De novo emergence of metabolically active protocells

TL;DR

The study demonstrates a minimal abiotic system in which four simple feedstocks spontaneously assemble into molybdenum-rich, hollow protocell-like compartments that grow and sustain non-equilibrium chemistry. The compartments synthesize diverse organic products, tracked by 13C labeling, LC-MS, and NMR, and can generate growth-competent seed particles, suggesting rudimentary inheritance-like propagation. The chemical dynamics persist under dark conditions and natural day-night cycles, and display remarkable parallels to oceanic molybdenum-rich blue vacuoles, indicating a plausible route to de novo protocell formation under environmental scaffolding. Together, these results propose dissipation-driven chemical complexification coupled to boundary formation as a plausible, testable mechanism for the abiotic emergence of life-like organization.

Abstract

A continuous route from a disordered soup of simple chemical feedstocks to a functional protocell -- a compartment that metabolizes, grows, and propagates -- remains elusive. Here, we show that a homogeneous aqueous chemical mixture containing phosphorus, iron, molybdenum salts and formaldehyde spontaneously self-organizes into compartments that couple robust non-equilibrium chemical dynamics to their own growth. These structures mature to a sustained, dissipative steady state and support an organic synthetic engine, producing diverse molecular species including many core biomolecular classes. Internal spherules that are themselves growth-competent are produced within the protocells, establishing a rudimentary mode of self-perpetuation. The chemical dynamics we observe in controlled laboratory conditions also occur in reaction mixtures exposed to natural day-night cycles. Strikingly, the morphology and chemical composition of the protocells in our experiments closely resemble molybdenum-rich microspheres recently discovered in current oceanic environments. Our work establishes a robust, testable route to de novo protocell formation. The emergence of life-like spatiotemporal organization and chemical dynamics from minimal initial conditions is more facile than previously thought and could be a recurring natural phenomenon.

Figures (12)

• Figure 1: Self-organization of molybdenum-rich microspheres requires four simple chemical precursors and results from selective elemental sequestration.a. Formation of microspheres is contingent on the presence of all four primary feedstocks: (NH4)2MoO4, FeSO4, HCHO, (NH4)2HPO4, suitably acidified (pH $\sim$ 2; details in the Supplementary Information). Sphere formation is only observed in the complete mixture in a region marked by the blue box. b. Optical micrograph of uniform microspheres. Inset: True color image highlighting the characteristic blue of the spheres. Scale bars, 2 $\mu$m. c. Energy-dispersive X-ray (EDX) spectroscopy showing the elemental composition of the spheres. Inset: Scanning electron microscopy (SEM) image showing the spherical particles on which the spectroscopy was performed. Scale bar, 2 $\mu$m. d, e. The spheres form via a selective elemental incorporation quantified by an enrichment factor (defined as the $\log_2$ fold change in elemental weight fractions; mean $\pm$ SEM, n = 5 replicates). This reveals an enrichment of molybdenum (Mo), nitrogen (N) and iron (Fe) alongside a relative depletion of carbon (C), oxygen (O) and phosphorus (P).
• Figure 2: The microspheres are soft, sticky compartments with heterogeneous interiors.a. SEM reveals an outer shell, indicating that the microspheres are characterized by a boundary wall and a lumen. Scale bar: $2~\mu m$. b. TEM shows contrast due to electron density differences, pointing to internal heterogeneity and sphere-like inclusions. Scale bar: $2~\mu m$. c. True color images of representative microsphere pairs exhibiting a stable contact indicating deformability and integrity of the boundary against fusion. Scale bar: $2~\mu m$. d. AFM measurements confirm mechanical softness and stickiness of the microspheres. The dashed line shows a guide to the eye, representing the stiffness of the AFM cantilever ($\sim$ 0.23 N/m).
• Figure 3: The compartments grow and mature, and have a capacity for self-perpetuation.a. Time-lapse brightfield microscopy snapshots showing the growth of a representative compartment. Scale bar, 2 $\mu m$. b. The mean radius (blue line) of the compartment population increases over time (individual compartment traces are shown in light grey). Inset: The polydispersity index (PDI) of the population decreases with time. c. The total mass of the compartment population increases over time, confirming material transfer from the solution. d. Time-resolved EDX spectra showing the dynamic elemental composition of the compartments. e. The absolute mass of all constituent elements increases throughout the growth process. f. Fold change in elemental weight fractions reveals a dynamic compositional evolution; the composition stabilizes after $\sim$4 hours. g. Transmission electron microscopy (TEM) images of compartments, 48 hours post formation, showing internal spherical structures. Scale bar, 2 $\mu m$. h. Time-lapse microscopy showing the growth of seed particles released from the lumen of mature compartments, 12 hours after formation, (indicated by red arrows) when exposed to the feedstock solution. Scale bar, 5 $\mu m$. i. EDX spectrum of the seed microspheres (P1) resulting from growth, demonstrating compositional similarity to the mature compartments (P0).
• Figure 4: The compartments are metabolically active chemical reactors that synthesize diverse biomolecular precursors.a. Isothermal calorimetry shows sustained exothermic activity in the complete reaction mixture (blue) compared to control mixtures lacking formaldehyde (red) over 21 days. b. Laboratory setup of the chemical reaction mixture exposed to a steady solar-spectrum simulating light source (AM1.5G; 1 Sun-equivalent irradiance). The reaction mixtures were infused with 13C-labeled formaldehyde. c. Quantitative analysis of 1-D 13C Nuclear Magnetic Resonance (NMR) spectra for the complete reaction mixture using 99% 13C-labeled formaldehyde shows the time-dependent emergence and increasing intensity of new molecular peaks. d. Liquid Chromatography (LC) analysis of the complete reaction mixture shows the appearance of numerous new peaks from day 2 to day 21. e. Mass Spectrometry (MS) plots of m/z versus intensity for the complete reaction mixture reveal the progressive appearance of many new peaks with increasing mass values from day 2 to day 21. f. Mass Spectrometry (MS) analysis of the complete reaction mixture shows the time-dependent emergence of new molecular species, along with an increase in their molecular abundance from day 2 to day 21. g. Comparison of the molecular-weight distributions in the compartment-enriched phase and the surrounding supernatant phase, showing that the compartments are enriched in higher-molecular-weight products. Experiments for this analysis were carried out by spiking with 1% 13C-labeled formaldehyde. Inset shows the plots for cumulative distribution function (CDF) for the two phases. Van Krevelen diagrams (H/C versus O/C) along with Multidimensional Stoichiometric Compound Classification (MSCC) krevelen1950graphicalkim2003graphicalrivas2018moving for all detected organic products shown for the protocell phase exposed to h. lab solar simulator and i. natural day-night cycles.
• Figure 5: The synthetic compartments exhibit similar morphology and chemical composition to naturally occurring molybdenum-rich microspheres in the ocean.a. SEM and b. brightfield microscopy images of the natural microspheres (referred to as "blue vacuoles") found within the Indo-Pacific sponge Theonella conica showing their hollow, shell-like morphology shoham_2024. Inset in panel b shows protocells obtained from our experiments 42 days after initiation of the reaction in laboratory conditions described in Fig. \ref{['fig:fig4']}. c. The EDX spectra of laboratory-formed compartments (4 hours, light blue; 24 hours, dark blue and 42 days, darker blue) are overlaid with the spectra obtained from oceanic microspheres (black) shoham_2024. d. Image from the chemical phase space of our experiment showing the formation of yellow structures, a color polymorphism also observed in the natural system (as seen in panel b, lower right image) and attributed to the redox chemistry of molybdenum saji2012molybdenum. Images in panels a and b and data in panel c are reproduced with permission.