2020
DOI: 10.1101/2020.06.18.158139
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The structure of autocatalytic networks, with application to early biochemistry

Abstract: Metabolism across all known living systems combines two key features. First, all of the molecules that are required are either available in the environment or can be built up from available resources via other reactions within the system. Second, the reactions proceed in a fast and synchronised fashion via catalysts that are also produced within the system. Building on early work by Stuart Kauffman, a precise mathematical model for describing such selfsustaining autocatalytic systems (RAF theory) has been deve… Show more

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Cited by 8 publications
(7 citation statements)
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References 34 publications
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“…Strikingly, the medium with just one organic cofactor, NAD, allowed for the production of the bacterial lipid precursor but not the archaeal, all RNA bases (UTP and CTP in only 10 metabolic networks) and only four amino acids—alanine, asparagine, aspartic acid and cysteine. As before [33] we note that NAD is converted to ATP in a reversible reaction used by 94% of all maxRAFs (both in the Rich or NAD-only media)—the Nicotinic Acid Mononucleotide Adenylyltransferase reaction. The implications of this interconversion in autocatalysis were previously explored [33], but here we expand on these with a broader perspective.…”
Section: Resultssupporting
confidence: 53%
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“…Strikingly, the medium with just one organic cofactor, NAD, allowed for the production of the bacterial lipid precursor but not the archaeal, all RNA bases (UTP and CTP in only 10 metabolic networks) and only four amino acids—alanine, asparagine, aspartic acid and cysteine. As before [33] we note that NAD is converted to ATP in a reversible reaction used by 94% of all maxRAFs (both in the Rich or NAD-only media)—the Nicotinic Acid Mononucleotide Adenylyltransferase reaction. The implications of this interconversion in autocatalysis were previously explored [33], but here we expand on these with a broader perspective.…”
Section: Resultssupporting
confidence: 53%
“…Previous work exposed the centrality of NAD in generating complex autocatalytic networks based on prokaryotic metabolism [31,33], and therefore here we proceeded to ask if maxRAFs could be found just with this one organic cofactor in the growth medium of all prokaryotes. In a medium with just NAD and no other organic cofactors, maxRAFs ranged in size from 3 to 232 reactions, with the same smallest RAF possible consisting of spontaneous reactions and with an average maxRAF size of 93 reactions (figure 1 b ; electronic supplementary material, data S5).…”
Section: Resultsmentioning
confidence: 99%
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“…Such a viable tier-1 system is here defined as a seed-dependent autocatalytic system (SDAS). SDASs are similar to pRAFs in the RAF theory [22], because neither can be constructed simply from the food set. However, they are not identical because SDASs require specific stoichiometric relationships among the involved reactions while RAF theory does not consider stoichiometry as its prerequisite.…”
Section: S2(f)-(h))mentioning
confidence: 99%
“…Such a viable tier-1 system is here defined as a seeddependent autocatalytic system (SDAS). SDASs are similar to pRAFs in the RAF theory (22), because neither can be constructed simply from the food set. However, they are not identical because SDASs require specific stoichiometric relationships among the involved reactions while RAF theory does not consider stoichiometry.…”
Section: Seeds and Tier-1 Seed-dependent Autocatalytic Systems (Sdass)mentioning
confidence: 99%