1
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Guo D, Zhang Z, Sun J, Zhao H, Hou W, Du N. A Fusion-Growth Protocell Model Based on Vesicle Interactions with Pyrite Particles. Molecules 2024; 29:2664. [PMID: 38893538 PMCID: PMC11173516 DOI: 10.3390/molecules29112664] [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: 04/25/2024] [Revised: 05/22/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Protocell models play a pivotal role in the exploration of the origin of life. Vesicles are one type of protocell model that have attracted much attention. Simple single-chain amphiphiles (SACs) and organic small molecules (OSMs) possess primitive relevance and were most likely the building blocks of protocells on the early Earth. OSM@SAC vesicles have been considered to be plausible protocell models. Pyrite (FeS2), a mineral with primitive relevance, is ubiquitous in nature and plays a crucial role in the exploration of the origin of life in the mineral-water interface scenario. "How do protocell models based on OSM@SAC vesicles interact with a mineral-water interface scenario that simulates a primitive Earth environment" remains an unresolved question. Hence, we select primitive relevant sodium monododecyl phosphate (SDP), isopentenol (IPN) and pyrite (FeS2) mineral particles to build a protocell model. The model investigates the basic physical and chemical properties of FeS2 particles and reveals the effects of the size, content and duration of interaction of FeS2 particles on IPN@SDP vesicles. This deepens the understanding of protocell growth mechanisms in scenarios of mineral-water interfaces in primitive Earth environments and provides new information for the exploration of the origin of life.
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Affiliation(s)
- Dong Guo
- Key Laboratory of Colloid and Interface Chemistry (Ministry of Education), School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Ziyue Zhang
- Key Laboratory of Colloid and Interface Chemistry (Ministry of Education), School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Jichao Sun
- Key Laboratory of Colloid and Interface Chemistry (Ministry of Education), School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Hui Zhao
- National Engineering Technology Research Center for Colloidal Materials, Shandong University, Jinan 250100, China
| | - Wanguo Hou
- Key Laboratory of Colloid and Interface Chemistry (Ministry of Education), School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
- National Engineering Technology Research Center for Colloidal Materials, Shandong University, Jinan 250100, China
| | - Na Du
- Key Laboratory of Colloid and Interface Chemistry (Ministry of Education), School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
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2
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Shinn EJ, Tajkhorshid E. Generating Concentration Gradients across Membranes for Molecular Dynamics Simulations of Periodic Systems. Int J Mol Sci 2024; 25:3616. [PMID: 38612428 PMCID: PMC11012027 DOI: 10.3390/ijms25073616] [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: 02/20/2024] [Revised: 03/15/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
The plasma membrane forms the boundary between a living entity and its environment and acts as a barrier to permeation and flow of substances. Several computational means of calculating permeability have been implemented for molecular dynamics (MD) simulations-based approaches. Except for double bilayer systems, most permeability studies have been performed under equilibrium conditions, in large part due to the challenges associated with creating concentration gradients in simulations utilizing periodic boundary conditions. To enhance the scientific understanding of permeation and complement the existing computational means of characterizing membrane permeability, we developed a non-equilibrium method that enables the generation and maintenance of steady-state gradients in MD simulations. We utilize PBCs advantageously by imposing a directional bias to the motion of permeants so that their crossing of the boundary replenishes the gradient, like a previous study on ions. Under these conditions, a net flow of permeants across membranes may be observed to determine bulk permeability by a direct application of J=PΔc. In the present study, we explore the results of its application to an exemplary O2 and POPC bilayer system, demonstrating accurate and precise permeability measurements. In addition, we illustrate the impact of permeant concentration and the choice of thermostat on the permeability. Moreover, we demonstrate that energetics of permeation can be closely examined by the dissipation of the gradient across the membrane to gain nuanced insights into the thermodynamics of permeability.
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Affiliation(s)
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Resource Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;
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3
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Ushiyama R, Nanjo S, Tsugane M, Sato R, Matsuura T, Suzuki H. Identifying Conditions for Protein Synthesis Inside Giant Vesicles Using Microfluidics toward Standardized Artificial Cell Production. ACS Synth Biol 2024; 13:68-76. [PMID: 38032418 DOI: 10.1021/acssynbio.3c00629] [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] [Indexed: 12/01/2023]
Abstract
To expand the range of practical applications of artificial cells, it is important to standardize the production process of giant (cell-sized) vesicles that encapsulate reconstituted biochemical reaction systems. For this purpose, a rapidly developing microfluidics-based giant vesicle generation system is a promising approach, similar to the droplet assay systems that are already widespread in the market. In this study, we examined the composition of the solutions used to generate vesicles encapsulating the in vitro transcription-translation (IVTT) system. We show that tuning of the lipid composition and adding poly(vinyl alcohol) to the outer solution improved the stability of the transition process into the lipid membrane so that protein synthesis proceeded in vesicles. The direct integration of α-hemolysin nanopores synthesized in situ was also demonstrated. These protein-synthesizing monodisperse giant vesicles can be prepared by using a simple microfluidic fabrication/operation with a commercial IVTT system.
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Affiliation(s)
- Ryota Ushiyama
- Department of Precision Mechanics, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Satoshi Nanjo
- Department of Precision Mechanics, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Mamiko Tsugane
- Department of Precision Mechanics, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Reiko Sato
- Department of Precision Mechanics, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Tomoaki Matsuura
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-i7E Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Hiroaki Suzuki
- Department of Precision Mechanics, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
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4
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Dávila MJ, Mayer C. Structural Phenomena in a Vesicle Membrane Obtained through an Evolution Experiment: A Study Based on MD Simulations. Life (Basel) 2023; 13:1735. [PMID: 37629592 PMCID: PMC10455627 DOI: 10.3390/life13081735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
The chemical evolution of biomolecules was clearly affected by the overall extreme environmental conditions found on Early Earth. Periodic temperature changes inside the Earth's crust may have played a role in the emergence and survival of functional peptides embedded in vesicular compartments. In this study, all-atom molecular dynamic (MD) simulations were used to elucidate the effect of temperature on the properties of functionalized vesicle membranes. A plausible prebiotic system was selected, constituted by a model membrane bilayer from an equimolar mixture of long-chain fatty acids and fatty amines, and an octapeptide, KSPFPFAA, previously identified as an optimized functional peptide in an evolution experiment. This peptide tends to form the largest spontaneous aggregates at higher temperatures, thereby enhancing the pore-formation process and the eventual transfer of essential molecules in a prebiotic scenario. The analyses also suggest that peptide-amphiphile interactions affect the structural properties of the membrane, with a significant increase in the degree of interdigitation at the lowest temperatures under study.
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Affiliation(s)
- María J. Dávila
- Institute of Physical Chemistry, CENIDE, University of Duisburg-Essen, 45141 Essen, Germany;
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5
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Zhang S, Lowe L, Anees P, Krishnan Y, Fai T, Szostak J, Wang A. Passive endocytosis in model protocells. Proc Natl Acad Sci U S A 2023; 120:e2221064120. [PMID: 37276401 PMCID: PMC10268330 DOI: 10.1073/pnas.2221064120] [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: 01/02/2023] [Accepted: 05/10/2023] [Indexed: 06/07/2023] Open
Abstract
Semipermeable membranes are a key feature of all living organisms. While specialized membrane transporters in cells can import otherwise impermeable nutrients, the earliest cells would have lacked a mechanism to import nutrients rapidly under nutrient-rich circumstances. Using both experiments and simulations, we find that a process akin to passive endocytosis can be recreated in model primitive cells. Molecules that are too impermeable to be absorbed can be taken up in a matter of seconds in an endocytic vesicle. The internalized cargo can then be slowly released over hours, into the main lumen or putative cytoplasm. This work demonstrates a way by which primitive life could have broken the symmetry of passive permeation prior to the evolution of protein transporters.
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Affiliation(s)
- Stephanie J. Zhang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA02114
| | - Lauren A. Lowe
- School of Chemistry, University of New South Wales Sydney, Bedegal Country, Sydney, NSW2052, Australia
- Australian Centre for Astrobiology, University of New South Wales Sydney, Bedegal Country, Sydney, NSW2052, Australia
- ARC Centre of Excellence in Synthetic Biology, University of New South Wales Sydney, Bedegal Country, Sydney, NSW2052, Australia
| | - Palapuravan Anees
- Neuroscience Institute, University of Chicago, Chicago, IL60637
- Department of Chemistry, University of Chicago, Chicago, IL60637
| | - Yamuna Krishnan
- Neuroscience Institute, University of Chicago, Chicago, IL60637
- Department of Chemistry, University of Chicago, Chicago, IL60637
- Institute of Biophysical Dynamics, University of Chicago, Chicago, IL60637
| | - Thomas G. Fai
- Department of Mathematics, Brandeis University, Waltham, MA02453
| | - Jack W. Szostak
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA02114
- Department of Chemistry, University of Chicago, Chicago, IL60637
- HHMI, Massachusetts General Hospital, Boston, MA02114
| | - Anna Wang
- School of Chemistry, University of New South Wales Sydney, Bedegal Country, Sydney, NSW2052, Australia
- Australian Centre for Astrobiology, University of New South Wales Sydney, Bedegal Country, Sydney, NSW2052, Australia
- ARC Centre of Excellence in Synthetic Biology, University of New South Wales Sydney, Bedegal Country, Sydney, NSW2052, Australia
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6
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Dagar S, Sarkar S, Rajamani S. Nonenzymatic Template-Directed Primer Extension Using 2'-3' Cyclic Nucleotides Under Wet-Dry Cycles. ORIGINS LIFE EVOL B 2023; 53:43-60. [PMID: 37243884 DOI: 10.1007/s11084-023-09636-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 04/15/2023] [Indexed: 05/29/2023]
Abstract
RNA World Hypothesis is centred around the idea of a period in the early history of life's origin, wherein nonenzymatic oligomerization and replication of RNA resulted in functional ribozymes. Previous studies in this endeavour have demonstrated template-directed primer extension using chemically modified nucleotides and primers. Nonetheless, similar studies that used non-activated nucleotides led to the formation of RNA only with abasic sites. In this study, we report template-directed primer extension with prebiotically relevant cyclic nucleotides, under dehydration-rehydration (DH-RH) cycles occurring at high temperature (90 °C) and alkaline conditions (pH 8). 2'-3' cyclic nucleoside monophosphates (cNMP) resulted in primer extension, while 3'-5' cNMP failed to do so. Intact extension of up to two nucleotide additions was observed with both canonical hydroxy-terminated (OH-primer) and activated amino-terminated (NH2-primer) primers. We demonstrate primer extension reactions using both purine and pyrimidine 2'-3' cNMPs, with higher product yield observed during cAMP additions. Further, the presence of lipid was observed to significantly enhance the extended product in cCMP reactions. In all, our study provides a proof-of-concept for nonenzymatic primer extension of RNA, using intrinsically activated prebiotically relevant cyclic nucleotides as monomers.
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Affiliation(s)
- Shikha Dagar
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Susovan Sarkar
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Sudha Rajamani
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India.
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7
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Zhang SJ, Lowe LA, Anees P, Krishnan Y, Fai TG, Szostak JW, Wang A. Passive endocytosis in model protocells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.07.522792. [PMID: 37205531 PMCID: PMC10187163 DOI: 10.1101/2023.01.07.522792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Semipermeable membranes are a key feature of all living organisms. While specialized membrane transporters in cells can import otherwise impermeable nutrients, the earliest cells would have lacked a mechanism to import nutrients rapidly under nutrient-rich circumstances. Using both experiments and simulations, we find that a process akin to passive endocytosis can be recreated in model primitive cells. Molecules that are too impermeable to be absorbed can be taken up in a matter of seconds in an endocytic vesicle. The internalized cargo can then be slowly released over hours, into the main lumen or putative cytoplasm. This work demonstrates a way by which primitive life could have broken the symmetry of passive permeation prior to the evolution of protein transporters.
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8
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Bailoni E, Partipilo M, Coenradij J, Grundel DAJ, Slotboom DJ, Poolman B. Minimal Out-of-Equilibrium Metabolism for Synthetic Cells: A Membrane Perspective. ACS Synth Biol 2023; 12:922-946. [PMID: 37027340 PMCID: PMC10127287 DOI: 10.1021/acssynbio.3c00062] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Indexed: 04/08/2023]
Abstract
Life-like systems need to maintain a basal metabolism, which includes importing a variety of building blocks required for macromolecule synthesis, exporting dead-end products, and recycling cofactors and metabolic intermediates, while maintaining steady internal physical and chemical conditions (physicochemical homeostasis). A compartment, such as a unilamellar vesicle, functionalized with membrane-embedded transport proteins and metabolic enzymes encapsulated in the lumen meets these requirements. Here, we identify four modules designed for a minimal metabolism in a synthetic cell with a lipid bilayer boundary: energy provision and conversion, physicochemical homeostasis, metabolite transport, and membrane expansion. We review design strategies that can be used to fulfill these functions with a focus on the lipid and membrane protein composition of a cell. We compare our bottom-up design with the equivalent essential modules of JCVI-syn3a, a top-down genome-minimized living cell with a size comparable to that of large unilamellar vesicles. Finally, we discuss the bottlenecks related to the insertion of a complex mixture of membrane proteins into lipid bilayers and provide a semiquantitative estimate of the relative surface area and lipid-to-protein mass ratios (i.e., the minimal number of membrane proteins) that are required for the construction of a synthetic cell.
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Affiliation(s)
- Eleonora Bailoni
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Michele Partipilo
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Jelmer Coenradij
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Douwe A. J. Grundel
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Dirk J. Slotboom
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Bert Poolman
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
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9
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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: 0] [Impact Index Per Article: 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.
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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
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10
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Towards an RNA/Peptides World by the Direct RNA Template Mechanism: The Emergence of Membrane-Stabilizing Peptides in RNA-Based Protocells. Life (Basel) 2023; 13:life13020523. [PMID: 36836881 PMCID: PMC9966593 DOI: 10.3390/life13020523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/29/2023] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
How functional peptides may have arisen is a significant problem for the scenario of the RNA world. An attractive idea, the direct RNA template (DRT) hypothesis, proposes that RNA molecules can bind amino acids specifically and promote the synthesis of corresponding peptides, thereby starting the RNA/peptides world. To investigate the plausibility of this idea, we modeled the emergence of a "membrane-stabilizing peptide" in RNA-based protocells-such a peptide was suggested to have appeared early in the RNA world based on experimental evidence. The computer simulation demonstrated that the protocells containing the "RNA gene" encoding this peptide may spread in the system owing to the peptide's function. The RNA gene may either originate de novo in protocells or emerge in protocells already containing ribozymes-here we adopt a nucleotide synthetase ribozyme as an example. Furthermore, interestingly, we show that a "nucleotide synthetase peptide" encoded by RNA (also via the DRT mechanism) may substitute the nucleotide synthetase ribozyme in evolution, which may represent how "functional-takeover" in the RNA world could have occurred. Overall, we conclude that the transition from the RNA world towards an RNA/peptides world may well have been mediated by the DRT mechanism. Remarkably, the successful modeling on the emergence of membrane-stabilizing peptide in RNA-based protocells is per se significant, which may imply a "promising" way for peptides to enter the RNA world, especially considering the weak interaction between RNA and the membrane in chemistry.
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11
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Martins FA, Freitas MP. Theoretical Exploitation of 1,2,3,4,5,6-Hexachloro- and 1,2,3,4,5,6-Hexafluorocyclohexane Isomers as Biologically Active Compounds. Chemphyschem 2023; 24:e202200450. [PMID: 36197010 DOI: 10.1002/cphc.202200450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/03/2022] [Indexed: 11/08/2022]
Abstract
Hexachlorocyclohexanes (HCHs) have been widely explored as biological compounds during the last century. However, most of them were banned due to their potential toxicity in humans, animals, and the environment. Revisiting HCHs to explore their biological activity while improving key features is valuable and may lead to a new class of pesticides that utilizes the biological response of HCHs without their toxic characteristics. In this sense, the fluorine atom can be a possible alternative since a large number of therapeutics and agrochemicals have been developed with this halogen in their structure. We have evaluated herein the conformational behavior of HCHs and their bioisosteric fluorinated compounds, namely, hexafluorocyclohexanes (HFHs), through quantum-chemical calculations. We also explored the potential of the HCH and HFH isomers as biological compounds by docking them inside three possible targets. It was demonstrated that HCH and HFH have similar ligand-protein interactions with three pockets: the picrotoxin and barbiturate sites of the GABAA receptor and the ryanodine receptor. The results support HFHs as possible alternatives for HCHs since the replacement of Cl with F does not forfeit the main ligand-protein interactions. Finally, we demonstrated that HFHs have a lower log P than HCHs by almost two logarithmic units. This result highlights the role of fluorine in distribution and bioaccumulation.
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Affiliation(s)
- Francisco A Martins
- Department of Chemistry, Institute of Natural Sciences, Federal University of Lavras, 37200-900, Lavras, MG, Brazil
| | - Matheus P Freitas
- Department of Chemistry, Institute of Natural Sciences, Federal University of Lavras, 37200-900, Lavras, MG, Brazil
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12
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Cao S, Ivanov T, de Souza Melchiors M, Landfester K, Caire da Silva L. Controlled Membrane Transport in Polymeric Biomimetic Nanoreactors. Chembiochem 2023; 24:e202200718. [PMID: 36715701 DOI: 10.1002/cbic.202200718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023]
Abstract
Polymersome-based biomimetic nanoreactors (PBNs) have generated great interest in nanomedicine and cell mimicry due to their robustness, tuneable chemistry, and broad applicability in biologically relevant fields. In this concept review, we mainly discuss the state of the art in functional polymersomes as biomimetic nanoreactors with membrane-controlled transport. PBNs that use environmental changes or external stimuli to adjust membrane permeability while maintaining structural integrity are highlighted. By encapsulating catalytic species, PBNs are able to convert inactive substrates into functional products in a controlled manner. In addition, special attention is paid to the use of PBNs as tailored artificial organelles with biomedical applications in vitro and in vivo, facilitating the fabrication of next-generation artificial organelles as therapeutic nanocompartments.
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Affiliation(s)
- Shoupeng Cao
- Department of Physical Chemistry of Polymers, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Tsvetomir Ivanov
- Department of Physical Chemistry of Polymers, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Marina de Souza Melchiors
- Department of Physical Chemistry of Polymers, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Katharina Landfester
- Department of Physical Chemistry of Polymers, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Lucas Caire da Silva
- Department of Physical Chemistry of Polymers, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
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13
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Sarkar S, Dagar S, Lahiri K, Rajamani S. pH-Responsive Self-Assembled Compartments as Tuneable Model Protocellular Membrane Systems. Chembiochem 2022; 23:e202200371. [PMID: 35968882 DOI: 10.1002/cbic.202200371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/10/2022] [Indexed: 01/25/2023]
Abstract
Prebiotically plausible single-chain amphiphiles are enticing as model protocellular compartments to study the emergence of cellular life, owing to their self-assembling properties. Here, we investigated the self-assembly behaviour of mono-N-dodecyl phosphate (DDP) and mixed systems of DDP with 1-dodecanol (DDOH) at varying pH conditions. Membranes composed of DDP showed pH-responsive vesicle formation in a wide range of pH with a low critical bilayer concentration (CBC). Further, the addition of DDOH to DDP membrane system enhanced vesicle formation and stability in alkaline pH regimes. We also compared the high-temperature behaviour of DDP and DDP:DDOH membranes with conventional fatty acid membranes. Both, DDP and DDP:DDOH mixed membranes possess packing that is similar to decanoic acid membrane. However, the micropolarity of these systems is similar to phospholipid membranes. Finally, the pH-dependent modulation of different phospholipid membranes doped with DDP was also demonstrated to engineer tuneable membranes with potential translational implications.
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Affiliation(s)
- Susovan Sarkar
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Shikha Dagar
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Kushan Lahiri
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Sudha Rajamani
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
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14
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Karoui H, Patwal PS, Pavan Kumar BVVS, Martin N. Chemical Communication in Artificial Cells: Basic Concepts, Design and Challenges. Front Mol Biosci 2022; 9:880525. [PMID: 35720123 PMCID: PMC9199989 DOI: 10.3389/fmolb.2022.880525] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/12/2022] [Indexed: 11/13/2022] Open
Abstract
In the past decade, the focus of bottom-up synthetic biology has shifted from the design of complex artificial cell architectures to the design of interactions between artificial cells mediated by physical and chemical cues. Engineering communication between artificial cells is crucial for the realization of coordinated dynamic behaviours in artificial cell populations, which would have implications for biotechnology, advanced colloidal materials and regenerative medicine. In this review, we focus our discussion on molecular communication between artificial cells. We cover basic concepts such as the importance of compartmentalization, the metabolic machinery driving signaling across cell boundaries and the different modes of communication used. The various studies in artificial cell signaling have been classified based on the distance between sender and receiver cells, just like in biology into autocrine, juxtacrine, paracrine and endocrine signaling. Emerging tools available for the design of dynamic and adaptive signaling are highlighted and some recent advances of signaling-enabled collective behaviours, such as quorum sensing, travelling pulses and predator-prey behaviour, are also discussed.
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Affiliation(s)
- Hedi Karoui
- Univ. Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, Pessac, France
| | - Pankaj Singh Patwal
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, India
| | - B. V. V. S. Pavan Kumar
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, India
- *Correspondence: B. V. V. S. Pavan Kumar, ; Nicolas Martin,
| | - Nicolas Martin
- Univ. Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, Pessac, France
- *Correspondence: B. V. V. S. Pavan Kumar, ; Nicolas Martin,
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15
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Dávila MJ, Mayer C. Membrane Structure Obtained in an Experimental Evolution Process. Life (Basel) 2022; 12:life12020145. [PMID: 35207433 PMCID: PMC8875328 DOI: 10.3390/life12020145] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 11/24/2022] Open
Abstract
Recently, an evolution experiment was carried out in a cyclic process, which involved periodic vesicle formation in combination with peptide and vesicle selection. As an outcome, an octapeptide (KSPFPFAA) was identified which rapidly integrated into the vesicle membrane and, according to its significant accumulation, is obviously connected to a particular advantage of the corresponding functionalized vesicle. Here we report a molecular dynamics study of the structural details of the functionalized vesicle membrane, which was a product of this evolution process and is connected to several survival mechanisms. In order to elucidate the particular advantage of this structure, we performed all-atom molecular dynamics simulations to examine structural changes and interactions of the peptide (KSPFPFAA) with the given octadecanoic acid/octadecylamine (1:1) bilayer under acidic conditions. The calculations clearly demonstrate the specific interactions between the peptide and the membrane and reveal the mechanisms leading to the improved vesicle survival.
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16
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Sebastianelli L, Mansy SS. Origins of life: Encapsulating Darwinian evolution. Curr Biol 2022; 32:R44-R46. [PMID: 35015996 DOI: 10.1016/j.cub.2021.11.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Encapsulation of RNA within model protocells promotes folding, promotes the binding of substrates, promotes catalysis, and protects against denaturation. A new study argues for an active role of lipid vesicles in the origins of life.
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Affiliation(s)
| | - Sheref S Mansy
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada.
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17
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Joshi MP, Steller L, Van Kranendonk MJ, Rajamani S. Influence of Metal Ions on Model Protoamphiphilic Vesicular Systems: Insights from Laboratory and Analogue Studies. Life (Basel) 2021; 11:life11121413. [PMID: 34947944 PMCID: PMC8708898 DOI: 10.3390/life11121413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 02/03/2023] Open
Abstract
Metal ions strongly affect the self-assembly and stability of membranes composed of prebiotically relevant amphiphiles (protoamphiphiles). Therefore, evaluating the behavior of such amphiphiles in the presence of ions is a crucial step towards assessing their potential as model protocell compartments. We have recently reported vesicle formation by N-acyl amino acids (NAAs), an interesting class of protoamphiphiles containing an amino acid linked to a fatty acid via an amide linkage. Herein, we explore the effect of ions on the self-assembly and stability of model N-oleoyl glycine (NOG)-based membranes. Microscopic analysis showed that the blended membranes of NOG and Glycerol 1-monooleate (GMO) were more stable than pure NOG vesicles, both in the presence of monovalent and divalent cations, with the overall vesicle stability being 100-fold higher in the presence of a monovalent cation. Furthermore, both pure NOG and NOG + GMO mixed systems were able to self-assemble into vesicles in natural water samples containing multiple ions that were collected from active hot spring sites. Our study reveals that several aspects of the metal ion stability of NAA-based membranes are comparable to those of fatty acid-based systems, while also confirming the robustness of compositionally heterogeneous membranes towards high metal ion concentrations. Pertinently, the vesicle formation by NAA-based systems in terrestrial hot spring samples indicates the conduciveness of these low ionic strength freshwater systems for facilitating prebiotic membrane-assembly processes. This further highlights their potential to serve as a plausible niche for the emergence of cellular life on the early Earth.
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Affiliation(s)
- Manesh Prakash Joshi
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
- Correspondence: (M.P.J.); (S.R.); Tel.: +91-20-2590-8061 (S.R.)
| | - Luke Steller
- Australian Centre for Astrobiology, and School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, NSW 2052, Australia; (L.S.); (M.J.V.K.)
| | - Martin J. Van Kranendonk
- Australian Centre for Astrobiology, and School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, NSW 2052, Australia; (L.S.); (M.J.V.K.)
| | - Sudha Rajamani
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
- Correspondence: (M.P.J.); (S.R.); Tel.: +91-20-2590-8061 (S.R.)
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18
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Papalazarou V, Maddocks ODK. Supply and demand: Cellular nutrient uptake and exchange in cancer. Mol Cell 2021; 81:3731-3748. [PMID: 34547236 DOI: 10.1016/j.molcel.2021.08.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/27/2021] [Accepted: 08/19/2021] [Indexed: 12/24/2022]
Abstract
Nutrient supply and demand delineate cell behavior in health and disease. Mammalian cells have developed multiple strategies to secure the necessary nutrients that fuel their metabolic needs. This is more evident upon disruption of homeostasis in conditions such as cancer, when cells display high proliferation rates in energetically challenging conditions where nutritional sources may be scarce. Here, we summarize the main routes of nutrient acquisition that fuel mammalian cells and their implications in tumorigenesis. We argue that the molecular mechanisms of nutrient acquisition not only tip the balance between nutrient supply and demand but also determine cell behavior upon nutrient limitation and energetic stress and contribute to nutrient partitioning and metabolic coordination between different cell types in inflamed or tumorigenic environments.
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Affiliation(s)
- Vasileios Papalazarou
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow G61 1QH, UK
| | - Oliver D K Maddocks
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow G61 1QH, UK.
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19
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Martin N, Douliez J. Fatty Acid Vesicles and Coacervates as Model Prebiotic Protocells. CHEMSYSTEMSCHEM 2021. [DOI: 10.1002/syst.202100024] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Nicolas Martin
- Univ. Bordeaux CNRS Centre de Recherche Paul Pascal UMR 5031 115 Avenue du Dr. Albert Schweitzer 33600 Pessac France
| | - Jean‐Paul Douliez
- Univ. Bordeaux INRAE Biologie du Fruit et Pathologie UMR 1332 71 Avenue Edouard Bourlaux 33140 Villenave d'Ornon France
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20
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Kierkegaard A, Sundbom M, Yuan B, Armitage JM, Arnot JA, Droge STJ, McLachlan MS. Bioconcentration of Several Series of Cationic Surfactants in Rainbow Trout. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:8888-8897. [PMID: 34133133 PMCID: PMC8277129 DOI: 10.1021/acs.est.1c02063] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/22/2021] [Accepted: 06/07/2021] [Indexed: 05/03/2023]
Abstract
Cationic surfactants have a strong affinity to sorb to phospholipid membranes and thus possess an inherent potential to bioaccumulate, but there are few measurements of bioconcentration in fish. We measured the bioconcentration of 10 alkylamines plus two quaternary ammonium compounds in juvenile rainbow trout at pH 7.6, and repeated the measurements at pH 6.2 for 6 of these surfactants. The BCF of the amines with chain lengths ≤ C14 was positively correlated with chain length, increasing ∼0.5 log units per carbon. Their BCF was also pH dependent and approximately proportional to the neutral fraction of the amine in the water. The BCFs of the quaternary ammonium compounds showed no pH dependence and were >2 orders of magnitude less than for amines of the same chain length at pH 7.6. This indicates that systemic uptake of permanently charged cationic surfactants is limited. The behavior of the quaternary ammonium compounds and the two C16 amines studied was consistent with previous observations that these surfactants accumulate primarily to the gills and external surfaces of the fish. At pH 7.6 the BCF exceeded 2000 L kg-1 for 4 amines with chains ≥ C13, showing that bioconcentration can be considerable for some longer chained cationic surfactants.
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Affiliation(s)
- Amelie Kierkegaard
- Department
of Environmental Science, Stockholm University, Stockholm SE-106 91, Sweden
| | - Marcus Sundbom
- Department
of Environmental Science, Stockholm University, Stockholm SE-106 91, Sweden
| | - Bo Yuan
- Department
of Environmental Science, Stockholm University, Stockholm SE-106 91, Sweden
| | - James M. Armitage
- AES
Armitage Environmental Sciences, Incorporated, Ottawa, Ontario K1L 8C3, Canada
| | - Jon A. Arnot
- ARC
Arnot Research and Consulting, Incorporated, Toronto, Ontario M4M 1W4, Canada
- Department
of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario MM1C 1A4, Canada
| | - Steven T. J. Droge
- Institute
for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam 1090 GE, The Netherlands
- Dutch
Board
for the Authorisation of Plant Protection Products and Biocides (Ctgb), Ede 6717 LL, The Netherlands
| | - Michael S. McLachlan
- Department
of Environmental Science, Stockholm University, Stockholm SE-106 91, Sweden
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21
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Toparlak Ö, Wang A, Mansy SS. Population-Level Membrane Diversity Triggers Growth and Division of Protocells. JACS AU 2021; 1:560-568. [PMID: 34467319 PMCID: PMC8395648 DOI: 10.1021/jacsau.0c00079] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Indexed: 06/01/2023]
Abstract
To date, multiple mechanisms have been described for the growth and division of model protocells, all of which exploit the lipid dynamics of fatty acids. In some examples, the more heterogeneous aggregate consisting of fatty acid and diacyl phospholipid or fatty acid and peptide grows at the expense of the more homogeneous aggregate containing a restricted set of lipids with similar dynamics. Imbalances between surface area and volume during growth can generate filamentous vesicles, which are typically divided by shear forces. Here, we describe another pathway for growth and division that depends simply on differences in the compositions of fatty acid membranes without additional components. Growth is driven by the thermodynamically favorable mixing of lipids between two populations, i.e., the system as a whole proceeds toward equilibrium. Division is the result of growth-induced curvature. Importantly, growth and division do not require a specific composition of lipids. For example, vesicles made from one type of lipid, e.g., short-chain fatty acids, grow and divide when fed with vesicles consisting of another type of lipid, e.g., long-chain fatty acids, and vice versa. After equilibration, additional rounds of growth and division could potentially proceed by the introduction of compositionally distinct aggregates. Since prebiotic synthesis likely gave rise to mixtures of lipids, the data are consistent with the presence of growing and dividing protocells on the prebiotic Earth.
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Affiliation(s)
- Ö.
Duhan Toparlak
- Department
of Cellular, Computational and Integrative Biology (D-CIBIO), University of Trento, Via Sommarive 9, 38123 Povo, TN, Italy
| | - Anna Wang
- School
of Chemistry and Australian Centre for Astrobiology, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Sheref S. Mansy
- Department
of Cellular, Computational and Integrative Biology (D-CIBIO), University of Trento, Via Sommarive 9, 38123 Povo, TN, Italy
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB T6G
2G2, Canada
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22
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Salvador López JM, Van Bogaert INA. Microbial fatty acid transport proteins and their biotechnological potential. Biotechnol Bioeng 2021; 118:2184-2201. [PMID: 33638355 DOI: 10.1002/bit.27735] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 01/08/2021] [Accepted: 02/24/2021] [Indexed: 12/11/2022]
Abstract
Fatty acid metabolism has been widely studied in various organisms. However, fatty acid transport has received less attention, even though it plays vital physiological roles, such as export of toxic free fatty acids or uptake of exogenous fatty acids. Hence, there are important knowledge gaps in how fatty acids cross biological membranes, and many mechanisms and proteins involved in these processes still need to be determined. The lack of information is more predominant in microorganisms, even though the identification of fatty acids transporters in these cells could lead to establishing new drug targets or improvements in microbial cell factories. This review provides a thorough analysis of the current information on fatty acid transporters in microorganisms, including bacteria, yeasts and microalgae species. Most available information relates to the model organisms Escherichia coli and Saccharomyces cerevisiae, but transport systems of other species are also discussed. Intracellular trafficking of fatty acids and their transport through organelle membranes in eukaryotic organisms is described as well. Finally, applied studies and engineering efforts using fatty acids transporters are presented to show the applied potential of these transporters and to stress the need for further identification of new transporters and their engineering.
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Affiliation(s)
- José M Salvador López
- BioPort Group, Faculty of Bioscience Engineering, Centre for Synthetic Biology (CSB), Ghent University, Ghent, Belgium
| | - Inge N A Van Bogaert
- BioPort Group, Faculty of Bioscience Engineering, Centre for Synthetic Biology (CSB), Ghent University, Ghent, Belgium
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23
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Sarkar S, Das S, Dagar S, Joshi MP, Mungi CV, Sawant AA, Patki GM, Rajamani S. Prebiological Membranes and Their Role in the Emergence of Early Cellular Life. J Membr Biol 2020; 253:589-608. [PMID: 33200235 DOI: 10.1007/s00232-020-00155-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/08/2020] [Indexed: 01/30/2023]
Abstract
Membrane compartmentalization is a fundamental feature of contemporary cellular life. Given this, it is rational to assume that at some stage in the early origins of life, membrane compartments would have potentially emerged to form a dynamic semipermeable barrier in primitive cells (protocells), protecting them from their surrounding environment. It is thought that such prebiological membranes would likely have played a crucial role in the emergence and evolution of life on the early Earth. Extant biological membranes are highly organized and complex, which is a consequence of a protracted evolutionary history. On the other hand, prebiotic membrane assemblies, which are thought to have preceded sophisticated contemporary membranes, are hypothesized to have been relatively simple and composed of single chain amphiphiles. Recent studies indicate that the evolution of prebiotic membranes potentially resulted from interactions between the membrane and its physicochemical environment. These studies have also speculated on the origin, composition, function and influence of environmental conditions on protocellular membranes as the niche parameters would have directly influenced their composition and biophysical properties. Nonetheless, the evolutionary pathways involved in the transition from prebiological membranes to contemporary membranes are largely unknown. This review critically evaluates existing research on prebiotic membranes in terms of their probable origin, composition, energetics, function and evolution. Notably, we outline new approaches that can further our understanding about how prebiotic membranes might have evolved in response to relevant physicochemical parameters that would have acted as pertinent selection pressures on the early Earth.
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Affiliation(s)
- Susovan Sarkar
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Souradeep Das
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Shikha Dagar
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Manesh Prakash Joshi
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Chaitanya V Mungi
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Anupam A Sawant
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Gauri M Patki
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Sudha Rajamani
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India.
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24
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Yun-Cárcamo S, Carrasco S, Rogan J, Correa-Burrows P, Valdivia JA. Stability and robustness of asymptotic autocatalytic systems. Sci Rep 2020; 10:15498. [PMID: 32968157 PMCID: PMC7511346 DOI: 10.1038/s41598-020-72580-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 08/21/2020] [Indexed: 11/09/2022] Open
Abstract
Here, we address the consequences of the extension in the space of a simple model of a system that is closed to efficient causation: the (M,R)-system model. To do so, we use a diffusion term to describe the collective motion of the nutrients’ concentration across the compartmentalized space that defines the organism. We show that the non-trivial stable steady state remains despite such generalization, as long as the system is small enough to deal with the transport of the precursors to feed the entire protocell and dispose of a sufficient concentration of it in its surroundings. Such consideration explains the emergence of a bifurcation with two parameters that we characterize. Finally, we show that the robustness of the system under catastrophic losses of catalysts also remains, preserving the original’s model character.
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Affiliation(s)
- Sohyoun Yun-Cárcamo
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, 7800024, Santiago, Chile.
| | - Sebastián Carrasco
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, 7800024, Santiago, Chile
| | - José Rogan
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, 7800024, Santiago, Chile
| | - Paulina Correa-Burrows
- Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, 7840390, Santiago, Chile
| | - Juan Alejandro Valdivia
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, 7800024, Santiago, Chile
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25
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Sarkar S, Dagar S, Verma A, Rajamani S. Compositional heterogeneity confers selective advantage to model protocellular membranes during the origins of cellular life. Sci Rep 2020; 10:4483. [PMID: 32161377 PMCID: PMC7066133 DOI: 10.1038/s41598-020-61372-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 02/24/2020] [Indexed: 12/21/2022] Open
Abstract
Protocellular membranes are thought to be composed of mixtures of single chain amphiphiles, such as fatty acids and their derivatives, moieties that would have been part of the complex prebiotic chemical landscape. The composition and physico-chemical properties of these prebiological membranes would have been significantly affected and regulated by their environment. In this study, pertinent properties were systematically characterized, under early Earth conditions. Two different fatty acids were mixed with their respective alcohol and/or glycerol monoester derivatives to generate combinations of binary and tertiary membrane systems. Their properties were then evaluated as a function of multiple factors including their stability under varying pH, varying Mg2+ ion concentrations, dilution regimes, and their permeability to calcein. Our results demonstrate how environmental constraints would have acted as important prebiotic selection pressures to shape the evolution of prebiological membranes. The study also illustrates that compositionally diverse membrane systems are more stable and robust to multiple selection pressures, thereby making them more suitable for supporting protocellular life.
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Affiliation(s)
- Susovan Sarkar
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Shikha Dagar
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Ajay Verma
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Sudha Rajamani
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India.
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26
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Membraneless polyester microdroplets as primordial compartments at the origins of life. Proc Natl Acad Sci U S A 2019; 116:15830-15835. [PMID: 31332006 DOI: 10.1073/pnas.1902336116] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Compartmentalization was likely essential for primitive chemical systems during the emergence of life, both for preventing leakage of important components, i.e., genetic materials, and for enhancing chemical reactions. Although life as we know it uses lipid bilayer-based compartments, the diversity of prebiotic chemistry may have enabled primitive living systems to start from other types of boundary systems. Here, we demonstrate membraneless compartmentalization based on prebiotically available organic compounds, α-hydroxy acids (αHAs), which are generally coproduced along with α-amino acids in prebiotic settings. Facile polymerization of αHAs provides a model pathway for the assembly of combinatorially diverse primitive compartments on early Earth. We characterized membraneless microdroplets generated from homo- and heteropolyesters synthesized from drying solutions of αHAs endowed with various side chains. These compartments can preferentially and differentially segregate and compartmentalize fluorescent dyes and fluorescently tagged RNA, providing readily available compartments that could have facilitated chemical evolution by protecting, exchanging, and encapsulating primitive components. Protein function within and RNA function in the presence of certain droplets is also preserved, suggesting the potential relevance of such droplets to various origins of life models. As a lipid amphiphile can also assemble around certain droplets, this further shows the droplets' potential compatibility with and scaffolding ability for nascent biomolecular systems that could have coexisted in complex chemical systems. These model compartments could have been more accessible in a "messy" prebiotic environment, enabling the localization of a variety of protometabolic and replication processes that could be subjected to further chemical evolution before the advent of the Last Universal Common Ancestor.
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27
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Ramadurai S, Sarangi NK, Maher S, MacConnell N, Bond AM, McDaid D, Flynn D, Keyes TE. Microcavity-Supported Lipid Bilayers; Evaluation of Drug-Lipid Membrane Interactions by Electrochemical Impedance and Fluorescence Correlation Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:8095-8109. [PMID: 31120755 DOI: 10.1021/acs.langmuir.9b01028] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Many drugs have intracellular or membrane-associated targets, thus understanding their interaction with the cell membrane is of value in drug development. Cell-free tools used to predict membrane interactions should replicate the molecular organization of the membrane. Microcavity array-supported lipid bilayer (MSLB) platforms are versatile biophysical models of the cell membrane that combine liposome-like membrane fluidity with stability and addressability. We used an MSLB herein to interrogate drug-membrane interactions across seven drugs from different classes, including nonsteroidal anti-inflammatories: ibuprofen (Ibu) and diclofenac (Dic); antibiotics: rifampicin (Rif), levofloxacin (Levo), and pefloxacin (Pef); and bisphosphonates: alendronate (Ale) and clodronate (Clo). Fluorescence lifetime correlation spectroscopy (FLCS) and electrochemical impedance spectroscopy (EIS) were used to evaluate the impact of drug on 1,2-dioleyl- sn-glycerophosphocholine and binary bilayers over physiologically relevant drug concentrations. Although FLCS data revealed Ibu, Levo, Pef, Ale, and Clo had no impact on lipid lateral mobility, EIS, which is more sensitive to membrane structural change, indicated modest but significant decreases to membrane resistivity consistent with adsorption but weak penetration of drugs at the membrane. Ale and Clo, evaluated at pH 5.25, did not impact the impedance of the membrane except at concentrations exceeding 4 mM. Conversely, Dic and Rif dramatically altered bilayer fluidity, suggesting their translocation through the bilayer, and EIS data showed that resistivity of the membrane decreased substantially with increasing drug concentration. Capacitance changes to the bilayer in most cases were insignificant. Using a Langmuir-Freundlich model to fit the EIS data, we propose Rsat as an empirical value that reflects permeation. Overall, the data indicate that Ibu, Levo, and Pef adsorb at the interface of the lipid membrane but Dic and Rif interact strongly, permeating the membrane core modifying the water/ion permeability of the bilayer structure. These observations are discussed in the context of previously reported data on drug permeability and log P.
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Affiliation(s)
- Sivaramakrishnan Ramadurai
- School of Chemical Sciences and National Centre for Sensor Research , Dublin City University , Dublin 9 , Ireland
| | - Nirod Kumar Sarangi
- School of Chemical Sciences and National Centre for Sensor Research , Dublin City University , Dublin 9 , Ireland
| | - Sean Maher
- School of Chemical Sciences and National Centre for Sensor Research , Dublin City University , Dublin 9 , Ireland
| | - Nicola MacConnell
- School of Chemical Sciences and National Centre for Sensor Research , Dublin City University , Dublin 9 , Ireland
| | - Alan M Bond
- School of Chemistry , Monash University , Clayton , Victoria 3800 , Australia
| | | | | | - Tia E Keyes
- School of Chemical Sciences and National Centre for Sensor Research , Dublin City University , Dublin 9 , Ireland
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28
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Lopez A, Fiore M. Investigating Prebiotic Protocells for A Comprehensive Understanding of the Origins of Life: A Prebiotic Systems Chemistry Perspective. Life (Basel) 2019; 9:E49. [PMID: 31181679 PMCID: PMC6616946 DOI: 10.3390/life9020049] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/21/2019] [Accepted: 06/06/2019] [Indexed: 01/06/2023] Open
Abstract
Protocells are supramolecular systems commonly used for numerous applications, such as the formation of self-evolvable systems, in systems chemistry and synthetic biology. Certain types of protocells imitate plausible prebiotic compartments, such as giant vesicles, that are formed with the hydration of thin films of amphiphiles. These constructs can be studied to address the emergence of life from a non-living chemical network. They are useful tools since they offer the possibility to understand the mechanisms underlying any living cellular system: Its formation, its metabolism, its replication and its evolution. Protocells allow the investigation of the synergies occurring in a web of chemical compounds. This cooperation can explain the transition between chemical (inanimate) and biological systems (living) due to the discoveries of emerging properties. The aim of this review is to provide an overview of relevant concept in prebiotic protocell research.
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Affiliation(s)
- Augustin Lopez
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Université de Lyon, Claude Bernard Lyon 1, 1 Rue Victor Grignard, Bâtiment Lederer, 69622 Villeurbanne CEDEX, France.
- Master de Biologie, École Normale Supérieure de Lyon, Université Claude Bernard Lyon I, Université de Lyon, 69342 Lyon CEDEX 07, France.
| | - Michele Fiore
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Université de Lyon, Claude Bernard Lyon 1, 1 Rue Victor Grignard, Bâtiment Lederer, 69622 Villeurbanne CEDEX, France.
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Yin S, Chen Y, Yu C, Ma W. From molecular to cellular form: modeling the first major transition during the arising of life. BMC Evol Biol 2019; 19:84. [PMID: 30943915 PMCID: PMC6448278 DOI: 10.1186/s12862-019-1412-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 03/21/2019] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND It has long been suggested that Darwinian evolution may have started at the molecular level and subsequently proceeded to a level with membrane boundary, i.e., of protocells. The transformation has been referred to as "the first major transition leading to life". However, so far, we actually have little knowledge about the relevant evolutionary mechanisms - and even about the plausibility - of such a transition. Here, based upon the scenario of the RNA world, we performed a computer simulation study to address this issue. RESULTS First, it was shown that at the molecular level, after the spread of one ribozyme (RNA replicase), another ribozyme (nucleotide synthetase) may emerge naturally in the system, and the two ribozymes would cooperate to spread in the naked scene. Then, when empty vesicles absorb the two ribozymes via "cytophagy", the resulting protocells may spread in the system and substitute the naked ribozymes. As for the driven power of such a transition, it was demonstrated that the membrane boundary's roles to ensure the cooperation between the two ribozymes and to prevent invasion of parasites are important. Beyond that, remarkably, it was found that another two factors may also have been significant: a possibly higher mobility of the raw materials in the environment (free water) and the protocells' potential capability to move around actively. Finally, the permeability of the membrane to raw materials was shown to be a major problem regarding the disadvantage for the cellular form. CONCLUSIONS The transition from the molecular level to the cellular level may have occurred naturally in early history of evolution. The evolutionary mechanisms for this process were complex. Besides the membrane boundary's roles to guarantee the molecular cooperation and to resist parasites, the greater chance for the protocells to access raw materials - either due to the diffusion of raw materials outside or the protocells' active movement, should also be highlighted, which may have at least to an extent compensated the disadvantage regarding the membrane's blocking effect against raw materials. The present study represents an effort of systematical exploration on this significant transition during the arising of life.
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Affiliation(s)
- Shaolin Yin
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China
| | - Yong Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China
| | - Chunwu Yu
- College of Computer Sciences, Wuhan University, Wuhan, 430072, People's Republic of China
| | - Wentao Ma
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China.
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30
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Poudyal RR, Guth-Metzler RM, Veenis AJ, Frankel EA, Keating CD, Bevilacqua PC. Template-directed RNA polymerization and enhanced ribozyme catalysis inside membraneless compartments formed by coacervates. Nat Commun 2019; 10:490. [PMID: 30700721 PMCID: PMC6353945 DOI: 10.1038/s41467-019-08353-4] [Citation(s) in RCA: 159] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 01/02/2019] [Indexed: 11/17/2022] Open
Abstract
Membraneless compartments, such as complex coacervates, have been hypothesized as plausible prebiotic micro-compartments due to their ability to sequester RNA; however, their compatibility with essential RNA World chemistries is unclear. We show that such compartments can enhance key prebiotically-relevant RNA chemistries. We demonstrate that template-directed RNA polymerization is sensitive to polycation identity, with polydiallyldimethylammonium chloride (PDAC) outperforming poly(allylamine), poly(lysine), and poly(arginine) in polycation/RNA coacervates. Differences in RNA diffusion rates between PDAC/RNA and oligoarginine/RNA coacervates imply distinct biophysical environments. Template-directed RNA polymerization is relatively insensitive to Mg2+ concentration when performed in PDAC/RNA coacervates as compared to buffer, even enabling partial rescue of the reaction in the absence of magnesium. Finally, we show enhanced activities of multiple nucleic acid enzymes including two ribozymes and a deoxyribozyme, underscoring the generality of this approach, in which functional nucleic acids like aptamers and ribozymes, and in some cases key cosolutes localize within the coacervate microenvironments. Membraneless compartments have been theorized to be prebiotic micro-compartments as they spontaneously encapsulate RNA and proteins. Here, the authors report membraneless compartments can enhance RNA chemistries, affecting template directed RNA polymerization and stimulating nucleic acid enzymes.
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Affiliation(s)
- Raghav R Poudyal
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA. .,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Rebecca M Guth-Metzler
- Department of Biochemistry, Microbiology, and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Andrew J Veenis
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Erica A Frankel
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.,The Dow Chemical Company, 400 Arcola Road, Collegeville, PA, 19426, USA
| | - Christine D Keating
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Philip C Bevilacqua
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA. .,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA. .,Department of Biochemistry, Microbiology, and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
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31
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Abstract
We propose a model whereby microscopic tunnels form in basalt glass in response to a natural proton flux from seawater into the glass. This flux is generated by the alteration of the glass as protons from water replace cations in the glass. In our proton gradient model, cells are gateways through which protons enter and alter the glass and through which cations leave the glass. In the process, tunnels are formed, and cells derive energy from the proton and ion fluxes. Proton flux from seawater into basalt glass would have occurred on Earth as soon as water accumulated on the surface and would have preceded biological redox catalysis. Tunnels in modern basalts are similar to tunnels in Archean basalts, which may be our earliest physical evidence of life. Proton gradients like those described in this paper certainly exist on other planetary bodies where silicate rocks are exposed to acidic to slightly alkaline water.
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Affiliation(s)
- Martin R Fisk
- 1 College of Earth, Ocean, and Atmospheric Sciences, Oregon State University , Corvallis, Oregon, USA
| | - Radu Popa
- 2 Department of Biological Sciences, University of Southern California , Los Angeles, California, USA
| | - David Wacey
- 3 Centre for Microscopy, Characterisation and Analysis, The University of Western Australia , Perth, Australia
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32
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Brea RJ, Bhattacharya A, Bhattacharya R, Song JJ, Sinha SK, Devaraj NK. Highly Stable Artificial Cells from Galactopyranose-Derived Single-Chain Amphiphiles. J Am Chem Soc 2018; 140:17356-17360. [PMID: 30495932 DOI: 10.1021/jacs.8b09388] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Single-chain amphiphiles (SCAs) that self-assemble into large vesicular structures are attractive components of synthetic cells because of the simplicity of bilayer formation and increased membrane permeability. However, SCAs commonly used for vesicle formation suffer from restricted working pH ranges, instability to divalent cations, and the inhibition of biocatalysts. Construction of more robust biocompatible membranes from SCAs would have significant benefits. We describe the formation of highly stable vesicles from alkyl galactopyranose thioesters. The compatibility of these uncharged SCAs with biomolecules makes possible the encapsulation of functional enzymes and nucleic acids during the vesicle generation process, enabling membrane protein reconstitution and compartmentalized nucleic acid amplification, even when charged precursors are supplied externally.
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33
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Chothe PP, Wu SP, Ye Z, Hariparsad N. Assessment of Transporter-Mediated and Passive Hepatic Uptake Clearance Using Rifamycin-SV as a Pan-Inhibitor of Active Uptake. Mol Pharm 2018; 15:4677-4688. [PMID: 29996058 DOI: 10.1021/acs.molpharmaceut.8b00654] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The use of in vitro data for the quantitative prediction of transporter-mediated clearance is critical. Central to this evaluation is the use of hepatocytes, since they contain the full complement of transporters and metabolic enzymes. In general, uptake clearance (CLuptake) is evaluated by measuring the appearance of compound in the cell. Passive clearance (CLpd) is often determined by conducting parallel studies at 4 °C or by attempting to saturate uptake pathways. Both approaches have their limitations. Recent studies have proposed the use of Rifamycin-SV (RFV) as a pan-inhibitor of hepatic uptake pathways. In our studies, we confirm that transport activity of all major hepatic uptake transporters is inhibited significantly by RFV at 1 mM (OATP1B1, 1B3, and 2B1 = NTCP (80%), OCT1 (65%), OAT2 (60%)). Under these incubation conditions, we found that the free intracellular concentration of RFV is ∼175 μM and that several major CYPs and UGTs can be reversibly inhibited. Using this approach, we also determined CLuptake and CLpd of nine known OATP substrates across three different lots of human hepatocytes. The scaling factors generated for these compounds at 37 °C with RFV and 4 °C were found to be similar. The CLpd of passively permeable compounds like metoprolol and semagacestat were found to be higher at 37 °C compared to 4 °C, indicating a temperature effect on these compounds. In addition, our data also suggests that incorporation of medium concentrations into CLuptake and CLpd calculations may be critical for highly protein bound and highly lipophilic drugs. Overall, our data indicate that RFV, instead of 4 °C, can be reliably used to measure CLuptake and CLpd of drugs.
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Affiliation(s)
- Paresh P Chothe
- Drug Metabolism and Pharmacokinetics , Vertex Pharmaceuticals Incorporated , Boston , Massachusetts 02210 , United States
| | - Shu-Pei Wu
- Drug Metabolism and Pharmacokinetics , Vertex Pharmaceuticals Incorporated , Boston , Massachusetts 02210 , United States
| | - Zhengqi Ye
- Drug Metabolism and Pharmacokinetics , Vertex Pharmaceuticals Incorporated , Boston , Massachusetts 02210 , United States
| | - Niresh Hariparsad
- Drug Metabolism and Pharmacokinetics , Vertex Pharmaceuticals Incorporated , Boston , Massachusetts 02210 , United States
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34
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Bonfio C, Godino E, Corsini M, Fabrizi de Biani F, Guella G, Mansy SS. Prebiotic iron–sulfur peptide catalysts generate a pH gradient across model membranes of late protocells. Nat Catal 2018. [DOI: 10.1038/s41929-018-0116-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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35
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Bolmatov D, Cai YQ, Zav'yalov D, Zhernenkov M. Crossover from picosecond collective to single particle dynamics defines the mechanism of lateral lipid diffusion. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2446-2455. [PMID: 30031781 DOI: 10.1016/j.bbamem.2018.07.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 07/04/2018] [Accepted: 07/13/2018] [Indexed: 10/28/2022]
Abstract
It has been widely accepted that the thermally excited motions of the molecules in a cell membrane is the prerequisite for a cell to carry its biological functions. On the other hand, the detailed mapping of the ultrafast picosecond single-molecule and the collective lipid dynamics in a cell membrane remains rather elusive. Here, we report all-atom molecular dynamics simulations of a 1,2-dipalmitoyl-sn-glycero-3-phosphocholine bilayer over a wide range of temperature. We elucidate a molecular mechanism underlying the lateral lipid diffusion in a cell membrane across the gel, rippled, and liquid phases using an analysis of the longitudinal and transverse current correlation spectra, the velocity auto-correlation functions, and the molecules mean square displacements. The molecular mechanism is based on the anomalous ultrafast vibrational properties of lipid molecules at the viscous-to-elastic crossover. The macroscopic lipid diffusion coefficients predicted by the proposed diffusion model are in a good agreement with experimentally observed values. Furthermore, we unveil the role of water confined at the water-lipid interface in triggering collective vibrations in a lipid bilayer.
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Affiliation(s)
- Dima Bolmatov
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, USA.
| | - Yong Q Cai
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | | | - Mikhail Zhernenkov
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA.
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36
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Tailoring the appearance: what will synthetic cells look like? Curr Opin Biotechnol 2018; 51:47-56. [DOI: 10.1016/j.copbio.2017.11.005] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 11/23/2022]
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37
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O’Flaherty D, Kamat NP, Mirza FN, Li L, Prywes N, Szostak JW. Copying of Mixed-Sequence RNA Templates inside Model Protocells. J Am Chem Soc 2018; 140:5171-5178. [PMID: 29608310 PMCID: PMC7547884 DOI: 10.1021/jacs.8b00639] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Indexed: 01/11/2023]
Abstract
The chemical replication of RNA inside fatty acid vesicles is a plausible step in the emergence of cellular life. On the primitive Earth, simple protocells with the ability to import nucleotides and short oligomers from their environment could potentially have replicated and retained larger genomic RNA oligonucleotides within a spatially defined compartment. We have previously shown that short 5'-phosphoroimidazolide-activated "helper" RNA oligomers enable the nonenzymatic copying of mixed-sequence templates in solution, using 5'-phosphoroimidazolide-activated mononucleotides. Here, we report that citrate-chelated Mg2+, a catalyst of nonenzymatic primer extension, enhances fatty acid membrane permeability to such short RNA oligomers up to the size of tetramers, without disrupting vesicle membranes. In addition, selective permeability of short, but not long, oligomers can be further enhanced by elevating the temperature. The ability to increase the permeability of fatty acid membranes to short oligonucleotides allows for the nonenzymatic copying of RNA templates containing all four nucleotides inside vesicles, bringing us one step closer to the goal of building a protocell capable of Darwinian evolution.
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Affiliation(s)
- Derek
K. O’Flaherty
- Howard
Hughes Medical Institute, Department of Molecular Biology, and Center
for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Neha P. Kamat
- Howard
Hughes Medical Institute, Department of Molecular Biology, and Center
for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Biomedical
Engineering Department, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Fatima N. Mirza
- Howard
Hughes Medical Institute, Department of Molecular Biology, and Center
for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Li Li
- Howard
Hughes Medical Institute, Department of Molecular Biology, and Center
for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Noam Prywes
- Howard
Hughes Medical Institute, Department of Molecular Biology, and Center
for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Jack W. Szostak
- Howard
Hughes Medical Institute, Department of Molecular Biology, and Center
for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
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38
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Shinde SV, Talukdar P. An anion receptor that facilitates transmembrane proton–anion symport by deprotonating its sulfonamide N–H proton. Chem Commun (Camb) 2018; 54:10351-10354. [DOI: 10.1039/c8cc04044c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Indole-based amide-sulfonamide derivatives were synthesized. The X-ray crystal structure and chloride binding studies in solution showed a 1 : 1 stoichiometry. The ion transport study indicated the proton–anion symport across the lipid bilayer membrane.
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Affiliation(s)
- Sopan Valiba Shinde
- Department of Chemistry
- Indian Institute of Science Education and Research Pune
- Pune 411008
- India
| | - Pinaki Talukdar
- Department of Chemistry
- Indian Institute of Science Education and Research Pune
- Pune 411008
- India
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39
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Qiao H, Hu N, Bai J, Ren L, Liu Q, Fang L, Wang Z. Encapsulation of Nucleic Acids into Giant Unilamellar Vesicles by Freeze-Thaw: a Way Protocells May Form. ORIGINS LIFE EVOL B 2017; 47:499-510. [PMID: 27807660 DOI: 10.1007/s11084-016-9527-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/19/2016] [Indexed: 12/27/2022]
Abstract
Protocells are believed to consist of a lipid membrane and encapsulated nucleic acid. As the lipid membrane is impermeable to macromolecules like nucleic acids, the processes by which nucleic acids become encapsulated inside lipid membrane compartments are still unknown. In this paper, a freeze-thaw method was modified and applied to giant unilamellar vesicles (GUVs) and deoxyribonucleic acid (DNA) in mixed solution resulting in the efficient encapsulation of 6.4 kb plasmid DNA and similar length linear DNA into GUVs. The mechanism of encapsulation was followed by observing the effect of freeze-thaw temperatures on GUV morphological change, DNA encapsulation and ice crystal formation, and analyzing their correlation. Following ice crystal formation, the shape of spherical GUVs was altered and membrane integrity was damaged and this was found to be a necessary condition for encapsulation. Heating alone had no effects on DNA encapsulation, but was helpful for restoring the spherical shape and membrane integrity of GUVs damaged during freezing. These results suggested that freeze-thaw could promote the encapsulation of DNA into GUVs by a mechanism: the vesicle membrane was breached by ice crystal formation during freezing, DNA entered into damaged GUVs through these membrane gaps and was encapsulated after the membrane was resealed during the thawing process. The process described herein therefore describes a simple way for the encapsulation of nucleic acids and potentially other macromolecules into lipid vesicles, a process by which early protocells might have formed.
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Affiliation(s)
- Hai Qiao
- State Key Laboratory of Ultrasound Engineering in Medicine Co-Founed by Chongqing and the Ministry of Science and Technology, Chongqing Key Laboratory of Biomedical Engineering, College of Biomedical Engineering, Chongqing Medical University, P. O. Box 153, No.1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Na Hu
- State Key Laboratory of Ultrasound Engineering in Medicine Co-Founed by Chongqing and the Ministry of Science and Technology, Chongqing Key Laboratory of Biomedical Engineering, College of Biomedical Engineering, Chongqing Medical University, P. O. Box 153, No.1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Jin Bai
- State Key Laboratory of Ultrasound Engineering in Medicine Co-Founed by Chongqing and the Ministry of Science and Technology, Chongqing Key Laboratory of Biomedical Engineering, College of Biomedical Engineering, Chongqing Medical University, P. O. Box 153, No.1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Lili Ren
- State Key Laboratory of Ultrasound Engineering in Medicine Co-Founed by Chongqing and the Ministry of Science and Technology, Chongqing Key Laboratory of Biomedical Engineering, College of Biomedical Engineering, Chongqing Medical University, P. O. Box 153, No.1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Qing Liu
- State Key Laboratory of Ultrasound Engineering in Medicine Co-Founed by Chongqing and the Ministry of Science and Technology, Chongqing Key Laboratory of Biomedical Engineering, College of Biomedical Engineering, Chongqing Medical University, P. O. Box 153, No.1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Liaoqiong Fang
- State Key Laboratory of Ultrasound Engineering in Medicine Co-Founed by Chongqing and the Ministry of Science and Technology, Chongqing Key Laboratory of Biomedical Engineering, College of Biomedical Engineering, Chongqing Medical University, P. O. Box 153, No.1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, People's Republic of China.
| | - Zhibiao Wang
- State Key Laboratory of Ultrasound Engineering in Medicine Co-Founed by Chongqing and the Ministry of Science and Technology, Chongqing Key Laboratory of Biomedical Engineering, College of Biomedical Engineering, Chongqing Medical University, P. O. Box 153, No.1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, People's Republic of China.
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40
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Ma W. What Does "the RNA World" Mean to "the Origin of Life"? Life (Basel) 2017; 7:life7040049. [PMID: 29186049 PMCID: PMC5745562 DOI: 10.3390/life7040049] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 10/30/2017] [Accepted: 11/24/2017] [Indexed: 12/30/2022] Open
Abstract
Corresponding to life’s two distinct aspects: Darwinian evolution and self-sustainment, the origin of life should also split into two issues: the origin of Darwinian evolution and the arising of self-sustainment. Because the “self-sustainment” we concern about life should be the self-sustainment of a relevant system that is “defined” by its genetic information, the self-sustainment could not have arisen before the origin of Darwinian evolution, which was just marked by the emergence of genetic information. The logic behind the idea of the RNA world is not as tenable as it has been believed. That is, genetic molecules and functional molecules, even though not being the same material, could have emerged together in the beginning and launched the evolution—provided that the genetic molecules can “simply” code the functional molecules. However, due to these or those reasons, alternative scenarios are generally much less convincing than the RNA world. In particular, when considering the accumulating experimental evidence that is supporting a de novo origin of the RNA world, it seems now quite reasonable to believe that such a world may have just stood at the very beginning of life on the Earth. Therewith, we acquire a concrete scenario for our attempts to appreciate those fundamental issues that are involved in the origin of life. In the light of those possible scenes included in this scenario, Darwinian evolution may have originated at the molecular level, realized upon a functional RNA. When two or more functional RNAs emerged, for their efficient cooperation, there should have been a selective pressure for the emergence of protocells. But it was not until the appearance of the “unitary-protocell”, which had all of its RNA genes linked into a chromosome, that Darwinian evolution made its full step towards the cellular level—no longer severely constrained by the low-grade evolution at the molecular level. Self-sustainment did not make sense before protocells emerged. The selection pressure that was favoring the exploration of more and more fundamental raw materials resulted in an evolutionary tendency of life to become more and more self-sustained. New functions for the entities to adapt to environments, including those that are involved in the self-sustainment per se, would bring new burdens to the self-sustainment—the advantage of these functions must overweigh the corresponding disadvantage.
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Affiliation(s)
- Wentao Ma
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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41
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Affiliation(s)
- Russell Perkins
- University of Colorado Boulder, 215 UCB, Boulder, Colorado 80309, United States
| | - Veronica Vaida
- University of Colorado Boulder, 215 UCB, Boulder, Colorado 80309, United States
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42
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Kee TP, Monnard PA. Chemical systems, chemical contiguity and the emergence of life. Beilstein J Org Chem 2017; 13:1551-1563. [PMID: 28904604 PMCID: PMC5564265 DOI: 10.3762/bjoc.13.155] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 07/11/2017] [Indexed: 12/17/2022] Open
Abstract
Charting the emergence of living cells from inanimate matter remains an intensely challenging scientific problem. The complexity of the biochemical machinery of cells with its exquisite intricacies hints at cells being the product of a long evolutionary process. Research on the emergence of life has long been focusing on specific, well-defined problems related to one aspect of cellular make-up, such as the formation of membranes or the build-up of information/catalytic apparatus. This approach is being gradually replaced by a more "systemic" approach that privileges processes inherent to complex chemical systems over specific isolated functional apparatuses. We will summarize the recent advances in system chemistry and show that chemical systems in the geochemical context imply a form of chemical contiguity in the syntheses of the various molecules that precede modern biomolecules.
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Affiliation(s)
- Terrence P Kee
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | - Pierre-Alain Monnard
- Institute of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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43
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Prebiotic selection for motifs in a model of template-free elongation of polymers within compartments. PLoS One 2017; 12:e0180208. [PMID: 28723913 PMCID: PMC5516967 DOI: 10.1371/journal.pone.0180208] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 06/12/2017] [Indexed: 01/08/2023] Open
Abstract
The transition from prelife where self-replication does not occur, to life which exhibits self-replication and evolution, has been a subject of interest for many decades. Membranes, forming compartments, seem to be a critical component of this transition as they provide several concurrent benefits. They maintain localized interactions, generate electro-chemical gradients, and help in selecting cooperative functions as they arise. These functions pave the way for the emergence and maintenance of simple metabolic cycles and polymers. In the context of origin of life, evolution of information-carrying molecules and RNA based enzymes within compartments has been subject to intensive theoretical and experimental research. Hence, many experimental efforts aim to produce compartments that contain elongating polynucleotides (also referred to as protocells), which store information and perform catalysis. Despite impressive experimental progress, we are still relatively ignorant about the dynamics by which elongating polynucleotides can produce more sophisticated behaviors. Here we perform computer simulations to couple information production through template-free elongation of polymers with dividing compartments. We find that polymers with a simple ability—biasing the concentration of monomers within their own compartment—can acquire a selective advantage in prelife. We further investigate whether such a mechanism allows for cooperative dynamics to dominate over purely competitive ones. We show that under this system of biased monomer addition, even without template-directed self-replication, genetic motifs can emerge, compete, cooperate, and ultimately survive within the population.
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Ronen R, Kaufman Y, Freger V. Formation of pore-spanning lipid membrane and cross-membrane water and ion transport. J Memb Sci 2017. [DOI: 10.1016/j.memsci.2016.09.059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Vieregg JR, Tang TYD. Polynucleotides in cellular mimics: Coacervates and lipid vesicles. Curr Opin Colloid Interface Sci 2016. [DOI: 10.1016/j.cocis.2016.09.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Strbak O, Kanuchova Z, Krafcik A. Proton Gradients as a Key Physical Factor in the Evolution of the Forced Transport Mechanism Across the Lipid Membrane. ORIGINS LIFE EVOL B 2016; 46:523-531. [PMID: 27038470 DOI: 10.1007/s11084-016-9496-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 12/15/2015] [Indexed: 12/29/2022]
Abstract
A critical phase in the transition from prebiotic chemistry to biological evolution was apparently an asymmetric ion flow across the lipid membrane. Due to imbalance in the ion flow, the early lipid vesicles could selectively take the necessary molecules from the environment, and release the side-products from the vesicle. Natural proton gradients played a definitively crucial role in this process, since they remain the basis of energy transfer in the present-day cells. On the basis of this supposition, and the premise of the early vesicle membrane's impermeability to protons, we have shown that the emergence of the proton gradient in the lipid vesicle could be a key physical factor in the evolution of the forced transport mechanism (pore formation and active transport) across the lipid bilayer. This driven flow of protons across the membrane is the result of the electrochemical proton gradient and osmotic pressures on the integrity of the lipid vesicle. At a critical number of new lipid molecules incorporated into the vesicle, the energies associated with the creation of the proton gradient exceed the bending stiffness of the lipid membrane, and overlap the free energy of the lipid bilayer pore formation.
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Affiliation(s)
- Oliver Strbak
- Department of Imaging Methods, Institute of Measurement Science, Slovak Academy of Sciences, Dubravska cesta 9, 841 04, Bratislava, Slovakia.
| | - Zuzana Kanuchova
- Astronomical Institute, Slovak Academy of Sciences, 059 60, Tatranska Lomnica, Slovakia
| | - Andrej Krafcik
- Department of Imaging Methods, Institute of Measurement Science, Slovak Academy of Sciences, Dubravska cesta 9, 841 04, Bratislava, Slovakia
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Weingart OG, Loessner MJ. Nerve cell-mimicking liposomes as biosensor for botulinum neurotoxin complete physiological activity. Toxicol Appl Pharmacol 2016; 313:16-23. [PMID: 27743862 DOI: 10.1016/j.taap.2016.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 09/02/2016] [Accepted: 10/10/2016] [Indexed: 10/20/2022]
Abstract
Botulinum neurotoxins (BoNT) are the most toxic substances known, and their neurotoxic properties and paralysing effects are exploited for medical treatment of a wide spectrum of disorders. To accurately quantify the potency of a pharmaceutical BoNT preparation, its physiological key activities (binding to membrane receptor, translocation, and proteolytic degradation of SNARE proteins) need to be determined. To date, this was only possible using animal models, or, to a limited extent, cell-based assays. We here report a novel in vitro system for BoNT/B analysis, based on nerve-cell mimicking liposomes presenting motoneuronal membrane receptors required for BoNT binding. Following triggered membrane translocation of the toxin's Light Chain, the endopeptidase activity can be quantitatively monitored employing a FRET-based reporter assay within the functionalized liposomes. We were able to detect BoNT/B physiological activity at picomolar concentrations in short time, opening the possibility for future replacement of animal experimentation in pharmaceutical BoNT testing.
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Affiliation(s)
- Oliver G Weingart
- Institute for Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, CH-8092 Zurich, Switzerland.
| | - Martin J Loessner
- Institute for Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, CH-8092 Zurich, Switzerland
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Fang B, Zhang M, Fan X, Ren F. The targeted proteins in tumor cells treated with the α-lactalbumin–oleic acid complex examined by descriptive and quantitative liquid chromatography–tandem mass spectrometry. J Dairy Sci 2016; 99:5991-6004. [DOI: 10.3168/jds.2016-10971] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 04/14/2016] [Indexed: 01/26/2023]
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49
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Zhernenkov M, Bolmatov D, Soloviov D, Zhernenkov K, Toperverg BP, Cunsolo A, Bosak A, Cai YQ. Revealing the mechanism of passive transport in lipid bilayers via phonon-mediated nanometre-scale density fluctuations. Nat Commun 2016; 7:11575. [PMID: 27175859 PMCID: PMC4865866 DOI: 10.1038/ncomms11575] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/10/2016] [Indexed: 12/21/2022] Open
Abstract
The passive transport of molecules through a cell membrane relies on thermal motions of the lipids. However, the nature of transmembrane transport and the precise mechanism remain elusive and call for a comprehensive study of phonon excitations. Here we report a high resolution inelastic X-ray scattering study of the in-plane phonon excitations in 1,2-dipalmitoyl-sn-glycero-3-phosphocholine above and below the main transition temperature. In the gel phase, for the first time, we observe low-frequency transverse modes, which exhibit a phonon gap when the lipid transitions into the fluid phase. We argue that the phonon gap signifies the formation of short-lived nanometre-scale lipid clusters and transient pores, which facilitate the passive molecular transport across the bilayer plane. Our findings suggest that the phononic motion of the hydrocarbon tails provides an effective mechanism of passive transport, and illustrate the importance of the collective dynamics of biomembranes. The molecular transport through bio-membranes of cells heavily relies on the dynamics of lipids, but the related mechanism remains unknown. Here, Zhernenkov et al. observe the propagating transverse phonon mode with a finite band gap and suggest its connection to short-lived local lipid clustering.
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Affiliation(s)
- Mikhail Zhernenkov
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Dima Bolmatov
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Dmitry Soloviov
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna 141980, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Kirill Zhernenkov
- Institut Nanosciences et Cryogénie, Commissariat à l'Energie Atomique, Grenoble 38054, France
| | - Boris P Toperverg
- Petersburg Nuclear Physics Institute, Gatchina 188300, Russia.,Institut Laue Langevin, 6, rue Jules Horowitz, Grenoble 38042, France
| | - Alessandro Cunsolo
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Alexey Bosak
- European Synchrotron Radiation Facility, Grenoble 38000, France
| | - Yong Q Cai
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, USA
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50
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Adamala KP, Engelhart AE, Szostak JW. Collaboration between primitive cell membranes and soluble catalysts. Nat Commun 2016; 7:11041. [PMID: 26996603 PMCID: PMC4802160 DOI: 10.1038/ncomms11041] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/15/2016] [Indexed: 12/23/2022] Open
Abstract
One widely held model of early life suggests primitive cells consisted of simple RNA-based catalysts within lipid compartments. One possible selective advantage conferred by an encapsulated catalyst is stabilization of the compartment, resulting from catalyst-promoted synthesis of key membrane components. Here we show model protocell vesicles containing an encapsulated enzyme that promotes the synthesis of simple fatty acid derivatives become stabilized to Mg2+, which is required for ribozyme activity and RNA synthesis. Thus, protocells capable of such catalytic transformations would have enjoyed a selective advantage over other protocells in high Mg2+ environments. The synthetic transformation requires both the catalyst and vesicles that solubilize the water-insoluble precursor lipid. We suggest that similar modified lipids could have played a key role in early life, and that primitive lipid membranes and encapsulated catalysts, such as ribozymes, may have acted in conjunction with each other, enabling otherwise-impossible chemical transformations within primordial cells. Early cells likely consisted of fatty acid vesicles enclosing magnesium-dependent ribozymes. Here, the authors show that fatty acid derivatives can form vesicles that, unlike those formed from only unmodified fatty acids, are stable in the presence of magnesium and could support ribozyme catalysis.
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Affiliation(s)
- Katarzyna P Adamala
- Howard Hughes Medical Institute and Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA
| | - Aaron E Engelhart
- Howard Hughes Medical Institute and Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute and Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA
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