‘Whole Organism’, Systems Biology, and Top-Down Criteria for Evaluating Scenarios for the Origin of Life

While most advances in the study of the origin of life on Earth (OoLoE) are piecemeal, tested against the laws of chemistry and physics, ultimately the goal is to develop an overall scenario for life’s origin(s). However, the dimensionality of non-equilibrium chemical systems, from the range of possible boundary conditions and chemical interactions, renders the application of chemical and physical laws difficult. Here we outline a set of simple criteria for evaluating OoLoE scenarios. These include the need for containment, steady energy and material flows, and structured spatial heterogeneity from the outset. The Principle of Continuity, the fact that all life today was derived from first life, suggests favoring scenarios with fewer non-analog (not seen in life today) to analog (seen in life today) transitions in the inferred first biochemical pathways. Top-down data also indicate that a complex metabolism predated ribozymes and enzymes, and that full cellular autonomy and motility occurred post-LUCA. Using these criteria, we find the alkaline hydrothermal vent microchamber complex scenario with a late evolving exploitation of the natural occurring pH (or Na+ gradient) by ATP synthase the most compelling. However, there are as yet so many unknowns, we also advocate for the continued development of as many plausible scenarios as possible.

Autocatalytic and oscillatory reaction networks that form guanidines and products of their cyclization

Autocatalytic and oscillatory networks of organic reactions are important for designing life-inspired materials and for better understanding the emergence of life on Earth; however, the diversity of the chemistries of these reactions is limited. In this work, we present the thiol-assisted formation of guanidines, which has a mechanism analogous to that of native chemical ligation. Using this reaction, we designed autocatalytic and oscillatory reaction networks that form substituted guanidines from thiouronium salts. The thiouronium salt-based oscillator show good stability of oscillations within a broad range of experimental conditions. By using nitrile-containing starting materials, we constructed an oscillator where the concentration of a bicyclic derivative of dihydropyrimidine oscillates. Moreover, the mixed thioester and thiouronium salt-based oscillator show unique responsiveness to chemical cues. The reactions developed in this work expand our toolbox for designing out-of-equilibrium chemical systems and link autocatalytic and oscillatory chemistry to the synthesis of guanidinium derivatives and the products of their transformations including analogs of nucleobases.

Self-sustained Marangoni Flows Driven by Chemical Reactions

Out-of-equilibrium chemical systems, comprising reaction networks and molecular self-assembly pathways, rely on the delivery of reagents. Rather than via external flow, diffusion or convection, we aim at self-sustained reagent delivery. Therefore, we explore how the coupling of Marangoni flow with chemical reactions can generate self-sustained flows, driven by said chemical reactions, and – in turn – sustained by the delivery of reagents for this reaction. We combine a photoacid generator with a pH-responsive surfactant, such that local UV exposure decreases the pH, increases the surface tension and triggers the emergence of a Marangoni flow. We study the impact of reagent concentrations and identify threshold conditions at which flow can emerge. Surprisingly, we unraveled an antagonistic influence of the reagents on key features of the flow such as interfacial velocity and duration, and rationalize these findings via a kinetic model. Our study displays the potential of reaction-driven flow to establish autonomous control in fuel delivery of out-of-equilibrium systems.

Self-sustained Marangoni Flows Driven by Chemical Reactions

Out-of-equilibrium chemical systems, comprising reaction networks and molecular self-assembly pathways, rely on the delivery of reagents. Rather than via external flow, diffusion or convection, we aim at self-sustained reagent delivery. Therefore, we explore how the coupling of Marangoni flow with chemical reactions can generate self-sustained flows, driven by said chemical reactions, and – in turn – sustained by the delivery of reagents for this reaction. We combine a photoacid generator with a pH-responsive surfactant, such that local UV exposure decreases the pH, increases the surface tension and triggers the emergence of a Marangoni flow. We study the impact of reagent concentrations and identify threshold conditions at which flow can emerge. Surprisingly, we unraveled an antagonistic influence of the reagents on key features of the flow such as interfacial velocity and duration, and rationalize these findings via a kinetic model. Our study displays the potential of reaction-driven flow to establish autonomous control in fuel delivery of out-of-equilibrium systems.

Standardized excitable elements for scalable engineering of far-from-equilibrium chemical networks

Engineered far-from-equilibrium synthetic chemical networks that pulse or switch states in response to environmental signals could precisely regulate the kinetics of chemical synthesis or self-assembly pathways. Currently, such networks must be extensively tuned to compensate for the different activities of and unintended reactions between different network chemical elements. Elements with standardized performance would allow rapid construction of networks with designed functions. Here we develop standardized excitable chemical elements, termed genelets, and use them to construct complex in vitro transcriptional networks. We develop a protocol for identifying >15 interchangeable genelet regulatory elements with uniform performance and minimal crosstalk. These elements can be combined to engineer feedforward and feedback modules whose dynamics are predicted by a simple kinetic model. We show modules can be rationally integrated and reorganized into networks that produce tunable temporal pulses and act as multi-state switchable memories. Standardized genelet elements, and the workflow to identify more, should make engineering complex far-from-equilibrium chemical dynamics routine.

Dissipation-driven selection of states in non-equilibrium chemical networks

Life has most likely originated as a consequence of processes taking place in non-equilibrium conditions (e.g. in the proximity of deep-sea thermal vents) selecting states of matter that would have been otherwise unfavorable at equilibrium. Here we present a simple chemical network in which the selection of states is driven by the thermodynamic necessity of dissipating heat as rapidly as possible in the presence of a thermal gradient: states participating to faster reactions contribute the most to the dissipation rate, and are the most populated ones in non-equilibrium steady-state conditions. Building upon these results, we show that, as the complexity of the chemical network increases, the velocity of the reaction path leading to a given state determines its selection, giving rise to non-trivial localization phenomena in state space. A byproduct of our studies is that, in the presence of a temperature gradient, thermophoresis-like behavior inevitably appears depending on the transport properties of each individual state, thus hinting at a possible microscopic explanation of this intriguing yet still not fully understood phenomenon.

Redox potential linked to water loss from proteins in evolution and development

As gene sequences change through evolution, and as the abundances of different proteins change through development, the distinct elemental composition of the proteins at different times can be represented as an overall chemical reaction. Compositional and thermodynamic analysis of these reactions leads to novel insight on biochemical changes and enables predictions of intensive variables including redox potential. The stoichiometric hydration state refers to the number of H2O in theoretical reactions to form the proteins from a set of thermodynamic components. By analyzing published phylostratigraphy and transcriptomic and proteomic datasets, I found that of proteins decreases on evolutionary timescales (from single-celled organisms to metazoans) and on developmental timescales in Bacillus subtilis biofilms. Moreover, values of computed for a developmental proteome of fruit flies are aligned with organismal water content from larva to adult stages. I present a thermodyamic model for the equilibrium chemical activity of target proteins in a genomic background. Conditions that maximize the activity of the target proteins are found by optimizing the values of water activity and oxygen fugacity, which are then combined to calculate effective values of redox potential (Eh). The effective Eh values during evolution range between values reported for mitochondria, the cytosol, and extracellular compartments. These results suggest a central role for water, and water activity, in the biochemistry of evolution and development.

On the use of catalysis to bias reaction pathways in out-of-equilibrium systems

We show, via simulations, how catalytic control over individual paths in a fuel-driven non-equilibrium chemical reaction network in batch or flow gives rise to responses in maximum conversion, lifetime and steady states.