Universal motifs and the diversity of autocatalytic systems

Abstract

Autocatalysis is essential for the origin of life and chemical evolution. However, the lack of a unified framework so far prevents a systematic study of autocatalysis. Here, we derive, from basic principles, general stoichiometric conditions for catalysis and autocatalysis in chemical reaction networks. This allows for a classification of minimal autocatalytic motifs called cores. While all known autocatalytic systems indeed contain minimal motifs, the classification also reveals hitherto unidentified motifs. We further examine conditions for kinetic viability of such networks, which depends on the autocatalytic motifs they contain and is notably increased by internal catalytic cycles. Finally, we show how this framework extends the range of conceivable autocatalytic systems, by applying our stoichiometric and kinetic analysis to autocatalysis emerging from coupled compartments. The unified approach to autocatalysis presented in this work lays a foundation toward the building of a systems-level theory of chemical evolution.

Elementary growth modes/vectors and minimal autocatalytic sets for kinetic/constraint-based models of cellular growth

“…Cellular growth is autocatalytic in the sense that the cell fabricates itself (thereby exchanging substrates/products with the environment). One needs to distinguish this notion of “network autocatalysis” from “autocatalytic subnetworks” (technically: autocatalytic cycles/cores) [3, 4].…”

Reciprocally-coupled Gating: Strange Loops in Bioenergetics, Genetics, and Catalysis

“…An important recent contribution derives a formal structure of autocatalysis from the matrix of stoichiometries, with reactions as columns and species as rows [15]. That matrix representation provided a unified framework for distinguishing their properties into only five distinct networks, which therefore compose a basis set for identifying autocatalytic subnetworks in arbitrarily large autocatalytic networks.…”

“…That matrix representation provided a unified framework for distinguishing their properties into only five distinct networks, which therefore compose a basis set for identifying autocatalytic subnetworks in arbitrarily large autocatalytic networks. That afforded a means to systematize the bewildering array of networks for modeling the emergence of life-like properties built by computational theorists as "Reflexive Autocatalytic Food Sets" (RAFS [23-29]) or GARDs [30], and show that they have the same formal structure [15]. Reflexive in this context simply refers to a closure property in which the product of the final catalyst provides the substrate for the first.…”

“…The first of these is a problem known variously as the error catastrophe [34], the "paradox of specificity" [35], or Eigen's Cliff [36]: high specificity conflicts with survival in error-prone systems, because side reactions (parasites) develop, leading to extinction. Solutions to this paradox invoked to rescue autocatalysis include compartmentation [15] and reaction-diffusion coupling [37], but these are unconvincing. Identifying a more fatal defect in autocatalytic sets, Wills argued that RAFS cannot, by themselves, account for the embedding of symbolic meaning into biomolecules [38][39][40][41][42] and hence that they cannot suffice to account for the emergence of biology.…”

“…The network is closed because the product of catalyst 5 is the substrate for catalyst 2. A and B were adapted from [15]. C. Elements of reciprocally coupled gating, presented as a strange loop [16].…”