molecular Medicine (IMM), State Key Laboratory of Oncogenes and Related Genes Renji Hospital, Shanghai Jiao Tong University School of Medicine, College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai 200240 China
| | - Juan Li
- Institute of Molecular Medicine (IMM), State Key Laboratory of Oncogenes and Related Genes Renji Hospital, Shanghai Jiao Tong University School of Medicine, College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai 200240 China.,MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences Hangzhou Zhejiang 310022 China
| | - Weihong Tan
- Institute of Molecular Medicine (IMM), State Key Laboratory of Oncogenes and Related Genes Renji Hospital, Shanghai Jiao Tong University School of Medicine, College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai 200240 China.,Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha Hunan 410082 China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences Hangzhou Zhejiang 310022 China
| |
Collapse
|
7
|
Kunnev D, Gospodinov A. Possible Emergence of Sequence Specific RNA Aminoacylation via Peptide Intermediary to Initiate Darwinian Evolution and Code Through Origin of Life. Life (Basel) 2018; 8:E44. [PMID: 30279401 PMCID: PMC6316189 DOI: 10.3390/life8040044] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/30/2018] [Accepted: 09/30/2018] [Indexed: 12/12/2022] Open
Abstract
One of the most intriguing questions in biological science is how life originated on Earth. A large number of hypotheses have been proposed to explain it, each putting an emphasis on different events leading to functional translation and self-sustained system. Here, we propose a set of interactions that could have taken place in the prebiotic environment. According to our hypothesis, hybridization-induced proximity of short aminoacylated RNAs led to the synthesis of peptides of random sequence. We postulate that among these emerged a type of peptide(s) capable of stimulating the interaction between specific RNAs and specific amino acids, which we call "bridge peptide" (BP). We conclude that translation should have emerged at the same time when the standard genetic code begun to evolve due to the stabilizing effect on RNA-peptide complexes with the help of BPs. Ribosomes, ribozymes, and the enzyme-directed RNA replication could co-evolve within the same period, as logical outcome of RNA-peptide world without the need of RNA only self-sustained step.
Collapse
Affiliation(s)
- Dimiter Kunnev
- Roswell Park Cancer Institute, Department of Molecular & Cellular Biology, Buffalo, NY 14263, USA.
| | - Anastas Gospodinov
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. 21, Sofia 1113, Bulgaria.
| |
Collapse
|
8
|
Vitas M, Dobovišek A. In the Beginning was a Mutualism - On the Origin of Translation. ORIGINS LIFE EVOL B 2018; 48:223-243. [PMID: 29713988 DOI: 10.1007/s11084-018-9557-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 04/23/2018] [Indexed: 12/28/2022]
Abstract
The origin of translation is critical for understanding the evolution of life, including the origins of life. The canonical genetic code is one of the most dominant aspects of life on this planet, while the origin of heredity is one of the key evolutionary transitions in living world. Why the translation apparatus evolved is one of the enduring mysteries of molecular biology. Assuming the hypothesis, that during the emergence of life evolution had to first involve autocatalytic systems which only subsequently acquired the capacity of genetic heredity, we propose and discuss possible mechanisms, basic aspects of the emergence and subsequent molecular evolution of translation and ribosomes, as well as enzymes as we know them today. It is possible, in this sense, to view the ribosome as a digital-to-analogue information converter. The proposed mechanism is based on the abilities and tendencies of short RNA and polypeptides to fold and to catalyse biochemical reactions. The proposed mechanism is in concordance with the hypothesis of a possible chemical co-evolution of RNA and proteins in the origin of the genetic code or even more generally at the early evolution of life on Earth. The possible abundance and availability of monomers at prebiotic conditions are considered in the mechanism. The hypothesis that early polypeptides were folding on the RNA scaffold is also considered and mutualism in molecular evolutionary development of RNA and peptides is favoured.
Collapse
Affiliation(s)
- Marko Vitas
- , Laze pri Borovnici 38, Borovnica, Slovenia.
| | - Andrej Dobovišek
- Faculty of Natural Sciences and Mathematics, University of Maribor, Koroška cesta 160, 2000, Maribor, Slovenia
| |
Collapse
|
9
|
Stadlbauer P, Šponer J, Costanzo G, Di Mauro E, Pino S, Šponer JE. Tetraloop-like geometries could form the basis of the catalytic activity of the most ancient ribooligonucleotides. Chemistry 2015; 21:3596-604. [PMID: 25640446 DOI: 10.1002/chem.201406140] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Indexed: 11/09/2022]
Abstract
The origin of the catalytic activity of ancient oligonucleotides is a largely unexplored field of contemporary science. In the current work we use molecular dynamics simulations to investigate the plausibility of tetraloop-like overhang geometries to initiate transphosphorylation reactions that lead to ligation and terminal cleavage in simple, Watson-Crick (WC) complementary oligoC/oligoG sequences observed experimentally. We show a series of examples of known tetraloop architectures, which can be adopted by the unpaired overhangs of short oligonucleotide sequences for a sufficiently long time to enable chemical reactions that lead to simple ribozyme-like catalytic activity. Thus, our computations demonstrate that the role of non-WC interactions at the emergence of the most ancient catalytic oligonucleotides could be more significant than ever believed.
Collapse
Affiliation(s)
- Petr Stadlbauer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno (Czech Republic)
| | | | | | | | | | | |
Collapse
|