Small-molecule autocatalytic networks are universal metabolic fossils

Xavier, Joana C.; Kauffman, Stuart

doi:10.1098/rsta.2021.0244

Cited by 22 publications

(32 citation statements)

References 73 publications

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“…Such sets of chemicals should play an important role in the analysis of the modular structure of CRS and pose valuable targets for the analysis of CRS corresponding to real biological systems, such as the ones constructed by Sousa et al. ( 2015 ) and Xavier and Kauffman ( 2022 ). Moreover, they bear interesting algebraic structures which lend themselves to future mathematical investigations.…”

Section: Discussionmentioning

confidence: 99%

Semigroup models for biochemical reaction networks

Loutchko

2023

J. Math. Biol.

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The catalytic reaction system (CRS) formalism by Hordijk and Steel is a versatile method to model autocatalytic biochemical reaction networks. It is particularly suited, and has been widely used, to study self-sustainment and self-generation properties. Its distinguishing feature is the explicit assignment of a catalytic function to chemicals that are part of the system. In this work, it is shown that the subsequent and simultaneous catalytic functions give rise to an algebraic structure of a semigroup with the additional compatible operation of idempotent addition and a partial order. The aim of this article is to demonstrate that such semigroup models are a natural setup to describe and analyze self-sustaining CRS. The basic algebraic properties of the models are established and the notion of the function of any set of chemicals on the whole CRS is made precise. This leads to a natural discrete dynamical system on the power set of chemicals, which is obtained by iteratively considering the self-action on a set of chemicals by its own function. The fixed points of this dynamical system are proven to correspond to self-sustaining sets of chemicals, which are functionally closed. Finally, as the main application, a theorem on the maximal self-sustaining set and a structure theorem on the set of functionally closed self-sustaining sets of chemicals are proven.

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Section: Discussionmentioning

confidence: 99%

Semigroup models for biochemical reaction networks

Loutchko

2023

J. Math. Biol.

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“…De novo purine production in extant biochemistry exhibits an autocatalytic dependence in the production of adenosine triphosphate (ATP) and PRPP, due to multiple steps requiring ATP as a phosphorylating agent (Fig. 1B) (8,9). This autocatalytic dependence may have been relaxed in primitive metabolism, where primitive phosphorylating agents could have been either pyrophosphate or acyl-phosphate (e.g., acetyl phosphate) (32)(33)(34).…”

Section: Non-atp Coupled Purine Production Enables Metabolic Expansio...mentioning

confidence: 99%

“…Many lines of evidence suggest that recovering continuity between ancient geochemistry and extant biochemistry might be impossible without the inclusion of a vast number of abiotic chemical reactions unrelated to modern biology. First, a recent analysis of organismal-scale metabolic networks reveals a high prevalence of autocatalytic subnetworks, in which the generation of several key biochemical coenzymes are required for their own synthesis ( 8, 9 ). Although autocatalysis has been proposed to have been a necessary feature for early evolutionary processes ( 8, 10 – 12 ), the widespread occurrence of such network motifs presents a problem for the initial emergence of ancient metabolism.…”

Section: Introductionmentioning

confidence: 99%

Primitive purine biosynthesis connects ancient geochemistry to modern metabolism

Goldford

Smith

Longo

et al. 2022

Preprint

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A major unresolved question in the origin of life is whether there exists a continuous path from geochemical precursors to the majority of molecules in the biosphere, due in part to the autocatalytic nature of metabolic networks in modern-day organisms and high rates of extinction throughout Earth's history. Here we simulated the emergence of ancient metabolic networks to identify a feasible path from simple geochemical precursors (e.g., phosphate, sulfide, ammonia, simple carboxylic acids, and metals) to contemporary biochemistry, using only known biochemical reactions and models of primitive coenzymes. We find that purine synthesis constitutes a bottleneck for metabolic expansion, and that non-autocatalytic phosphoryl coupling agents are sufficient to enable expansion from geochemistry to modern metabolic networks. Our model predicts distinct phases of metabolic evolution, characterized by the sequential emergence of key molecules (carboxylic acids, amino acids, sugars), purines/nucleotide cofactors (ATP, NAD+), flavins, and quinones, respectively. Early phases in the resulting expansion are associated with enzymes that are metal-dependent and structurally symmetric, consistent with models of early biochemical evolution. The production of quinones in the last phase of metabolic expansion permits oxygenic photosynthesis and the production of O2, leading to a >30% increase in biomolecules. These results reveal a feasible trajectory from simple geochemical precursors to the vast majority of core biochemistry.

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“…Still at the molecular scale, Xavier and Kauffman's article Small-molecule autocatalytic networks are universal metabolic fossils [171] focuses on the emergence of early metabolism. They investigate small-molecule reflexively autocatalytic food-generated networks, proving that these structures can be generated from all the hitherto annotated prokaryotic metabolic networks in the KEGG database.…”

Section: Summary Of the Theme Issuementioning

confidence: 99%

From the origin of life to pandemics: Emergent phenomena in complex systems

Artime,

De Domenico

2022

Preprint

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When a large number of similar entities interact among each other and with their environment at a low scale, unexpected outcomes at higher spatio-temporal scales might spontaneously arise. This nontrivial phenomenon, known as emergence, characterizes a broad range of distinct complex systems -from physical to biological and social ones -and is often related to collective behavior. It is ubiquitous, from non-living entities such as oscillators that under specific conditions synchronize, to living ones, such as birds flocking or fish schooling. Despite the ample phenomenological evidence of the existence of systems' emergent properties, central theoretical questions to the study of emergence remain still unanswered, such as the lack of a widely accepted, rigorous definition of the phenomenon or the identification of the essential physical conditions that favour emergence. We offer here a general overview of the phenomenon of emergence and sketch current and future challenges on the topic. Our short review also serves as an introduction to the Theme Issue Emergent phenomena in complex physical and socio-technical systems: from cells to societies, where we provide a synthesis of the contents tackled in the Issue and outline how they relate to these challenges, spanning from current advances in our understanding on the origin of life to the large-scale propagation of infectious diseases.

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Small-molecule autocatalytic networks are universal metabolic fossils

Cited by 22 publications

References 73 publications

Semigroup models for biochemical reaction networks

Semigroup models for biochemical reaction networks

Primitive purine biosynthesis connects ancient geochemistry to modern metabolism

From the origin of life to pandemics: Emergent phenomena in complex systems

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