Unified representation of Life's basic properties by a 3-species Stochastic Cubic Autocatalytic Reaction-Diffusion system of equations

Muñuzuri, Alberto P.; Pérez–Mercader, Juan

doi:10.1016/j.plrev.2022.03.003

Cited by 21 publications

(9 citation statements)

References 67 publications

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“…It is unclear how an inherently informatic, networklevel property such as code degeneracy would arise on the basis of tracing the individual origins of the ribosome's chemical components and interaction partners in isolation from this wider network (93). Recent discoveries have shown that 'biological' attributes such as selfreproduction, adaptation and evolvability (which together characterize much of biological agency) are intrinsically linked to one another through an elegant coupling of Hopf and Turing instabilities within a small network of reactions with a cubic autocatalytic motif (94). These attributes are observable even in the absence of the intricacies of macromolecular mechanisms or a diversified biochemical metabolic network.…”

Section: Implications For Prebiotic Chemistrymentioning

confidence: 99%

The modular biochemical reaction network structure of cellular translation

Cuevas-Zuviría

Fer

Adam³

et al. 2023

Preprint

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Translation is a foundational attribute of all living cells. At the heart of cellular operation, it is a chemical information decoding process that begins with an input string of nucleotides and ends with the synthesis of a specific output string of peptides. The translation process is interconnected with gene expression, physiological regulation, transcription, and responses to signaling molecules, among other cellular functions. However, the underlying biochemical connections between translation, metabolism and polymer biosynthesis that enable translation to occur have not been comprehensively mapped. Here we present a multilayer graph of biochemical reactions describing the translation, polymer biosynthesis and metabolism networks of an Escherichia coli cell. Contrary to our predictions of a continuous mass distribution, the compounds that compose these three layers are distinctly aggregated into three modes regardless of their layer categorization. Multimodal mass distributions are well-known in ecosystems, but this is the first such distribution reported at the biochemical level. The connectivity distributions of the translation and metabolic networks are each likely to be heavy-tailed, but the polymer biosynthesis network is not. A multimodal mass-connectivity distribution indicates that the translation and metabolism networks are each distinct, adaptive biochemical modules, and that the gaps between the modes reflect evolved responses to the functional use of metabolite, polypeptide and polynucleotide compounds. The chemical reaction network of cellular translation opens new avenues for exploring complex adaptive phenomena such as percolation and phase changes in biochemical contexts.

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Section: Implications For Prebiotic Chemistrymentioning

confidence: 99%

The modular biochemical reaction network structure of cellular translation

Cuevas-Zuviría

Fer

Adam³

et al. 2023

Preprint

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“…Such configurations can be: heritable, because autocatalysis can lead to dynamics resembling reproduction (Muñuzuri and Pé rez-Mercader, 2022) influencing adjacent reactor states; mutable, because bistable chemical systems can switch between attractors in response to perturbations (Peng et al, 2020;Soai et al, 2003); and selectable, because different spatial configurations may have different propensities to persist in terms of likelihoods to occupy previously unoccupied sites or to recover from perturbations. The modeled system provides a tractable basis for assessing the extent to which spatial configurations of attractors can be heritable, mutable, and selectable (HMS) under prebiotically possible conditions.…”

Section: Introductionmentioning

confidence: 99%

Heritable, mutable, and selectable spatial patterns from bistable chemical reaction networks in weakly-coupled reactor arrays

Peng

Plum

Adam

2023

Preprint

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The origins of genetic information processing remain a mystery in prebiotic chemistry research. Genetic systems encode information as digital sequences of nucleotide residues and require multiple interdependent and complex machineries that were likely to have been established late in the prebiotic evolutionary process. Candidate predecessor systems are potentially insightful for examining how genetic systems could have been scaffolded by alternatives that were simpler, yet capable of performing comparable functions. Some researchers have proposed that relative concentrations of simple chemical species (i.e., chemical compositions) could encode heritable information in an analog manner. While conceptually plausible, it is also difficult to explain how most forms of analog inheritance (which can be highly sensitive to interference) could underpin emergent characteristics that are necessary for adaptive evolution afforded by high-fidelity, polymer-based digital inheritance. Here, by simulating bistable reaction systems with two simple autocatalytic cycles in two-dimensional lattices of connected flow reactors, we show that without linear polymers, it is still possible to encode spatial configurations of discrete states of chemical compositions that are heritable and mutable. Different configurations can have differing likelihoods of propagating to new reactors or recovering from perturbations, which means that they can respond to at least some types of selective environments or conditions. Taken together, these spatial configurations are heritable, mutable, and selectable (HMS). They are similar to analog inheritance because they depend on chemical compositions, and they are similar to digital inheritance because they consist of spatially distributed, discretized units. Although such discrete HMS spatial configurations are far less heritable, more mutable, and less selectable than nucleotide-sequence-based digital inheritance, they represent a possible bridge between analog and digital inheritance in complex chemical systems.

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“…30 A recent study in 2022 by Munũzuri and Peŕez-Mercader demonstrated that a number of these behaviors become apparent in systems with as few as three unique molecular compounds, provided there are both Hopf and Turing instabilities present. 31 It seems likely that examples of primitive "life-like" autocatalytic systems that can be generated from only smallmolecule reactions will become increasingly more common, at least in the laboratory setting, but the question still remains: how probable are abiotic autocatalytic networks, especially in the context of natural environmental settings like those of early Earth? The unique capabilities of autocatalysis make a compelling case for assessing their generic pervasiveness, but searching for autocatalytic systems is an inherently difficult problem, 32 even though some researchers have attempted to use algorithms based on simple chemical principles to identify and design abiotic autocatalytic cycles.…”

Section: Introductionmentioning

confidence: 99%

“…The Whitesides group in 2016 engineered an autocatalytic reaction network capable of bistability and oscillatory behavior based on simple α-aminothioesters, disulfides, electron-deficient olefins, and the auto-amplification of cysteamine . A recent study in 2022 by Muñuzuri and Pérez-Mercader demonstrated that a number of these behaviors become apparent in systems with as few as three unique molecular compounds, provided there are both Hopf and Turing instabilities present …”

Section: Introductionmentioning

confidence: 99%

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Assessment of Stoichiometric Autocatalysis across Element Groups

Peng,

Adam,

Fahrenbach

et al. 2023

J. Am. Chem. Soc.

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Autocatalysis has been proposed to play critical roles during abiogenesis. These proposals are at odds with a limited number of known examples of abiotic (and, in particular, inorganic) autocatalytic systems that might reasonably function in a prebiotic environment. In this study, we broadly assess the occurrence of stoichiometries that can support autocatalytic chemical systems through comproportionation. If the product of a comproportionation reaction can be coupled with an auxiliary oxidation or reduction pathway that furnishes a reactant, then a Comproportionation-based Autocatalytic Cycle (CompAC) can exist. Using this strategy, we surveyed the literature published in the past two centuries for reactions that can be organized into CompACs that consume some chemical species as food to synthesize more autocatalysts. 226 CompACs and 44 Broad-sense CompACs were documented, and we found that each of the 18 groups, lanthanoid series, and actinoid series in the periodic table has at least two CompACs. Our findings demonstrate that stoichiometric relationships underpinning abiotic autocatalysis could broadly exist across a range of geochemical and cosmochemical conditions, some of which are substantially different from the modern Earth. Meanwhile, the observation of some autocatalytic systems requires effective spatial or temporal separation between the food chemicals while allowing comproportionation and auxiliary reactions to proceed, which may explain why naturally occurring autocatalytic systems are not frequently observed. The collated CompACs and the conditions in which they might plausibly support complex, “life-like” chemical dynamics can directly aid an expansive assessment of life’s origins and provide a compendium of alternative hypotheses concerning false-positive biosignatures.

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Unified representation of Life's basic properties by a 3-species Stochastic Cubic Autocatalytic Reaction-Diffusion system of equations

Cited by 21 publications

References 67 publications

The modular biochemical reaction network structure of cellular translation

The modular biochemical reaction network structure of cellular translation

Heritable, mutable, and selectable spatial patterns from bistable chemical reaction networks in weakly-coupled reactor arrays

Assessment of Stoichiometric Autocatalysis across Element Groups

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