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Guo D, Zhang Z, Sun J, Hou W, Du N. A primitive cell model involving Vesicles, microtubules and asters. J Colloid Interface Sci 2024; 675:700-711. [PMID: 38996700 DOI: 10.1016/j.jcis.2024.07.045] [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: 03/11/2024] [Revised: 06/25/2024] [Accepted: 07/05/2024] [Indexed: 07/14/2024]
Abstract
HYPOTHESIS Simple single-chain amphiphiles (sodium monododecyl phosphate, SDP) and organic small molecules (isopentenol, IPN), both of primitive relevance, are proved to have been the building blocks of protocells on the early Earth. How do SDP-based membrane and coexisting IPN come together in specific ways to produce more complex chemical entities? What kind of cell-like behavior can be endowed with this protocell model? These are important questions in the pre-life chemical origin scenario that have not been answered to date. EXPERIMENTS The phase behavior and formation mechanism of the aggregates for SDP/IPN/H2O ternary system were characterized and studied by different electron microscopy, fluorescent probe technology, DLS, IR, ESI-MS, SAXS, etc. The stability (freeze-thaw and wet-dry treatments) and cell-like behavior (chemical signaling communication) were tested via simulating particular scenarios. FINDINGS Vesicles, microtubules and asters phases resembling the morphology and structure of modern cells/organelles were obtained. The intermolecular hydrogen bonding is the main driving force for the emergence of the aggregates. The protocell models not only display remarkable stabilities by simulating the primordial Earth's diurnal temperature differences and ocean tides but also are able to exhibit cell-like behavior of chemical signaling transition.
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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, PR China
| | - Ziyue Zhang
- Key Laboratory of Colloid and Interface Chemistry (Ministry of Education), School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China
| | - Jichao Sun
- Key Laboratory of Colloid and Interface Chemistry (Ministry of Education), School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China
| | - Wanguo Hou
- Key Laboratory of Colloid and Interface Chemistry (Ministry of Education), School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China; National Engineering Technology Research Center for Colloidal Materials, Shandong University, Jinan 250100, PR China
| | - Na Du
- Key Laboratory of Colloid and Interface Chemistry (Ministry of Education), School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China.
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2
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O'Connor PBF. The Evolutionary Transition of the RNA World to Obcells to Cellular-Based Life. J Mol Evol 2024; 92:278-285. [PMID: 38683368 DOI: 10.1007/s00239-024-10171-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 04/08/2024] [Indexed: 05/01/2024]
Abstract
The obcell hypothesis is a proposed route for the RNA world to develop into a primitive cellular one. It posits that this transition began with the emergence of the proto-ribosome which enabled RNA to colonise the external surface of lipids by the synthesis of amphipathic peptidyl-RNAs. The obcell hypothesis also posits that the emergence of a predation-based ecosystem provided a selection mechanism for continued sophistication amongst early life forms. Here, I argue for this hypothesis owing to its significant explanatory power; it offers a rationale why a ribosome which initially was capable only of producing short non-coded peptides was advantageous and it forgoes issues related to maintaining a replicating RNA inside a lipid enclosure. I develop this model by proposing that the evolutionary selection for improved membrane anchors resulted in the emergence of primitive membrane pores which enabled obcells to gradually evolve into a cellular morphology. Moreover, I introduce a model of obcell production which advances that tRNAs developed from primers of the RNA world.
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3
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Hertle L, Sevim S, Zhu J, Pustovalov V, Veciana A, Llacer-Wintle J, Landers FC, Ye H, Chen XZ, Vogler H, Grossniklaus U, Puigmartí-Luis J, Nelson BJ, Pané S. A Naturally Inspired Extrusion-Based Microfluidic Approach for Manufacturing Tailorable Magnetic Soft Continuum Microrobotic Devices. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2402309. [PMID: 38780003 DOI: 10.1002/adma.202402309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/15/2024] [Indexed: 05/25/2024]
Abstract
Soft materials play a crucial role in small-scale robotic applications by closely mimicking the complex motion and morphing behavior of organisms. However, conventional fabrication methods face challenges in creating highly integrated small-scale soft devices. In this study, microfluidics is leveraged to precisely control reaction-diffusion (RD) processes to generate multifunctional and compartmentalized calcium-cross-linkable alginate-based microfibers. Under RD conditions, sophisticated alginate-based fibers are produced for magnetic soft continuum robotics applications with customizable features, such as geometry (compact or hollow), degree of cross-linking, and the precise localization of magnetic nanoparticles (inside the core, surrounding the fiber, or on one side). This fine control allows for tuning the stiffness and magnetic responsiveness of the microfibers. Additionally, chemically cleavable regions within the fibers enable disassembly into smaller robotic units or roll-up structures under a rotating magnetic field. These findings demonstrate the versatility of microfluidics in processing highly integrated small-scale devices.
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Affiliation(s)
- Lukas Hertle
- Multi-Scale Robotics Lab, Institute of Robotics and Intelligent Systems, ETH Zurich, Tannenstrasse 3, Zurich, 8092, Switzerland
| | - Semih Sevim
- Multi-Scale Robotics Lab, Institute of Robotics and Intelligent Systems, ETH Zurich, Tannenstrasse 3, Zurich, 8092, Switzerland
| | - Jiawei Zhu
- Multi-Scale Robotics Lab, Institute of Robotics and Intelligent Systems, ETH Zurich, Tannenstrasse 3, Zurich, 8092, Switzerland
| | - Vitaly Pustovalov
- Multi-Scale Robotics Lab, Institute of Robotics and Intelligent Systems, ETH Zurich, Tannenstrasse 3, Zurich, 8092, Switzerland
| | - Andrea Veciana
- Multi-Scale Robotics Lab, Institute of Robotics and Intelligent Systems, ETH Zurich, Tannenstrasse 3, Zurich, 8092, Switzerland
| | - Joaquin Llacer-Wintle
- Multi-Scale Robotics Lab, Institute of Robotics and Intelligent Systems, ETH Zurich, Tannenstrasse 3, Zurich, 8092, Switzerland
| | - Fabian C Landers
- Multi-Scale Robotics Lab, Institute of Robotics and Intelligent Systems, ETH Zurich, Tannenstrasse 3, Zurich, 8092, Switzerland
| | - Hao Ye
- Multi-Scale Robotics Lab, Institute of Robotics and Intelligent Systems, ETH Zurich, Tannenstrasse 3, Zurich, 8092, Switzerland
| | - Xiang-Zhong Chen
- Multi-Scale Robotics Lab, Institute of Robotics and Intelligent Systems, ETH Zurich, Tannenstrasse 3, Zurich, 8092, Switzerland
- Institute of Optoelectronics State Key Laboratory of Photovoltaic Science and Technology Shanghai Frontiers Science Research Base of Intelligent Optoelectronics and Perception, Fudan University, Shanghai, 200433, P. R. China
- Yiwu Research Institute of Fudan University, Yiwu, Zhejiang, 322000, China
| | - Hannes Vogler
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, Zurich, 8008, Switzerland
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, Zurich, 8008, Switzerland
| | - Josep Puigmartí-Luis
- Departament de Ciència dels Materials i Química Física Institut de Química Teòrica i Computacional, University of Barcelona, Martí i Franquès, 1, Barcelona, 08028, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, Barcelona, 08010, Spain
| | - Bradley J Nelson
- Multi-Scale Robotics Lab, Institute of Robotics and Intelligent Systems, ETH Zurich, Tannenstrasse 3, Zurich, 8092, Switzerland
| | - Salvador Pané
- Multi-Scale Robotics Lab, Institute of Robotics and Intelligent Systems, ETH Zurich, Tannenstrasse 3, Zurich, 8092, Switzerland
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4
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Malaterre C. Is Life Binary or Gradual? Life (Basel) 2024; 14:564. [PMID: 38792586 PMCID: PMC11121977 DOI: 10.3390/life14050564] [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: 02/23/2024] [Revised: 04/15/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
The binary nature of life is deeply ingrained in daily experiences, evident in the stark distinctions between life and death and the living and the inert. While this binary perspective aligns with disciplines like medicine and much of biology, uncertainties emerge in fields such as microbiology, virology, synthetic biology, and systems chemistry, where intermediate entities challenge straightforward classification as living or non-living. This contribution explores the motivations behind both binary and non-binary conceptualizations of life. Despite the perceived necessity to unequivocally define life, especially in the context of origin of life research and astrobiology, mounting evidence indicates a gray area between what is intuitively clearly alive and what is distinctly not alive. This prompts consideration of a gradualist perspective, depicting life as a spectrum with varying degrees of "lifeness". Given the current state of science, the existence or not of a definite threshold remains open. Nevertheless, shifts in epistemic granularity and epistemic perspective influence the framing of the question, and scientific advancements narrow down possible answers: if a threshold exists, it can only be at a finer level than what is intuitively taken as living or non-living. This underscores the need for a more refined distinction between the inanimate and the living.
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Affiliation(s)
- Christophe Malaterre
- Département de Philosophie, Université du Québec à Montréal, Montreal, QC H3C 3P8, Canada;
- Centre Interuniversitaire de Recherche sur la Science et la Technologie (CIRST), Montreal, QC H3C 3P8, Canada
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5
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Rasmussen B, Muhling JR, Tosca NJ. Nanoparticulate apatite and greenalite in oldest, well-preserved hydrothermal vent precipitates. SCIENCE ADVANCES 2024; 10:eadj4789. [PMID: 38277446 PMCID: PMC10816723 DOI: 10.1126/sciadv.adj4789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/28/2023] [Indexed: 01/28/2024]
Abstract
Paleoarchean jaspilites are used to track ancient ocean chemistry and photoautotrophy because they contain hematite interpreted to have formed following biological oxidation of vent-derived Fe(II) and seawater P-scavenging. However, recent studies have triggered debate about ancient seawater Fe and P deposition. Here, we report greenalite and fluorapatite (FAP) nanoparticles in the oldest, well-preserved jaspilites from the ~3.5-billion-year Dresser Formation, Pilbara Craton, Australia. We argue that both phases are vent plume particles, whereas coexisting hematite is linked to secondary oxidation. Geochemical modeling predicts that hydrothermal alteration of seafloor basalts by anoxic, sulfate-free seawater releases Fe(II) and P that simultaneously precipitate as greenalite and FAP upon venting. The formation, transport, and preservation of FAP nanoparticles indicate that seawater P concentrations were ≥1 to 2 orders of magnitude higher than in modern deepwater. We speculate that Archean seafloor vents were nanoparticle "factories" that, on prebiotic Earth, produced countless Fe(II)- and P-rich templates available for catalysis and biosynthesis.
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Affiliation(s)
- Birger Rasmussen
- School of Earth Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Janet R. Muhling
- School of Earth Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Nicholas J. Tosca
- Department of Earth Sciences, University of Cambridge, Cambridge CB2 3EQ, UK
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6
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Cho Y, Choi YJ, Kaser SJ, Meacham R, Christoff-Tempesta T, Wu S, Zuo X, Ortony JH. Geometric Transformations Afforded by Rotational Freedom in Aramid Amphiphile Nanostructures. J Am Chem Soc 2023; 145:22954-22963. [PMID: 37819710 DOI: 10.1021/jacs.3c04598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Molecular self-assembly in water leads to nanostructure geometries that can be tuned owing to the highly dynamic nature of amphiphiles. There is growing interest in strongly interacting amphiphiles with suppressed dynamics, as they exhibit ultrastability in extreme environments. However, such amphiphiles tend to assume a limited range of geometries upon self-assembly due to the specific spatial packing induced by their strong intermolecular interactions. To overcome this limitation while maintaining structural robustness, we incorporate rotational freedom into the aramid amphiphile molecular design by introducing a diacetylene moiety between two aramid units, resulting in diacetylene aramid amphiphiles (D-AAs). This design strategy enables rotations along the carbon-carbon sp hybridized bonds of an otherwise fixed aramid domain. We show that varying concentrations and equilibration temperatures of D-AA in water lead to self-assembly into four different nanoribbon geometries: short, extended, helical, and twisted nanoribbons, all while maintaining robust structure with thermodynamic stability. We use advanced microscopy, X-ray scattering, spectroscopic techniques, and two-dimensional (2D) NMR to understand the relationship between conformational freedom within strongly interacting amphiphiles and their self-assembly pathways.
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Affiliation(s)
- Yukio Cho
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yu-Jin Choi
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Samuel J Kaser
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Rebecca Meacham
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ty Christoff-Tempesta
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Siyu Wu
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Xiaobing Zuo
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Julia H Ortony
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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7
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Howlett MG, Fletcher SP. From autocatalysis to survival of the fittest in self-reproducing lipid systems. Nat Rev Chem 2023; 7:673-691. [PMID: 37612460 DOI: 10.1038/s41570-023-00524-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2023] [Indexed: 08/25/2023]
Abstract
Studying autocatalysis - in which molecules catalyse their own formation - might help to explain the emergence of chemical systems that exhibit traits normally associated with biology. When coupled to other processes, autocatalysis can lead to complex systems-level behaviour in apparently simple mixtures. Lipids are an important class of chemicals that appear simple in isolation, but collectively show complex supramolecular and mesoscale dynamics. Here we discuss autocatalytic lipids as a source of extraordinary behaviour such as primitive chemical evolution, chemotaxis, temporally controllable materials and even as supramolecular catalysts for continuous synthesis. We survey the literature since the first examples of lipid autocatalysis and highlight state-of-the-art synthetic systems that emulate life, displaying behaviour such as metabolism and homeostasis, with special consideration for generating structural complexity and out-of-equilibrium models of life. Autocatalytic lipid systems have enormous potential for building complexity from simple components, and connections between physical effects and molecular reactivity are only just beginning to be discovered.
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Affiliation(s)
- Michael G Howlett
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Stephen P Fletcher
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.
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8
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Sepulveda RV, Sbarbaro C, Opazo MC, Duarte Y, González-Nilo F, Aguayo D. Insights into Early Steps of Decanoic Acid Self-Assemblies under Prebiotic Temperatures Using Molecular Dynamics Simulations. MEMBRANES 2023; 13:membranes13050469. [PMID: 37233530 DOI: 10.3390/membranes13050469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/18/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023]
Abstract
The origin of life possibly required processes in confined systems that facilitated simple chemical reactions and other more complex reactions impossible to achieve under the condition of infinite dilution. In this context, the self-assembly of micelles or vesicles derived from prebiotic amphiphilic molecules is a cornerstone in the chemical evolution pathway. A prime example of these building blocks is decanoic acid, a short-chain fatty acid capable of self-assembling under ambient conditions. This study explored a simplified system made of decanoic acids under temperatures ranging from 0 °C to 110 °C to replicate prebiotic conditions. The study revealed the first point of aggregation of decanoic acid into vesicles and examined the insertion of a prebiotic-like peptide in a primitive bilayer. The information gathered from this research provides critical insights into molecule interactions with primitive membranes, allowing us to understand the first nanometric compartments needed to trigger further reactions that were essential for the origin of life.
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Affiliation(s)
- Romina V Sepulveda
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Av. República 330, Santiago 8370146, Chile
| | - Christopher Sbarbaro
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Av. República 330, Santiago 8370146, Chile
| | - Ma Cecilia Opazo
- Instituto de Ciencias Naturales, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Manuel Montt 948, Providencia 7500000, Chile
| | - Yorley Duarte
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Av. República 330, Santiago 8370146, Chile
| | - Fernando González-Nilo
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Av. República 330, Santiago 8370146, Chile
| | - Daniel Aguayo
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Av. República 330, Santiago 8370146, Chile
- Agricultura Digital, Servicio Agrícola, Salinas y Fabres S.A., Ruta 5 Sur, Parcela 165, Hijuela Larga, Paine 9540000, Chile
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9
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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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10
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Ju Y, Zhang H, Wang X, Liu Y, Yang Y, Kan G, Yu K, Jiang J. Abiotic synthesis with plausible emergence for primitive phospholipid in aqueous microdroplets. J Colloid Interface Sci 2023; 634:535-542. [PMID: 36549202 DOI: 10.1016/j.jcis.2022.12.056] [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: 08/09/2022] [Revised: 10/08/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022]
Abstract
Phospholipids are the protective layer of modern cells, but it is challenging for the formation of phospholipids that require a simple abiotic synthesis before the advent of primitive cells. Here, we reported the abiotic synthesis for lysophosphatidic acids (LPAs) with prebiotically plausible reactants in aqueous microdroplets under ambient conditions. The LPAs formation is carried out by fusing two microdroplets streams: one contains glycerol and pyrophosphate in water and the other one contains fatty acids in acetonitrile. Compared with the bulk solution, LPAs were generated in microdroplets without the addition of catalyst and heating. Conditions of reactant concentrations and microdroplet size varied and suggested that LPAs formation occurred near or at the microdroplet surface. The LPAs formation also showed chemoselective toward on chain-length of fatty acids. Finally, the formation of LPAs underwent two-step reactions with glycerol phosphorylation eliminating one water molecule followed by esterification with fatty acids. These results also implicated that pyrophosphate functioned as both catalysts and precursors in prebiotic LPAs synthesis. The approach using fusion aqueous microdroplets has desirable features in studying the substance exchange and interaction in atmosphere.
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Affiliation(s)
- Yun Ju
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, PR China; School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, Heilongjiang 150090, PR China
| | - Hong Zhang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, PR China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, PR China.
| | - Xiaofei Wang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, PR China
| | - Yaqi Liu
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, PR China
| | - Yali Yang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, PR China; School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, Heilongjiang 150090, PR China
| | - Guangfeng Kan
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, PR China
| | - Kai Yu
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, PR China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, PR China
| | - Jie Jiang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, PR China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, PR China; School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, Heilongjiang 150090, PR China.
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11
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Self-Similar Patterns from Abiotic Decarboxylation Metabolism through Chemically Oscillating Reactions: A Prebiotic Model for the Origin of Life. Life (Basel) 2023; 13:life13020551. [PMID: 36836908 PMCID: PMC9960873 DOI: 10.3390/life13020551] [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: 11/26/2022] [Revised: 02/03/2023] [Accepted: 02/11/2023] [Indexed: 02/18/2023] Open
Abstract
The origin of life must have included an abiotic stage of carbon redox reactions that involved electron transport chains and the production of lifelike patterns. Chemically oscillating reactions (COR) are abiotic, spontaneous, out-of-equilibrium, and redox reactions that involve the decarboxylation of carboxylic acids with strong oxidants and strong acids to produce CO2 and characteristic self-similar patterns. Those patterns have circular concentricity, radial geometries, characteristic circular twins, colour gradients, cavity structures, and branching to parallel alignment. We propose that COR played a role during the prebiotic cycling of carboxylic acids, furthering the new model for geology where COR can also explain the patterns of diagenetic spheroids in sediments. The patterns of COR in Petri dishes are first considered and compared to those observed in some eukaryotic lifeforms. The molecular structures and functions of reactants in COR are then compared to key biological metabolic processes. We conclude that the newly recognised similarities in compositions and patterns warrant future research to better investigate the role of halogens in biochemistry; COR in life-forms, including in humans; and the COR-stage of prebiotic carbon cycling on other planets, such as Mars.
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12
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Nader S, Baccouche A, Connolly F, Abou-Ghanem M, Styler SA, Lewis JD, Pink D, Mansy SS. Model Atmospheric Aerosols Convert to Vesicles upon Entry into Aqueous Solution. ACS EARTH & SPACE CHEMISTRY 2023; 7:252-259. [PMID: 36704180 PMCID: PMC9869892 DOI: 10.1021/acsearthspacechem.2c00328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 06/18/2023]
Abstract
Aerosols are abundant on the Earth and likely played a role in prebiotic chemistry. Aerosol particles coagulate, divide, and sample a wide variety of conditions conducive to synthesis. While much work has centered on the generation of aerosols and their chemistry, little effort has been expended on their fate after settling. Here, using a laboratory model, we show that aqueous aerosols transform into cell-sized protocellular structures upon entry into aqueous solution containing lipid. Such processes provide for a heretofore unexplored pathway for the assembly of the building blocks of life from disparate geochemical regions within cell-like vesicles with a lipid bilayer in a manner that does not lead to dilution. The efficiency of aerosol to vesicle transformation is high with prebiotically plausible lipids, such as decanoic acid and decanol, that were previously shown to be capable of forming growing and dividing vesicles. The high transformation efficiency with 10-carbon lipids in landing solutions is consistent with the surface properties and dynamics of short-chain lipids. Similar processes may be operative today as fatty acids are common constituents of both contemporary aerosols and the sea. Our work highlights a new pathway that may have facilitated the emergence of the Earth's first cells.
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Affiliation(s)
- Serge Nader
- Department
of Chemistry, University of Alberta, Edmonton, AlbertaT6G 2N4, Canada
| | - Alexandre Baccouche
- Department
of Chemistry, University of Alberta, Edmonton, AlbertaT6G 2N4, Canada
| | - Fiona Connolly
- Department
of Chemistry, University of Alberta, Edmonton, AlbertaT6G 2N4, Canada
| | - Maya Abou-Ghanem
- Department
of Chemistry, University of Alberta, Edmonton, AlbertaT6G 2N4, Canada
| | - Sarah A. Styler
- Department
of Chemistry, University of Alberta, Edmonton, AlbertaT6G 2N4, Canada
| | - John D. Lewis
- Department
of Oncology, University of Alberta, Edmonton, AlbertaT6G 2E1, Canada
| | - Desmond Pink
- Nanostics
Inc., Edmonton, AlbertaT5J 4P6, Canada
| | - Sheref S. Mansy
- Department
of Chemistry, University of Alberta, Edmonton, AlbertaT6G 2N4, Canada
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13
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Boyd MA, Thavarajah W, Lucks JB, Kamat NP. Robust and tunable performance of a cell-free biosensor encapsulated in lipid vesicles. SCIENCE ADVANCES 2023; 9:eadd6605. [PMID: 36598992 PMCID: PMC9812392 DOI: 10.1126/sciadv.add6605] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 11/23/2022] [Indexed: 05/21/2023]
Abstract
Cell-free systems have enabled the development of genetically encoded biosensors to detect a range of environmental and biological targets. Encapsulation of these systems in synthetic membranes to form artificial cells can reintroduce features of the cellular membrane, including molecular containment and selective permeability, to modulate cell-free sensing capabilities. Here, we demonstrate robust and tunable performance of a transcriptionally regulated, cell-free riboswitch encapsulated in lipid membranes, allowing the detection of fluoride, an environmentally important molecule. Sensor response can be tuned by varying membrane composition, and encapsulation protects from sensor degradation, facilitating detection in real-world samples. These sensors can detect fluoride using two types of genetically encoded outputs, enabling detection of fluoride at the Environmental Protection Agency maximum contaminant level of 0.2 millimolars. This work demonstrates the capacity of bilayer membranes to confer tunable permeability to encapsulated, genetically encoded sensors and establishes the feasibility of artificial cell platforms to detect environmentally relevant small molecules.
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Affiliation(s)
- Margrethe A. Boyd
- Department of Biomedical Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Walter Thavarajah
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, USA
- Center for Water Research, Northwestern University, Evanston, IL, USA
| | - Julius B. Lucks
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, USA
- Center for Water Research, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Corresponding author. (N.P.K.); (J.B.L.)
| | - Neha P. Kamat
- Department of Biomedical Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Corresponding author. (N.P.K.); (J.B.L.)
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14
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Wang X, Hu J, Liu S. Overcoming the Dilemma of Permeability and Stability of Polymersomes through Traceless Cross-Linking. Acc Chem Res 2022; 55:3404-3416. [PMID: 36351034 DOI: 10.1021/acs.accounts.2c00442] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In nature, cells are highly compartmentalized into many organelles that are well separated from the rest of the cellular space by unique membrane structures, which are of crucial importance to allow cells to perform various physiological functions in such a small and crowded space. Learning from the ubiquitous membrane structures of cells and organelles has continuously inspired the development of artificial self-assembled nanostructures, with lipid vesicles (liposomes) and polymer vesicles (polymersomes) being the most representative examples. Similar to the membrane-bound structures of cells and organelles, both liposomes and polymersomes contain an aqueous interior enclosed by a bilayer membrane. Therefore, liposomes and polymersomes have been extensively investigated to mimic the fundamental structures and functions of living cells. For example, liposomes and polymersomes have been successfully engineered as nanocarriers, smart nanoreactors, artificial organelles, and so on. Notably, living cells can exchange both energy and materials with surrounding environments, benefiting from the selective permeability of lipid membranes. The permselectivity of cell membranes is thus an essential attribute of living organisms. Compared to liposomes, polymersomes have increased structural stability but low membrane permeability. Indeed, polymersomes are almost impermeable to small molecules, ions, and even water molecules. To improve the permeability of polymersomes, much effort has been devoted to the incorporation of channel proteins, the coassembly of oppositely charged block copolymers (BCPs), the development of stimuli-responsive BCPs, and so on. Despite great achievements, these approaches generally lead to decreased stability of polymersomes and, sometimes, polymersome disintegration. In this Account, we discuss our recent efforts to reconcile the stability and permeability of polymersomes via a traceless cross-linking approach. Although cross-linking reactions within bilayer membranes generally lead to decreased permeability, the traceless cross-linking approach can concurrently improve the stability and permeability of polymersomes. Specifically, stimuli-responsive polymersomes undergo either covalent cross-linking or noncovalent cross-linking reactions under specific stimuli to increase bilayer stability, while the cross-linking processes can concurrently permeabilize polymersome bilayers through cross-linking-driven hydrophobic-to-hydrophilic transitions. Notably, unlike conventional cross-linking processes requiring additional cross-linkers, the traceless cross-linking process does not involve extra cross-linking agents but takes full advantage of the in situ generated active moieties. By taking advantage of the simultaneous modulation of the stability and permeability of polymersomes via traceless cross-linking, these polymersomes can be further engineered as smart nanocarriers and nanoreactors. The robustness and generality of this approach have been validated by both extracellular and intracellular stimuli such as light irradiation, glutathione, and hydrogen peroxide. Moreover, many functional groups such as fluorescent dyes and contrast agents can be integrated into this versatile platform as well, enabling the construction of theranostic nanovectors capable of responding to pathological microenvironments. This Account provides a new approach to regulating the permeability of polymersomes while maintaining their structural stability.
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Affiliation(s)
- Xiaorui Wang
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, and CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China.,Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Biomaterials Research Center, School of Biomedical Engineering, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Jinming Hu
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, and CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Shiyong Liu
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, and CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
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15
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Bhattacharya D, Kleeblatt DC, Statt A, Reinhart WF. Predicting aggregate morphology of sequence-defined macromolecules with recurrent neural networks. SOFT MATTER 2022; 18:5037-5051. [PMID: 35748651 DOI: 10.1039/d2sm00452f] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Self-assembly of dilute sequence-defined macromolecules is a complex phenomenon in which the local arrangement of chemical moieties can lead to the formation of long-range structure. The dependence of this structure on the sequence necessarily implies that a mapping between the two exists, yet it has been difficult to model so far. Predicting the aggregation behavior of these macromolecules is challenging due to the lack of effective order parameters, a vast design space, inherent variability, and high computational costs associated with currently available simulation techniques. Here, we accurately predict the morphology of aggregates self-assembled from sequence-defined macromolecules using supervised machine learning. We find that regression models with implicit representation learning perform significantly better than those based on engineered features such as k-mer counting, and a recurrent-neural-network-based regressor performs the best out of nine model architectures we tested. Furthermore, we demonstrate the high-throughput screening of monomer sequences using the regression model to identify candidates for self-assembly into selected morphologies. Our strategy is shown to successfully identify multiple suitable sequences in every test we performed, so we hope the insights gained here can be extended to other increasingly complex design scenarios in the future, such as the design of sequences under polydispersity and at varying environmental conditions.
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Affiliation(s)
- Debjyoti Bhattacharya
- Materials Science and Engineering, Pennsylvania State University, University Park, PA 16802, USA.
| | - Devon C Kleeblatt
- Materials Science and Engineering, Pennsylvania State University, University Park, PA 16802, USA.
| | - Antonia Statt
- Materials Science and Engineering, Grainger College of Engineering, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - Wesley F Reinhart
- Materials Science and Engineering, Pennsylvania State University, University Park, PA 16802, USA.
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA 16802, USA
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16
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Imai M, Sakuma Y, Kurisu M, Walde P. From vesicles toward protocells and minimal cells. SOFT MATTER 2022; 18:4823-4849. [PMID: 35722879 DOI: 10.1039/d1sm01695d] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In contrast to ordinary condensed matter systems, "living systems" are unique. They are based on molecular compartments that reproduce themselves through (i) an uptake of ingredients and energy from the environment, and (ii) spatially and timely coordinated internal chemical transformations. These occur on the basis of instructions encoded in information molecules (DNAs). Life originated on Earth about 4 billion years ago as self-organised systems of inorganic compounds and organic molecules including macromolecules (e.g. nucleic acids and proteins) and low molar mass amphiphiles (lipids). Before the first living systems emerged from non-living forms of matter, functional molecules and dynamic molecular assemblies must have been formed as prebiotic soft matter systems. These hypothetical cell-like compartment systems often are called "protocells". Other systems that are considered as bridging units between non-living and living systems are called "minimal cells". They are synthetic, autonomous and sustainable reproducing compartment systems, but their constituents are not limited to prebiotic substances. In this review, we focus on both membrane-bounded (vesicular) protocells and minimal cells, and provide a membrane physics background which helps to understand how morphological transformations of vesicle systems might have happened and how vesicle reproduction might be coupled with metabolic reactions and information molecules. This research, which bridges matter and life, is a great challenge in which soft matter physics, systems chemistry, and synthetic biology must take joined efforts to better understand how the transformation of protocells into living systems might have occurred at the origin of life.
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Affiliation(s)
- Masayuki Imai
- Department of Physics, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba, Sendai 980-8578, Japan.
| | - Yuka Sakuma
- Department of Physics, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba, Sendai 980-8578, Japan.
| | - Minoru Kurisu
- Department of Physics, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba, Sendai 980-8578, Japan.
| | - Peter Walde
- Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, CH-8093 Zürich, Switzerland
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17
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Takamiya H, Kouduka M, Furutani H, Mukai H, Nakagawa K, Yamamoto T, Kato S, Kodama Y, Tomioka N, Ito M, Suzuki Y. Copper-Nanocoated Ultra-Small Cells in Grain Boundaries Inside an Extinct Vent Chimney. Front Microbiol 2022; 13:864205. [PMID: 35747369 PMCID: PMC9209642 DOI: 10.3389/fmicb.2022.864205] [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: 01/28/2022] [Accepted: 05/09/2022] [Indexed: 11/18/2022] Open
Abstract
Chemosynthetic organisms flourish around deep-sea hydrothermal vents where energy-rich fluids are emitted from metal sulfide chimneys. However, microbial life hosted in mineral assemblages in extinct chimneys lacking fluid venting remains largely unknown. The interior of extinct chimneys remains anoxic where the percolation of oxygenated seawater is limited within tightly packed metal sulfide grains. Given the scarcity of photosynthetic organics in deep seawater, anaerobic microbes might inhabit the grain boundaries energetically depending on substrates derived from rock-water interactions. In this study, we reported ultra-small cells directly visualized in grain boundaries of CuFeS2 inside an extinct metal sulfide chimney from the southern Mariana Trough. Nanoscale solid analyses reveal that ultra-small cells are coated with Cu2O nanocrystals in grain boundaries enriched with C, N, and P. In situ spectroscopic and spectrometric characterizations demonstrate the distribution of organics with amide groups and a large molecular organic compound in the grain boundaries. We inferred that the ultra-small cells are anaerobes because of the fast dissolution of Cu2O nanocrystals in oxygenated solution. This Cu2O property also excludes the possibility of microbial contamination from ambient seawater during sampling. It is shown by 16S rRNA gene sequence analysis that the chimney interior is dominated by Pacearchaeota known to have anaerobic metabolisms and ultra-small cells. Our results support the potential existence of photosynthesis-independent microbial ecosystems in grain boundaries in submarine metal sulfides deposits on the early Earth.
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Affiliation(s)
- Hinako Takamiya
- Department of Earth and Planetary Science, The University of Tokyo, Bunkyo City, Japan
| | - Mariko Kouduka
- Department of Earth and Planetary Science, The University of Tokyo, Bunkyo City, Japan
| | - Hitoshi Furutani
- Department of Earth and Planetary Science, The University of Tokyo, Bunkyo City, Japan
| | - Hiroki Mukai
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Kaoru Nakagawa
- Solutions COE, Analytical & Measuring Instruments Division, Shimadzu Corporation, Kyoto, Japan
| | - Takushi Yamamoto
- Solutions COE, Analytical & Measuring Instruments Division, Shimadzu Corporation, Kyoto, Japan
| | - Shingo Kato
- Japan Collection of Microorganisms (JCM), RIKEN BioResource Research Center, Tsukuba, Japan
| | | | - Naotaka Tomioka
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Japan
| | - Motoo Ito
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Japan
| | - Yohey Suzuki
- Department of Earth and Planetary Science, The University of Tokyo, Bunkyo City, Japan
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18
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The Bootstrap Model of Prebiotic Networks of Proteins and Nucleic Acids. Life (Basel) 2022; 12:life12050724. [PMID: 35629391 PMCID: PMC9144896 DOI: 10.3390/life12050724] [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: 03/31/2022] [Revised: 05/08/2022] [Accepted: 05/10/2022] [Indexed: 11/17/2022] Open
Abstract
It is not known how life arose from prebiotic physical chemistry. How did fruitful cell-like associations emerge from the two polymer types—informational (nucleic acids, xNAs = DNA or RNA) and functional (proteins)? Our model shows how functional networks could bootstrap from random sequence-independent initial states. For proteins, we adopt the foldamer hypothesis: through persistent nonequilibrium prebiotic syntheses, short random peptides fold and catalyze the elongation of others. The xNAs enter through random binding to the peptides, and all chains can mutate. Chains grow inside colloids that split when they’re large, coupling faster growth speeds to bigger populations. Random and useless at first, these folding and binding events grow protein—xNA networks that resemble today’s protein–protein networks.
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19
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Gözen I, Köksal ES, Põldsalu I, Xue L, Spustova K, Pedrueza-Villalmanzo E, Ryskulov R, Meng F, Jesorka A. Protocells: Milestones and Recent Advances. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2106624. [PMID: 35322554 DOI: 10.1002/smll.202106624] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/06/2022] [Indexed: 06/14/2023]
Abstract
The origin of life is still one of humankind's great mysteries. At the transition between nonliving and living matter, protocells, initially featureless aggregates of abiotic matter, gain the structure and functions necessary to fulfill the criteria of life. Research addressing protocells as a central element in this transition is diverse and increasingly interdisciplinary. The authors review current protocell concepts and research directions, address milestones, challenges and existing hypotheses in the context of conditions on the early Earth, and provide a concise overview of current protocell research methods.
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Affiliation(s)
- Irep Gözen
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Oslo, 0318, Norway
| | - Elif Senem Köksal
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Oslo, 0318, Norway
| | - Inga Põldsalu
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Oslo, 0318, Norway
| | - Lin Xue
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Oslo, 0318, Norway
| | - Karolina Spustova
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Oslo, 0318, Norway
| | - Esteban Pedrueza-Villalmanzo
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Göteborg, SE-412 96, Sweden
- Department of Physics, University of Gothenburg, Universitetsplatsen 1, Gothenburg, 40530, Sweden
| | - Ruslan Ryskulov
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Göteborg, SE-412 96, Sweden
| | - Fanda Meng
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Göteborg, SE-412 96, Sweden
- School of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250000, China
| | - Aldo Jesorka
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Göteborg, SE-412 96, Sweden
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20
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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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21
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Lu H, Aida H, Kurokawa M, Chen F, Xia Y, Xu J, Li K, Ying BW, Yomo T. Primordial mimicry induces morphological change in Escherichia coli. Commun Biol 2022; 5:24. [PMID: 35017623 PMCID: PMC8752768 DOI: 10.1038/s42003-021-02954-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 12/07/2021] [Indexed: 11/09/2022] Open
Abstract
The morphology of primitive cells has been the subject of extensive research. A spherical form was commonly presumed in prebiotic studies but lacked experimental evidence in living cells. Whether and how the shape of living cells changed are unclear. Here we exposed the rod-shaped bacterium Escherichia coli to a resource utilization regime mimicking a primordial environment. Oleate was given as an easy-to-use model prebiotic nutrient, as fatty acid vesicles were likely present on the prebiotic Earth and might have been used as an energy resource. Six evolutionary lineages were generated under glucose-free but oleic acid vesicle (OAV)-rich conditions. Intriguingly, fitness increase was commonly associated with the morphological change from rod to sphere and the decreases in both the size and the area-to-volume ratio of the cell. The changed cell shape was conserved in either OAVs or glucose, regardless of the trade-offs in carbon utilization and protein abundance. Highly differentiated mutations present in the genome revealed two distinct strategies of adaption to OAV-rich conditions, i.e., either directly targeting the cell wall or not. The change in cell morphology of Escherichia coli for adapting to fatty acid availability supports the assumption of the primitive spherical form. Lu et al. investigate the evolution of the shape of living cells by generating six experimental lineages of the rod-shaped E. coli under glucose-free conditions in the presence of oleic acid mimicking a primordial environment. The authors show that the morphological changes from rod to sphere accompanied fitness increases and adaptation amongst fatty acid availability supports the assumption of a primitive spherical form.
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Affiliation(s)
- Hui Lu
- Biomedical Synthetic Biology Research Center, School of Life Sciences, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, PR China
| | - Honoka Aida
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Masaomi Kurokawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Feng Chen
- School of Software Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, PR China
| | - Yang Xia
- Biomedical Synthetic Biology Research Center, School of Life Sciences, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, PR China
| | - Jian Xu
- Biomedical Synthetic Biology Research Center, School of Life Sciences, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, PR China
| | - Kai Li
- Biomedical Synthetic Biology Research Center, School of Life Sciences, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, PR China
| | - Bei-Wen Ying
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8572, Japan.
| | - Tetsuya Yomo
- Biomedical Synthetic Biology Research Center, School of Life Sciences, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, PR China.
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22
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Thoma J, Burmann BM. Architects of their own environment: How membrane proteins shape the Gram-negative cell envelope. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:1-34. [PMID: 35034716 DOI: 10.1016/bs.apcsb.2021.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Gram-negative bacteria are surrounded by a complex multilayered cell envelope, consisting of an inner and an outer membrane, and separated by the aqueous periplasm, which contains a thin peptidoglycan cell wall. These bacteria employ an arsenal of highly specialized membrane protein machineries to ensure the correct assembly and maintenance of the membranes forming the cell envelope. Here, we review the diverse protein systems, which perform these functions in Escherichia coli, such as the folding and insertion of membrane proteins, the transport of lipoproteins and lipopolysaccharide within the cell envelope, the targeting of phospholipids, and the regulation of mistargeted envelope components. Some of these protein machineries have been known for a long time, yet still hold surprises. Others have only recently been described and some are still missing pieces or yet remain to be discovered.
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Affiliation(s)
- Johannes Thoma
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Göteborg, Sweden; Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden.
| | - Björn M Burmann
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Göteborg, Sweden; Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
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23
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Boyd MA, Davis AM, Chambers NR, Tran P, Prindle A, Kamat NP. Vesicle-Based Sensors for Extracellular Potassium Detection. Cell Mol Bioeng 2021; 14:459-469. [PMID: 34777604 DOI: 10.1007/s12195-021-00688-7] [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: 02/22/2021] [Accepted: 07/07/2021] [Indexed: 10/20/2022] Open
Abstract
Introduction The design of sensors that can detect biological ions in situ remains challenging. While many fluorescent indicators exist that can provide a fast, easy readout, they are often nonspecific, particularly to ions with similar charge states. To address this issue, we developed a vesicle-based sensor that harnesses membrane channels to gate access of potassium (K+) ions to an encapsulated fluorescent indicator. Methods We assembled phospholipid vesicles that incorporated valinomycin, a K+ specific membrane transporter, and that encapsulated benzofuran isophthalate (PBFI), a K+ sensitive dye that nonspecifically fluoresces in the presence of other ions, like sodium (Na+). The specificity, kinetics, and reversibility of encapsulated PBFI fluorescence was determined in a plate reader and fluorimeter. The sensors were then added to E. coli bacterial cultures to evaluate K+ levels in media as a function of cell density. Results Vesicle sensors significantly improved specificity of K+ detection in the presence of a competing monovalent ion, sodium (Na+), and a divalent cation, calcium (Ca2+), relative to controls where the dye was free in solution. The sensor was able to report both increases and decreases in K+ concentration. Finally, we observed our vesicle sensors could detect changes in K+ concentration in bacterial cultures. Conclusion Our data present a new platform for extracellular ion detection that harnesses ion-specific membrane transporters to improve the specificity of ion detection. By changing the membrane transporter and encapsulated sensor, our approach should be broadly useful for designing biological sensors that detect an array of biological analytes in traditionally hard-to-monitor environments. Supplementary Information The online version contains supplementary material available at 10.1007/s12195-021-00688-7.
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Affiliation(s)
- Margrethe A Boyd
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL 60208 USA
| | - Anna M Davis
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL 60208 USA
| | - Nora R Chambers
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL 60208 USA
| | - Peter Tran
- Department of Chemical and Biological Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL 60208 USA
| | - Arthur Prindle
- Center for Synthetic Biology, McCormick School of Engineering, Northwestern University, Evanston, IL 60208 USA.,Department of Chemical and Biological Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL 60208 USA.,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 USA
| | - Neha P Kamat
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL 60208 USA.,Center for Synthetic Biology, McCormick School of Engineering, Northwestern University, Evanston, IL 60208 USA
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24
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Abbas M, Lipiński WP, Nakashima KK, Huck WTS, Spruijt E. A short peptide synthon for liquid-liquid phase separation. Nat Chem 2021; 13:1046-1054. [PMID: 34645986 DOI: 10.1038/s41557-021-00788-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 08/13/2021] [Indexed: 11/09/2022]
Abstract
Liquid-liquid phase separation of disordered proteins has emerged as a ubiquitous route to membraneless compartments in living cells, and similar coacervates may have played a role when the first cells formed. However, existing coacervates are typically made of multiple macromolecular components, and designing short peptide analogues capable of self-coacervation has proven difficult. Here we present a short peptide synthon for phase separation, made of only two dipeptide stickers linked via a flexible, hydrophilic spacer. These small-molecule compounds self-coacervate into micrometre-sized liquid droplets at sub-millimolar concentrations, which retain up to 75 wt% water. The design is general and we derive guidelines for the required sticker hydrophobicity and spacer polarity. To illustrate their potential as protocells, we create a disulfide-linked derivative that undergoes reversible compartmentalization controlled by redox chemistry. The resulting coacervates sequester and melt nucleic acids, and act as microreactors that catalyse two different anabolic reactions yielding molecules of increasing complexity. This provides a stepping stone for new coacervate-based protocells made of single peptide species.
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Affiliation(s)
- Manzar Abbas
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Wojciech P Lipiński
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Karina K Nakashima
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
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25
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Rubio-Sánchez R, O'Flaherty DK, Wang A, Coscia F, Petris G, Di Michele L, Cicuta P, Bonfio C. Thermally Driven Membrane Phase Transitions Enable Content Reshuffling in Primitive Cells. J Am Chem Soc 2021; 143:16589-16598. [PMID: 34597506 PMCID: PMC8607435 DOI: 10.1021/jacs.1c06595] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
Self-assembling single-chain amphiphiles
available in the prebiotic
environment likely played a fundamental role in the advent of primitive
cell cycles. However, the instability of prebiotic fatty acid-based
membranes to temperature and pH seems to suggest that primitive cells
could only host prebiotically relevant processes in a narrow range
of nonfluctuating environmental conditions. Here we propose that membrane
phase transitions, driven by environmental fluctuations, enabled the
generation of daughter protocells with reshuffled content. A reversible
membrane-to-oil phase transition accounts for the dissolution of fatty
acid-based vesicles at high temperatures and the concomitant release
of protocellular content. At low temperatures, fatty acid bilayers
reassemble and encapsulate reshuffled material in a new cohort of
protocells. Notably, we find that our disassembly/reassembly cycle
drives the emergence of functional RNA-containing primitive cells
from parent nonfunctional compartments. Thus, by exploiting the intrinsic
instability of prebiotic fatty acid vesicles, our results point at
an environmentally driven tunable prebiotic process, which supports
the release and reshuffling of oligonucleotides and membrane components,
potentially leading to a new generation of protocells with superior
traits. In the absence of protocellular transport machinery, the environmentally
driven disassembly/assembly cycle proposed herein would have plausibly
supported protocellular content reshuffling transmitted to primitive
cell progeny, hinting at a potential mechanism important to initiate
Darwinian evolution of early life forms.
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Affiliation(s)
- Roger Rubio-Sánchez
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, U.K
| | - Derek K O'Flaherty
- Department of Chemistry, University of Guelph, Guelph ON N1G 1Y4, Canada
| | - Anna Wang
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Francesca Coscia
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K.,Fondazione Human Technopole, Structural Biology Research Centre, Milan 20157, Italy
| | - Gianluca Petris
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
| | - Lorenzo Di Michele
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, U.K.,Department of Chemistry and fabriCELL, Imperial College London, Molecular Sciences Research Hub, London W12 0BZ, U.K
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, U.K
| | - Claudia Bonfio
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K.,Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
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26
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Urakami N, Sakuma Y, Chiba T, Imai M. Vesicle deformation and division induced by flip-flops of lipid molecules. SOFT MATTER 2021; 17:8434-8445. [PMID: 34473188 DOI: 10.1039/d1sm00847a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We investigated the deformation of small unilamellar vesicles (SUVs) induced by flip-flops of lipids using coarse-grained molecular dynamics simulations. In the case of single-component SUVs composed of zero spontaneous curvature lipids (ZLs), the flip-flop of ZLs deformed stomatocyte-shaped SUVs into an oblate shape, whereas pear-shaped SUVs were deformed into a prolate shape. These two equilibrium shapes comply with the local minima of elastic energy. In the case of binary vesicles composed of ZLs and negative spontaneous curvature lipids (NLs), the vesicle deformation pathway depended on the initial NL distribution in the bilayer. If the initial difference in the NL concentration between the outer and inner leaflets was small, the flip-flop of ZLs and NLs rapidly deformed pear-shaped SUVs into an equilibrium prolate shape. On the other hand, when NLs were localised in the inner leaflet, the flip-flop of ZLs and NLs deformed pear-shaped SUVs into a limiting shape and then induced vesicle division. Because the flip-flop rate of NLs is much faster than that of ZLs, the total free energy was first relaxed by the flip-flop of NLs and then by that of ZLs. This kinetic effect is responsible for the observed vesicle division induced by flip-flops.
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Affiliation(s)
- Naohito Urakami
- Department of Physics and Informatics, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8512, Japan.
| | - Yuka Sakuma
- Department of Physics, Tohoku University, Aoba, Sendai 980-8578, Japan
| | - Toshikaze Chiba
- Department of Physics, Tohoku University, Aoba, Sendai 980-8578, Japan
| | - Masayuki Imai
- Department of Physics, Tohoku University, Aoba, Sendai 980-8578, Japan
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27
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Song Q, Dong Q, Dong XH, Zhu YL, Li W. Self-Assembly Behaviors of Giant Amphiphiles Containing Cubic Cage-like “Monomers”. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c01431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Qingliang Song
- State Key Laboratory of Molecular Engineering of Polymers, Key Laboratory of Computational Physical Sciences, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Qingshu Dong
- State Key Laboratory of Molecular Engineering of Polymers, Key Laboratory of Computational Physical Sciences, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Xue-Hui Dong
- South China Advanced Institute for Soft Matter Science and Technology, School of Molecular Science and Engineering and State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou 510640, China
| | - You-Liang Zhu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Weihua Li
- State Key Laboratory of Molecular Engineering of Polymers, Key Laboratory of Computational Physical Sciences, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
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28
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Kawakita A, Uchida N, Ryu Y, Muraoka T. Self-assembly of Amphiphilic Peptide in Phospholipid Membrane. J PHOTOPOLYM SCI TEC 2021. [DOI: 10.2494/photopolymer.34.155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anju Kawakita
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology
| | - Noriyuki Uchida
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology
| | - Yunosuke Ryu
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology
| | - Takahiro Muraoka
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology
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29
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Abstract
The detection of ethanolamine (NH2CH2CH2OH) in a molecular cloud in the interstellar medium confirms that a precursor of phospholipids is efficiently formed by interstellar chemistry. Hence, ethanolamine could have been transferred from the proto-Solar nebula to planetesimals and minor bodies of the Solar System and thereafter to our planet. The prebiotic availability of ethanolamine on early Earth could have triggered the formation of efficient and permeable amphiphilic molecules such as phospholipids, thus playing a relevant role in the evolution of the first cellular membranes needed for the emergence of life. Cell membranes are a key element of life because they keep the genetic material and metabolic machinery together. All present cell membranes are made of phospholipids, yet the nature of the first membranes and the origin of phospholipids are still under debate. We report here the presence of ethanolamine in space, NH2CH2CH2OH, which forms the hydrophilic head of the simplest and second-most-abundant phospholipid in membranes. The molecular column density of ethanolamine in interstellar space is N = (1.51± 0.07)× 1013 cm−2, implying a molecular abundance with respect to H2 of (0.9−1.4) × 10−10. Previous studies reported its presence in meteoritic material, but they suggested that it is synthesized in the meteorite itself by decomposition of amino acids. However, we find that the proportion of the molecule with respect to water in the interstellar medium is similar to the one found in the meteorite (10−6). These results indicate that ethanolamine forms efficiently in space and, if delivered onto early Earth, could have contributed to the assembling and early evolution of primitive membranes.
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30
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Wei C, Pohorille A. Fast bilayer-micelle fusion mediated by hydrophobic dipeptides. Biophys J 2021; 120:2330-2342. [PMID: 33887225 DOI: 10.1016/j.bpj.2021.04.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/15/2021] [Accepted: 04/02/2021] [Indexed: 11/30/2022] Open
Abstract
To understand the transition from inanimate matter to life, we studied a process that directly couples simple metabolism to evolution via natural selection, demonstrated experimentally by Adamala and Szostak. In this process, dipeptides synthesized inside precursors of cells promote absorption of fatty acid micelles to vesicles, inducing their preferential growth and division at the expense of other vesicles. The process is explained on the basis of coarse-grained molecular dynamics simulations, each extending for tens of microseconds, carried out to model fusion between a micelle and a membrane, both made of fatty acids in the absence and presence of hydrophobic dipeptides. In all systems with dipeptides, but not in their absence, fusion events were observed. They involve the formation of a stalk made by hydrophobic chains from the micelle and the membrane, similar to that postulated for vesicle-vesicle fusion. The emergence of a stalk is facilitated by transient clusters of dipeptides, side chains of which form hydrophobic patches at the membrane surface. Committor probability calculations indicate that the size of a patch is a suitable reaction coordinate and allows for identifying the transition state for fusion. Free-energy barrier to fusion is greatly reduced in the presence of dipeptides to only 4-5 kcal/mol, depending on the hydrophobicity of side chains. The mechanism of mediated fusion, which is expected to apply to other small peptides and hydrophobic molecules, provides a robust means by which a nascent metabolism can confer evolutionary advantage to precursors of cells.
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Affiliation(s)
- Chenyu Wei
- NASA Ames Research Center, Moffett Field, California; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
| | - Andrew Pohorille
- NASA Ames Research Center, Moffett Field, California; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California.
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31
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Omarova M, Zhang Y, Mkam Tsengam IK, He J, Yu T, Zhang D, John V. Hydrophobe Containing Polypeptoids Complex with Lipids and Induce Fusogenesis of Lipid Vesicles. J Phys Chem B 2021; 125:3145-3152. [PMID: 33730500 PMCID: PMC8041297 DOI: 10.1021/acs.jpcb.0c11477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/07/2021] [Indexed: 12/19/2022]
Abstract
The hydrophobic effect of alkyl group insertion into phospholipid bilayers is exploited in modifying and modulating vesicle structure. We show that amphiphilic polypeptoids (peptide mimics) with n-decyl side chains, which we term as hydrophobe-containing polypeptoids (HCPs), can insert the alkyl hydrophobes into the membrane bilayer of phospholipid-based vesicles. Such insertion leads to disruption of the liposomes and the formation of HCP-lipid complexes that are colloidally stable in aqueous solution. Interestingly, when these complexes are added to fresh liposomes, remnant uncomplexed hydrophobes (the n-decyl groups) bridge liposomes and fuse them. The fusion leads to the engulfing of liposomes and the formation of multilayered vesicles. The morphology of the liposome system can be changed from stopping fusion and forming clustered vesicles to the continued formation of multilayered liposomes simply by controlling the amount of the HCP-lipid complex added. The entire procedure occurs in aqueous systems without the addition of any other solvents. There are several implications to these observations including the biological relevance of mimicking fusogenic proteins such as the SNARE proteins and the development of new drug delivery technologies to impact delivery to cell organelles.
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Affiliation(s)
- Marzhana Omarova
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Yueheng Zhang
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Igor Kevin Mkam Tsengam
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Jibao He
- Coordinated
Instrumentation Facility, Tulane University, New Orleans, Louisiana 70118, United States
| | - Tianyi Yu
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Donghui Zhang
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Vijay John
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
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32
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Giant Vesicles Produced with Phosphatidylcholines (PCs) and Phosphatidylethanolamines (PEs) by Water-in-Oil Inverted Emulsions. Life (Basel) 2021; 11:life11030223. [PMID: 33801936 PMCID: PMC7998898 DOI: 10.3390/life11030223] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 11/30/2022] Open
Abstract
(1) Background: giant vesicles (GVs) are widely employed as models for studying physicochemical properties of bio-membranes and artificial cell construction due to their similarities to natural cell membranes. Considering the critical roles of GVs, various methods have been developed to prepare them. Notably, the water-in-oil (w/o) inverted emulsion-transfer method is reported to be the most promising, owning to the relatively higher productivity and better encapsulation efficiency of biomolecules. Previously, we successfully established an improved approach to acquire detailed information of 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)-derived GVs with imaging flow cytometry (IFC); (2) Methods: we prepared GVs with different lipid compositions, including phosphatidylcholines (PCs), phosphatidylethanolamines (PEs), and PC/PE mixtures by w/o inverted emulsion methods. We comprehensively compared the yield, purity, size, and encapsulation efficiency of the resulting vesicles; (3) Results: the relatively higher productivities of GVs could be obtained from POPC, 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1,2-dilauroyl-sn-glycero-3-phosphoethanolamine (DLPE), DOPC: DLPE (7:3), and POPC: DLPE (6:4) pools. Furthermore, we also demonstrate that these GVs are stable during long term preservation in 4 °C. (4) Conclusions: our results will be useful for the analytical study of GVs and GV-based applications.
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33
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Abstract
Giant unilamellar vesicles (GUVs) have gained great popularity as mimicries for cellular membranes. As their sizes are comfortably above the optical resolution limit, and their lipid composition is easily controlled, they are ideal for quantitative light microscopic investigation of dynamic processes in and on membranes. However, reconstitution of functional proteins into the lumen or the GUV membrane itself has proven technically challenging. In recent years, a selection of techniques has been introduced that tremendously improve GUV-assay development and enable the precise investigation of protein-membrane interactions under well-controlled conditions. Moreover, due to these methodological advances, GUVs are considered important candidates as protocells in bottom-up synthetic biology. In this review, we discuss the state of the art of the most important vesicle production and protein encapsulation methods and highlight some key protein systems whose functional reconstitution has advanced the field.
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Affiliation(s)
- Thomas Litschel
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; ,
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; ,
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34
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Jia TZ, Caudan M, Mamajanov I. Origin of Species before Origin of Life: The Role of Speciation in Chemical Evolution. Life (Basel) 2021; 11:154. [PMID: 33671365 PMCID: PMC7922636 DOI: 10.3390/life11020154] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/11/2021] [Accepted: 02/15/2021] [Indexed: 11/17/2022] Open
Abstract
Speciation, an evolutionary process by which new species form, is ultimately responsible for the incredible biodiversity that we observe on Earth every day. Such biodiversity is one of the critical features which contributes to the survivability of biospheres and modern life. While speciation and biodiversity have been amply studied in organismic evolution and modern life, it has not yet been applied to a great extent to understanding the evolutionary dynamics of primitive life. In particular, one unanswered question is at what point in the history of life did speciation as a phenomenon emerge in the first place. Here, we discuss the mechanisms by which speciation could have occurred before the origins of life in the context of chemical evolution. Specifically, we discuss that primitive compartments formed before the emergence of the last universal common ancestor (LUCA) could have provided a mechanism by which primitive chemical systems underwent speciation. In particular, we introduce a variety of primitive compartment structures, and associated functions, that may have plausibly been present on early Earth, followed by examples of both discriminate and indiscriminate speciation affected by primitive modes of compartmentalization. Finally, we discuss modern technologies, in particular, droplet microfluidics, that can be applied to studying speciation phenomena in the laboratory over short timescales. We hope that this discussion highlights the current areas of need in further studies on primitive speciation phenomena while simultaneously proposing directions as important areas of study to the origins of life.
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Affiliation(s)
- Tony Z. Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan;
- Blue Marble Space Institute of Science, 1001 4th Ave., Suite 3201, Seattle, WA 98154, USA
| | - Melina Caudan
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan;
| | - Irena Mamajanov
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan;
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35
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Kotopoulou E, Lopez‐Haro M, Calvino Gamez JJ, García‐Ruiz JM. Nanoscale Anatomy of Iron-Silica Self-Organized Membranes: Implications for Prebiotic Chemistry. Angew Chem Int Ed Engl 2021; 60:1396-1402. [PMID: 33022871 PMCID: PMC7839773 DOI: 10.1002/anie.202012059] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Indexed: 12/26/2022]
Abstract
Iron-silica self-organized membranes, so-called chemical gardens, behave as fuel cells and catalyze the formation of amino/carboxylic acids and RNA nucleobases from organics that were available on early Earth. Despite their relevance for prebiotic chemistry, little is known about their structure and mineralogy at the nanoscale. Studied here are focused ion beam milled sections of iron-silica membranes, grown from synthetic and natural, alkaline, serpentinization-derived fluids thought to be widespread on early Earth. Electron microscopy shows they comprise amorphous silica and iron nanoparticles of large surface areas and inter/intraparticle porosities. Their construction resembles that of a heterogeneous catalyst, but they can also exhibit a bilayer structure. Surface-area measurements suggest that membranes grown from natural waters have even higher catalytic potential. Considering their geochemically plausible precipitation in the early hydrothermal systems where abiotic organics were produced, iron-silica membranes might have assisted the generation and organization of the first biologically relevant organics.
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Affiliation(s)
- Electra Kotopoulou
- Instituto Andaluz de Ciencias de la TierraConsejo Superior de Investigaciones Científicas- Universidad de GranadaAvda. de las Palmeras 418100GranadaSpain
| | - Miguel Lopez‐Haro
- Departamento de Ciencia de los Materiales e Ingeniería Metalúrgica y Química InorgánicaFacultad de CienciasUniversidad de CadizCampus Rio San PedroPuerto Real11510CádizSpain
| | - Jose Juan Calvino Gamez
- Departamento de Ciencia de los Materiales e Ingeniería Metalúrgica y Química InorgánicaFacultad de CienciasUniversidad de CadizCampus Rio San PedroPuerto Real11510CádizSpain
| | - Juan Manuel García‐Ruiz
- Instituto Andaluz de Ciencias de la TierraConsejo Superior de Investigaciones Científicas- Universidad de GranadaAvda. de las Palmeras 418100GranadaSpain
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36
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Banger A, Sindram J, Otten M, Kania J, Wilms D, Strzelczyk A, Miletic S, Marlovits TC, Karg M, Hartmann L. Synthesis and self-assembly of amphiphilic precision glycomacromolecules. Polym Chem 2021. [DOI: 10.1039/d1py00422k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Amphiphilic precision glycomacromolecules (APG) are synthesized using solid-phase synthesis and studied for their self-assembly behavior and as inhibitors of bacterial adhesion.
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Affiliation(s)
- Alexander Banger
- Institute of Organic and Macromolecular Chemistry, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Julian Sindram
- Insitute of Physical Chemistry I: Colloids and Nanooptics, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Marius Otten
- Insitute of Physical Chemistry I: Colloids and Nanooptics, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Jessica Kania
- Institute of Organic and Macromolecular Chemistry, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Dimitri Wilms
- Institute of Organic and Macromolecular Chemistry, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Alexander Strzelczyk
- Institute of Organic and Macromolecular Chemistry, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Sean Miletic
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany
| | - Thomas C. Marlovits
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Deutsches Elektronen-Synchrotron Zentrum (DESY), Hamburg, Germany
| | - Matthias Karg
- Insitute of Physical Chemistry I: Colloids and Nanooptics, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Laura Hartmann
- Institute of Organic and Macromolecular Chemistry, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
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37
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Van Kranendonk MJ, Baumgartner R, Djokic T, Ota T, Steller L, Garbe U, Nakamura E. Elements for the Origin of Life on Land: A Deep-Time Perspective from the Pilbara Craton of Western Australia. ASTROBIOLOGY 2021; 21:39-59. [PMID: 33404294 DOI: 10.1089/ast.2019.2107] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
For decades, deep sea hydrothermal vents have been a preferred setting for the Origin of Life, but "The Water Problem" as relates to polymerization of organic molecules, together with a propensity to dilute critical prebiotic elements as well as a number of other crucial factors, suggests that a terrestrial hot spring field with the capacity for wet-dry cycling and element concentration may represent a more likely candidate. Here, we investigate a 3.5 billion-year-old, anoxic hot spring setting from the Pilbara Craton (Australia) and show that its hydrothermal veins and compositionally varied pools and springs concentrated all of the essential elements required for prebiotic chemistry (including B, Zn, Mn, and K, in addition to C, H, N, O, P, and S). Temporal variability (seasonal to decadal), together with the known propensity of hot springs for wet-dry cycling and information exchange, would lead to innovation pools with peaks of fitness for developing molecules. An inference from the chemical complexity of the Pilbara analogue is that life could perhaps get started quickly on planets with volcanoes, silicate rocks, an exposed land surface, and water, ingredients that should form the backbone in the search for life in the Universe.
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Affiliation(s)
- Martin J Van Kranendonk
- Australian Centre for Astrobiology, School of Biological Earth and Environmental Sciences, University of New South Wales Sydney, Kensington, Australia
- Pheasant Memorial Laboratory, Institute for Planetary Materials, Okayama University, Misasa, Japan
| | - Raphael Baumgartner
- Australian Centre for Astrobiology, School of Biological Earth and Environmental Sciences, University of New South Wales Sydney, Kensington, Australia
| | - Tara Djokic
- Australian Centre for Astrobiology, School of Biological Earth and Environmental Sciences, University of New South Wales Sydney, Kensington, Australia
| | - Tsutomu Ota
- Pheasant Memorial Laboratory, Institute for Planetary Materials, Okayama University, Misasa, Japan
| | - Luke Steller
- Australian Centre for Astrobiology, School of Biological Earth and Environmental Sciences, University of New South Wales Sydney, Kensington, Australia
| | - Ulf Garbe
- Australian Nuclear Science and Technology Organisation, Kirrawee, Australia
| | - Eizo Nakamura
- Pheasant Memorial Laboratory, Institute for Planetary Materials, Okayama University, Misasa, Japan
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38
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Boyd MA, Kamat NP. Designing Artificial Cells towards a New Generation of Biosensors. Trends Biotechnol 2020; 39:927-939. [PMID: 33388162 DOI: 10.1016/j.tibtech.2020.12.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/25/2020] [Accepted: 12/01/2020] [Indexed: 01/31/2023]
Abstract
The combination of biological and synthetic materials has great potential to generate new types of biosensors. Toward this goal, recent advances in artificial cell development have demonstrated the capacity to detect a variety of analytes and environmental changes by encapsulating genetically encoded sensors within bilayer membranes, expanding the contexts within which biologically based sensing can operate. This chassis not only acts as a container for cell-free sensors, but can also play an active role in artificial cell sensing by serving as an additional gate mediating the transfer of environmental information. Here, we focus on recent progress toward stimuli-responsive artificial cells and discuss strategies for membrane functionalization in order to expand cell-free biosensing capabilities and applications.
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Affiliation(s)
- Margrethe A Boyd
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Neha P Kamat
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.
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39
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Kotopoulou E, Lopez‐Haro M, Calvino Gamez JJ, García‐Ruiz JM. Nanoscale Anatomy of Iron‐Silica Self‐Organized Membranes: Implications for Prebiotic Chemistry. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202012059] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Electra Kotopoulou
- Instituto Andaluz de Ciencias de la Tierra Consejo Superior de Investigaciones Científicas- Universidad de Granada Avda. de las Palmeras 4 18100 Granada Spain
| | - Miguel Lopez‐Haro
- Departamento de Ciencia de los Materiales e Ingeniería Metalúrgica y Química Inorgánica Facultad de Ciencias Universidad de Cadiz Campus Rio San Pedro Puerto Real 11510 Cádiz Spain
| | - Jose Juan Calvino Gamez
- Departamento de Ciencia de los Materiales e Ingeniería Metalúrgica y Química Inorgánica Facultad de Ciencias Universidad de Cadiz Campus Rio San Pedro Puerto Real 11510 Cádiz Spain
| | - Juan Manuel García‐Ruiz
- Instituto Andaluz de Ciencias de la Tierra Consejo Superior de Investigaciones Científicas- Universidad de Granada Avda. de las Palmeras 4 18100 Granada Spain
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40
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Kundu N, Mondal D, Sarkar N. Dynamics of the vesicles composed of fatty acids and other amphiphile mixtures: unveiling the role of fatty acids as a model protocell membrane. Biophys Rev 2020; 12:1117-1131. [PMID: 32926295 PMCID: PMC7575682 DOI: 10.1007/s12551-020-00753-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 09/03/2020] [Indexed: 01/31/2023] Open
Abstract
Fundamental research at the interface of chemistry and biology has the potential to shine light on the question of how living cells can be synthesized from inanimate matter thereby providing plausible pathways for the emergence of cellular life. Compartmentalization of different biochemical reactions within a membrane bound water environment is considered an essential first step in any origin of life pathway. It has been suggested that fatty acid-based vesicles can be considered a model protocell having the potential for change via Darwinian evolution. As such, protocell models have the potential to assist in furthering our understanding of the origin of life in the laboratory. Fatty acids, both by themselves and in mixtures with other amphiphiles, can form different self-assembled structures depending on their surroundings. Recent studies of fatty acid-based membranes have suggested likely pathways of protocell growth, division and membrane permeabilisation for the transport of different nutrients, such as nucleotides across the membrane. In this review, different dynamic processes related to the growth and division of the protocell membrane are discussed and possible pathways for transition of the protocell to the modern cell are explored. These areas of research may lead to a better understanding of the synthesis of artificial cell-like entities and thus herald the possibility of creating new form of life distinct from existing biology. Graphical Abstract Table of Content (TOC) only.
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Affiliation(s)
- Niloy Kundu
- Environment Research Group, R&D Department, Tata Steel Ltd, Jamshedpur, 831007, India.
| | - Dipankar Mondal
- Institute for System Genetics and Department of Cell Biology, New York University, Langone Medical Center, New York, 10016, USA
- Department of Chemistry, Indian Institute of Technology, Kharagpur, WB, 721302, India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology, Kharagpur, WB, 721302, India
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41
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Osinski G, Cockell C, Pontefract A, Sapers H. The Role of Meteorite Impacts in the Origin of Life. ASTROBIOLOGY 2020; 20:1121-1149. [PMID: 32876492 PMCID: PMC7499892 DOI: 10.1089/ast.2019.2203] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The conditions, timing, and setting for the origin of life on Earth and whether life exists elsewhere in our solar system and beyond represent some of the most fundamental scientific questions of our time. Although the bombardment of planets and satellites by asteroids and comets has long been viewed as a destructive process that would have presented a barrier to the emergence of life and frustrated or extinguished life, we provide a comprehensive synthesis of data and observations on the beneficial role of impacts in a wide range of prebiotic and biological processes. In the context of previously proposed environments for the origin of life on Earth, we discuss how meteorite impacts can generate both subaerial and submarine hydrothermal vents, abundant hydrothermal-sedimentary settings, and impact analogues for volcanic pumice rafts and splash pools. Impact events can also deliver and/or generate many of the necessary chemical ingredients for life and catalytic substrates such as clays as well. The role that impact cratering plays in fracturing planetary crusts and its effects on deep subsurface habitats for life are also discussed. In summary, we propose that meteorite impact events are a fundamental geobiological process in planetary evolution that played an important role in the origin of life on Earth. We conclude with the recommendation that impact craters should be considered prime sites in the search for evidence of past life on Mars. Furthermore, unlike other geological processes such as volcanism or plate tectonics, impact cratering is ubiquitous on planetary bodies throughout the Universe and is independent of size, composition, and distance from the host star. Impact events thus provide a mechanism with the potential to generate habitable planets, moons, and asteroids throughout the Solar System and beyond.
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Affiliation(s)
- G.R. Osinski
- Institute for Earth and Space Exploration, University of Western Ontario, London, Canada
- Department of Earth Sciences, University of Western Ontario, London, Canada
- Address correspondence to: Dr. Gordon Osinski, Department of Earth Sciences, 1151 Richmond Street, University of Western Ontario, London ON, N6A 5B7, Canada
| | - C.S. Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - A. Pontefract
- Department of Biology, Georgetown University, Washington, DC, USA
| | - H.M. Sapers
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
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42
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Ellery A. How to Build a Biological Machine Using Engineering Materials and Methods. Biomimetics (Basel) 2020; 5:biomimetics5030035. [PMID: 32722540 PMCID: PMC7558640 DOI: 10.3390/biomimetics5030035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/14/2020] [Accepted: 07/19/2020] [Indexed: 01/09/2023] Open
Abstract
We present work in 3D printing electric motors from basic materials as the key to building a self-replicating machine to colonise the Moon. First, we explore the nature of the biological realm to ascertain its essence, particularly in relation to the origin of life when the inanimate became animate. We take an expansive view of this to ascertain parallels between the biological and the manufactured worlds. Life must have emerged from the available raw material on Earth and, similarly, a self-replicating machine must exploit and leverage the available resources on the Moon. We then examine these lessons to explore the construction of a self-replicating machine using a universal constructor. It is through the universal constructor that the actuator emerges as critical. We propose that 3D printing constitutes an analogue of the biological ribosome and that 3D printing may constitute a universal construction mechanism. Following a description of our progress in 3D printing motors, we suggest that this engineering effort can inform biology, that motors are a key facet of living organisms and illustrate the importance of motors in biology viewed from the perspective of engineering (in the Feynman spirit of “what I cannot create, I cannot understand”).
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Affiliation(s)
- Alex Ellery
- Space Exploration Engineering Group, Department of Mechanical & Aerospace Engineering, Carleton University, Ottawa, ON K1S 5B6, Canada
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Toparlak ÖD, Karki M, Egas Ortuno V, Krishnamurthy R, Mansy SS. Cyclophospholipids Increase Protocellular Stability to Metal Ions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1903381. [PMID: 31523894 DOI: 10.1002/smll.201903381] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/21/2019] [Indexed: 06/10/2023]
Abstract
Model protocells have long been constructed with fatty acids, because these lipids are prebiotically plausible and can, at least theoretically, support a protocell life cycle. However, fatty acid protocells are stable only within a narrow range of pH and metal ion concentration. This instability is particularly problematic as the early Earth would have had a range of conditions, and extant life is completely reliant on metal ions for catalysis and the folding and activity of biological polymers. Here, prebiotically plausible monoacyl cyclophospholipids are shown to form robust vesicles that survive a broad range of pH and high concentrations of Mg2+ , Ca2+ , and Na+ . Importantly, stability to Mg2+ and Ca2+ is improved by the presence of environmental concentrations of Na+ . These results suggest that cyclophospholipids, or lipids with similar characteristics, may have played a central role during the emergence of Darwinian evolution.
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Affiliation(s)
- Ö Duhan Toparlak
- Department CIBIO, University of Trento, via Sommarive 9, 38123, Povo, Italy
| | - Megha Karki
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Veronica Egas Ortuno
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Sheref S Mansy
- Department CIBIO, University of Trento, via Sommarive 9, 38123, Povo, Italy
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Damer B, Deamer D. The Hot Spring Hypothesis for an Origin of Life. ASTROBIOLOGY 2020; 20:429-452. [PMID: 31841362 PMCID: PMC7133448 DOI: 10.1089/ast.2019.2045] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 10/23/2019] [Indexed: 05/05/2023]
Abstract
We present a testable hypothesis related to an origin of life on land in which fluctuating volcanic hot spring pools play a central role. The hypothesis is based on experimental evidence that lipid-encapsulated polymers can be synthesized by cycles of hydration and dehydration to form protocells. Drawing on metaphors from the bootstrapping of a simple computer operating system, we show how protocells cycling through wet, dry, and moist phases will subject polymers to combinatorial selection and draw structural and catalytic functions out of initially random sequences, including structural stabilization, pore formation, and primitive metabolic activity. We propose that protocells aggregating into a hydrogel in the intermediate moist phase of wet-dry cycles represent a primitive progenote system. Progenote populations can undergo selection and distribution, construct niches in new environments, and enable a sharing network effect that can collectively evolve them into the first microbial communities. Laboratory and field experiments testing the first steps of the scenario are summarized. The scenario is then placed in a geological setting on the early Earth to suggest a plausible pathway from life's origin in chemically optimal freshwater hot spring pools to the emergence of microbial communities tolerant to more extreme conditions in dilute lakes and salty conditions in marine environments. A continuity is observed for biogenesis beginning with simple protocell aggregates, through the transitional form of the progenote, to robust microbial mats that leave the fossil imprints of stromatolites so representative in the rock record. A roadmap to future testing of the hypothesis is presented. We compare the oceanic vent with land-based pool scenarios for an origin of life and explore their implications for subsequent evolution to multicellular life such as plants. We conclude by utilizing the hypothesis to posit where life might also have emerged in habitats such as Mars or Saturn's icy moon Enceladus. "To postulate one fortuitously catalyzed reaction, perhaps catalyzed by a metal ion, might be reasonable, but to postulate a suite of them is to appeal to magic." -Leslie Orgel.
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Affiliation(s)
- Bruce Damer
- Department of Biomolecular Engineering, University of California, Santa Cruz, California
| | - David Deamer
- Department of Biomolecular Engineering, University of California, Santa Cruz, California
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45
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Meza U, Delgado-Ramírez M, Romero-Méndez C, Sánchez-Armass S, Rodríguez-Menchaca AA. Functional marriage in plasma membrane: Critical cholesterol level-optimal protein activity. Br J Pharmacol 2020; 177:2456-2465. [PMID: 32060896 DOI: 10.1111/bph.15027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/14/2020] [Accepted: 02/06/2020] [Indexed: 12/13/2022] Open
Abstract
In physiology, homeostasis refers to the condition where a system exhibits an optimum functional level. In contrast, any variation from this optimum is considered as a dysfunctional or pathological state. In this review, we address the proposal that a critical cholesterol level in the plasma membrane is required for the proper functioning of transmembrane proteins. Thus, membrane cholesterol depletion or enrichment produces a loss or gain of direct cholesterol-protein interaction and/or changes in the physical properties of the plasma membrane, which affect the basal or optimum activity of transmembrane proteins. Whether or not this functional switching is a generalized mechanism exhibited for all transmembrane proteins, or if it works just for an exclusive group of them, is an open question and an attractive subject to explore at a basic, pharmacological and clinical level.
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Affiliation(s)
- Ulises Meza
- Departamento de Fisiología y Biofísica, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - Mayra Delgado-Ramírez
- Departamento de Fisiología y Biofísica, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - Catalina Romero-Méndez
- Departamento de Fisiología y Biofísica, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - Sergio Sánchez-Armass
- Departamento de Fisiología y Biofísica, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - Aldo A Rodríguez-Menchaca
- Departamento de Fisiología y Biofísica, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
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Lancet D, Segrè D, Kahana A. Twenty Years of "Lipid World": A Fertile Partnership with David Deamer. Life (Basel) 2019; 9:E77. [PMID: 31547028 PMCID: PMC6958426 DOI: 10.3390/life9040077] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/08/2019] [Accepted: 09/10/2019] [Indexed: 12/17/2022] Open
Abstract
"The Lipid World" was published in 2001, stemming from a highly effective collaboration with David Deamer during a sabbatical year 20 years ago at the Weizmann Institute of Science in Israel. The present review paper highlights the benefits of this scientific interaction and assesses the impact of the lipid world paper on the present understanding of the possible roles of amphiphiles and their assemblies in the origin of life. The lipid world is defined as a putative stage in the progression towards life's origin, during which diverse amphiphiles or other spontaneously aggregating small molecules could have concurrently played multiple key roles, including compartment formation, the appearance of mutually catalytic networks, molecular information processing, and the rise of collective self-reproduction and compositional inheritance. This review brings back into a broader perspective some key points originally made in the lipid world paper, stressing the distinction between the widely accepted role of lipids in forming compartments and their expanded capacities as delineated above. In the light of recent advancements, we discussed the topical relevance of the lipid worldview as an alternative to broadly accepted scenarios, and the need for further experimental and computer-based validation of the feasibility and implications of the individual attributes of this point of view. Finally, we point to possible avenues for exploring transition paths from small molecule-based noncovalent structures to more complex biopolymer-containing proto-cellular systems.
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Affiliation(s)
- Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610010, Israel.
| | - Daniel Segrè
- Bioinformatics Program, Department of Biology, Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.
| | - Amit Kahana
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610010, Israel.
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47
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Lancet D, Zidovetzki R, Markovitch O. Systems protobiology: origin of life in lipid catalytic networks. J R Soc Interface 2019; 15:rsif.2018.0159. [PMID: 30045888 PMCID: PMC6073634 DOI: 10.1098/rsif.2018.0159] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/29/2018] [Indexed: 12/17/2022] Open
Abstract
Life is that which replicates and evolves, but there is no consensus on how life emerged. We advocate a systems protobiology view, whereby the first replicators were assemblies of spontaneously accreting, heterogeneous and mostly non-canonical amphiphiles. This view is substantiated by rigorous chemical kinetics simulations of the graded autocatalysis replication domain (GARD) model, based on the notion that the replication or reproduction of compositional information predated that of sequence information. GARD reveals the emergence of privileged non-equilibrium assemblies (composomes), which portray catalysis-based homeostatic (concentration-preserving) growth. Such a process, along with occasional assembly fission, embodies cell-like reproduction. GARD pre-RNA evolution is evidenced in the selection of different composomes within a sparse fitness landscape, in response to environmental chemical changes. These observations refute claims that GARD assemblies (or other mutually catalytic networks in the metabolism first scenario) cannot evolve. Composomes represent both a genotype and a selectable phenotype, anteceding present-day biology in which the two are mostly separated. Detailed GARD analyses show attractor-like transitions from random assemblies to self-organized composomes, with negative entropy change, thus establishing composomes as dissipative systems—hallmarks of life. We show a preliminary new version of our model, metabolic GARD (M-GARD), in which lipid covalent modifications are orchestrated by non-enzymatic lipid catalysts, themselves compositionally reproduced. M-GARD fills the gap of the lack of true metabolism in basic GARD, and is rewardingly supported by a published experimental instance of a lipid-based mutually catalytic network. Anticipating near-future far-reaching progress of molecular dynamics, M-GARD is slated to quantitatively depict elaborate protocells, with orchestrated reproduction of both lipid bilayer and lumenal content. Finally, a GARD analysis in a whole-planet context offers the potential for estimating the probability of life's emergence. The invigorated GARD scrutiny presented in this review enhances the validity of autocatalytic sets as a bona fide early evolution scenario and provides essential infrastructure for a paradigm shift towards a systems protobiology view of life's origin.
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Affiliation(s)
- Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Raphael Zidovetzki
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA 92521, USA
| | - Omer Markovitch
- Origins Center, Center for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Groningen, the Netherlands.,Blue Marble Space Institute of Science, Seattle, WA, USA
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48
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Deshpande S, Wunnava S, Hueting D, Dekker C. Membrane Tension-Mediated Growth of Liposomes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1902898. [PMID: 31365179 DOI: 10.1002/smll.201902898] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/18/2019] [Indexed: 05/22/2023]
Abstract
Recent years have seen a tremendous interest in the bottom-up reconstitution of minimal biomolecular systems, with the ultimate aim of creating an autonomous synthetic cell. One of the universal features of living systems is cell growth, where the cell membrane expands through the incorporation of newly synthesized lipid molecules. Here, the gradual tension-mediated growth of cell-sized (≈10 µm) giant unilamellar vesicles (GUVs) is demonstrated, to which nanometer-sized (≈30 nm) small unilamellar vesicles (SUVs) are provided, that act as a lipid source. By putting tension on the GUV membranes through a transmembrane osmotic pressure, SUV-GUV fusion events are promoted and substantial growth of the GUV is caused, even up to doubling its volume. Thus, experimental evidence is provided that membrane tension alone is sufficient to bring about membrane fusion and growth is demonstrated for both pure phospholipid liposomes and for hybrid vesicles with a mixture of phospholipids and fatty acids. The results show that growth of liposomes can be realized in a protein-free minimal system, which may find useful applications in achieving autonomous synthetic cells that are capable of undergoing a continuous growth-division cycle.
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Affiliation(s)
- Siddharth Deshpande
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Sreekar Wunnava
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - David Hueting
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
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49
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Affiliation(s)
- Kilian Vogele
- Physik-DepartmentTechnische Universitat Munchen, TU München Garching Germany
| | - Tobias Pirzer
- Physik-DepartmentTechnische Universitat Munchen, TU München Garching Germany
| | - Friedrich C. Simmel
- Physik-DepartmentTechnische Universitat Munchen, TU München Garching Germany
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50
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Possible Roles of Amphiphilic Molecules in the Origin of Biological Homochirality. Symmetry (Basel) 2019. [DOI: 10.3390/sym11080966] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
A review. The question of homochirality is an intriguing problem in the field of chemistry, and is deeply related to the origin of life. Though amphiphiles and their supramolecular assembly have attracted less attention compared to biomacromolecules such as RNA and proteins, the lipid world hypothesis sheds new light on the origin of life. This review describes how amphiphilic molecules are possibly involved in the scenario of homochirality. Some prebiotic conditions relevant to amphiphilic molecules will also be described. It could be said that the chiral properties of amphiphilic molecules have various interesting features such as compositional information, spontaneous formation, the ability to exchange components, fission and fusion, adsorption, and permeation. This review aims to clarify the roles of amphiphiles regarding homochirality, and to determine what kinds of physical properties of amphiphilic molecules could have played a role in the scenario of homochirality.
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