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Frenkel-Pinter M, Haynes JW, Mohyeldin AM, C M, Sargon AB, Petrov AS, Krishnamurthy R, Hud NV, Williams LD, Leman LJ. Mutually stabilizing interactions between proto-peptides and RNA. Nat Commun 2020; 11:3137. [PMID: 32561731 PMCID: PMC7305224 DOI: 10.1038/s41467-020-16891-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/28/2020] [Indexed: 12/16/2022] Open
Abstract
The close synergy between peptides and nucleic acids in current biology is suggestive of a functional co-evolution between the two polymers. Here we show that cationic proto-peptides (depsipeptides and polyesters), either produced as mixtures from plausibly prebiotic dry-down reactions or synthetically prepared in pure form, can engage in direct interactions with RNA resulting in mutual stabilization. Cationic proto-peptides significantly increase the thermal stability of folded RNA structures. In turn, RNA increases the lifetime of a depsipeptide by >30-fold. Proto-peptides containing the proteinaceous amino acids Lys, Arg, or His adjacent to backbone ester bonds generally promote RNA duplex thermal stability to a greater magnitude than do analogous sequences containing non-proteinaceous residues. Our findings support a model in which tightly-intertwined biological dependencies of RNA and protein reflect a long co-evolutionary history that began with rudimentary, mutually-stabilizing interactions at early stages of polypeptide and nucleic acid co-existence.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,NASA Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jay W Haynes
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Ahmad M Mohyeldin
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Martin C
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Alyssa B Sargon
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Anton S Petrov
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,NASA Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ramanarayanan Krishnamurthy
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA.,Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Nicholas V Hud
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Loren Dean Williams
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA. .,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA. .,NASA Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Luke J Leman
- NSF/NASA Center for Chemical Evolution, Atlanta, GA, USA. .,Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA.
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Frenkel-Pinter M, Samanta M, Ashkenasy G, Leman LJ. Prebiotic Peptides: Molecular Hubs in the Origin of Life. Chem Rev 2020; 120:4707-4765. [PMID: 32101414 DOI: 10.1021/acs.chemrev.9b00664] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mousumi Samanta
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Luke J Leman
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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3
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Schreiber A, Huber MC, Schiller SM. Prebiotic Protocell Model Based on Dynamic Protein Membranes Accommodating Anabolic Reactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:9593-9610. [PMID: 31287709 DOI: 10.1021/acs.langmuir.9b00445] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The nature of the first prebiotic compartments and their possible minimal molecular composition is of great importance in the origin of life scenarios. Current protocell model membranes are proposed to be lipid-based. This paradigm has several shortcomings such as limited membrane stability of monoacyl lipid-based membranes (e.g., fatty acids), missing pathways to synthesize protocell membrane components (e.g., phospholipids) under early earth conditions, and the requirement for different classes of molecules for the formation of compartments and the catalysis of reactions. Amino acids on the other hand are known to arise and persist with remarkable abundance under early earth conditions since the fundamental Miller-Urey experiments. They were also postulated early to form protocellular structures, for example, proteinoid capsules. Here, we present a protocell model constituted by membranes assembled from amphiphilic proteins based on prebiotic amino acids. Self-assembled dynamic protein membrane-based compartments (PMBCs) are impressively stable and compatible with prevalent cellular membrane constituents forming protein-only or protein-lipid hybrid membranes. They can embed processes essential for extant living cells, such as enclosure of molecules, membrane fusion, phase separation, and complex biosynthetic elements from modern cells demonstrating "upward" compatibility. Our findings suggest that prebiotic PMBCs represent a new type of protocell as a possible ancestor of current lipid-based cells. The presented prebiotic PMBC model can be used to design artificial cells, important for the study of structural, catalytic, and evolutionary pathways related to the emergence of life.
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Affiliation(s)
- Andreas Schreiber
- Zentrum für Biosystemanalyse (ZBSA) , Albert-Ludwigs-Universität Freiburg , 7 Habsburgerstrasse 49 , D-79104 Freiburg , Germany
- Faculty of Biology , University of Freiburg , Schänzlestrasse 1 , D-79104 Freiburg , Germany
| | - Matthias C Huber
- Zentrum für Biosystemanalyse (ZBSA) , Albert-Ludwigs-Universität Freiburg , 7 Habsburgerstrasse 49 , D-79104 Freiburg , Germany
- Faculty of Biology , University of Freiburg , Schänzlestrasse 1 , D-79104 Freiburg , Germany
| | - Stefan M Schiller
- Zentrum für Biosystemanalyse (ZBSA) , Albert-Ludwigs-Universität Freiburg , 7 Habsburgerstrasse 49 , D-79104 Freiburg , Germany
- Faculty of Biology , University of Freiburg , Schänzlestrasse 1 , D-79104 Freiburg , Germany
- BIOSS Centre for Biological Signalling Studies , University of Freiburg , Schänzlestrasse 18 , D-79104 Freiburg , Germany
- IMTEK Department of Microsystems Engineering , University of Freiburg , Georges-Köhler-Allee 103 , D-79110 Freiburg , Germany
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies , University of Freiburg , Georges-Köhler-Allee 105 , D-79110 Freiburg , Germany
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Shen G, Fang H, Song Y, Bielska AA, Wang Z, Taylor JSA. Phospholipid conjugate for intracellular delivery of peptide nucleic acids. Bioconjug Chem 2009; 20:1729-36. [PMID: 19678628 DOI: 10.1021/bc900048y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptide nucleic acids (PNAs) have a number of attractive features that have made them an ideal choice for antisense and antigene-based tools, probes, and drugs, but their poor membrane permeability has limited their application as therapeutic or diagnostic agents. Herein, we report a general method for the synthesis of phospholipid-PNAs (LP-PNAs) and compare the effect of noncleavable lipids and bioreductively cleavable lipids (L and LSS) and phospholipid (LP) on the splice-correcting bioactivity of a PNA bearing the cell penetrating Arg9 group (PNA-R9). While the three constructs show similar and increasing bioactivity at 1-3 microM, the activity of LP-PNA-R9 continues to increase from 4-6 microM, while the activity of L-PNA-R9 remains constant and that of LSS-PNA-R9 decreases rapidly in parallel with their relative cytotoxicity. The activity of both LP-PNA-R9 and L-PNA-R9 dramatically increased in the presence of chloroquine, as expected for an endocytotic entry mechanism. The constructs were also found to have CMC values of 1.0 and 4.5 microM, respectively, in 150 mM NaCl, pH 7 water, suggesting that micelle formation may play a hitherto unrecognized role in modulating toxicity and/or facilitating endocytosis.
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Affiliation(s)
- Gang Shen
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, USA
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Yiadom KPAB, Hammamieh R, Ukpabi N, Tsang P, Yang DCH. A peptide from the extension of Lys-tRNA synthetase binds to transfer RNA and DNA. Peptides 2003; 24:987-98. [PMID: 14499277 DOI: 10.1016/s0196-9781(03)00188-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Eukaryotic aminoacyl-tRNA synthetases have dispensable extensions appended at the amino- or carboxyl-terminus as compared to their bacterial counterparts. While a synthetic peptide corresponding to the basic amino-terminal extension in yeast Asp-tRNA synthetase binds to DNA, the extension in the intact protein evidently binds to tRNA and enhances the tRNA specificity of Asp-tRNA synthetase. On the other hand, the amino-terminal extension in human Asp-tRNA synthetase, both within the intact protein and as a synthetic peptide, binds to tRNA. Here, the tRNA binding of a synthetic peptide, hKRS(Arg(25)-Glu(42)), corresponding to the amino-terminal extension of human Lys-tRNA synthetase (hKRS) was analyzed. This basic peptide bound to tRNA(Phe) and the apparent-binding constant increased with increasing concentrations of Mg(2+). The hKRS peptide also bound to DNA and polyphosphate; however, the apparent DNA-binding constants decreased at increasing concentrations of Mg(2+). The ability of the hKRS peptide to adopt alpha-helical conformation was demonstrated by NMR and circular dichroism. A Lys-rich peptide derived from the elongation factor 1alpha was also examined and bound to DNA but not to tRNA.
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MESH Headings
- Amino Acid Sequence
- Cations, Divalent/chemistry
- Circular Dichroism
- DNA/chemistry
- DNA/metabolism
- DNA-Binding Proteins/chemical synthesis
- DNA-Binding Proteins/chemistry
- DNA-Binding Proteins/metabolism
- Humans
- Hydrogen-Ion Concentration
- Lysine-tRNA Ligase/chemistry
- Magnesium Chloride/chemistry
- Magnetic Resonance Spectroscopy
- Models, Molecular
- Molecular Sequence Data
- Molecular Weight
- Peptide Elongation Factor 1/chemistry
- Peptides/chemical synthesis
- Peptides/chemistry
- Peptides/metabolism
- Polyphosphates/chemistry
- Protein Binding
- Protein Structure, Secondary
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- RNA, Transfer, Met/chemistry
- RNA, Transfer, Met/metabolism
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/metabolism
- RNA-Binding Proteins/chemical synthesis
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/metabolism
- Sodium Chloride/chemistry
- Spectrometry, Fluorescence
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Trifluoroethanol/chemistry
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