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Autocatalytic sets in E. coli metabolism

BACKGROUND: A central unsolved problem in early evolution concerns self-organization towards higher complexity in chemical reaction networks. In theory, autocatalytic sets have useful properties to help model such transitions. Autocatalytic sets are chemical reaction systems in which molecules belon...

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Autores principales: Sousa, Filipa L, Hordijk, Wim, Steel, Mike, Martin, William F
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer International Publishing 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4429071/
https://www.ncbi.nlm.nih.gov/pubmed/25995773
http://dx.doi.org/10.1186/s13322-015-0009-7
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author Sousa, Filipa L
Hordijk, Wim
Steel, Mike
Martin, William F
author_facet Sousa, Filipa L
Hordijk, Wim
Steel, Mike
Martin, William F
author_sort Sousa, Filipa L
collection PubMed
description BACKGROUND: A central unsolved problem in early evolution concerns self-organization towards higher complexity in chemical reaction networks. In theory, autocatalytic sets have useful properties to help model such transitions. Autocatalytic sets are chemical reaction systems in which molecules belonging to the set catalyze the synthesis of other members of the set. Given an external supply of starting molecules – the food set – and the conditions that (i) all reactions are catalyzed by at least one molecule, and (ii) each molecule can be constructed from the food set by a sequence of reactions, the system becomes a reflexively autocatalytic food-generated network (RAF set). Autocatalytic networks and RAFs have been studied extensively as mathematical models for understanding the properties and parameters that influence self-organizational tendencies. However, despite their appeal, the relevance of RAFs for real biochemical networks that exist in nature has, so far, remained virtually unexplored. RESULTS: Here we investigate the best-studied metabolic network, that of Escherichia coli, for the existence of RAFs. We find that the largest RAF encompasses almost the entire E. coli cytosolic reaction network. We systematically study its structure by considering the impact of removing catalysts or reactions. We show that, without biological knowledge, finding the minimum food set that maintains a given RAF is NP-complete. We apply a randomized algorithm to find (approximately) smallest subsets of the food set that suffice to sustain the original RAF. CONCLUSIONS: The existence of RAF sets within a microbial metabolic network indicates that RAFs capture properties germane to biological organization at the level of single cells. Moreover, the interdependency between the different metabolic modules, especially concerning cofactor biosynthesis, points to the important role of spontaneous (non-enzymatic) reactions in the context of early evolution. [Figure: see text] ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13322-015-0009-7) contains supplementary material, which is available to authorized users.
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spelling pubmed-44290712015-05-18 Autocatalytic sets in E. coli metabolism Sousa, Filipa L Hordijk, Wim Steel, Mike Martin, William F J Syst Chem Research Article BACKGROUND: A central unsolved problem in early evolution concerns self-organization towards higher complexity in chemical reaction networks. In theory, autocatalytic sets have useful properties to help model such transitions. Autocatalytic sets are chemical reaction systems in which molecules belonging to the set catalyze the synthesis of other members of the set. Given an external supply of starting molecules – the food set – and the conditions that (i) all reactions are catalyzed by at least one molecule, and (ii) each molecule can be constructed from the food set by a sequence of reactions, the system becomes a reflexively autocatalytic food-generated network (RAF set). Autocatalytic networks and RAFs have been studied extensively as mathematical models for understanding the properties and parameters that influence self-organizational tendencies. However, despite their appeal, the relevance of RAFs for real biochemical networks that exist in nature has, so far, remained virtually unexplored. RESULTS: Here we investigate the best-studied metabolic network, that of Escherichia coli, for the existence of RAFs. We find that the largest RAF encompasses almost the entire E. coli cytosolic reaction network. We systematically study its structure by considering the impact of removing catalysts or reactions. We show that, without biological knowledge, finding the minimum food set that maintains a given RAF is NP-complete. We apply a randomized algorithm to find (approximately) smallest subsets of the food set that suffice to sustain the original RAF. CONCLUSIONS: The existence of RAF sets within a microbial metabolic network indicates that RAFs capture properties germane to biological organization at the level of single cells. Moreover, the interdependency between the different metabolic modules, especially concerning cofactor biosynthesis, points to the important role of spontaneous (non-enzymatic) reactions in the context of early evolution. [Figure: see text] ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13322-015-0009-7) contains supplementary material, which is available to authorized users. Springer International Publishing 2015-04-01 2015 /pmc/articles/PMC4429071/ /pubmed/25995773 http://dx.doi.org/10.1186/s13322-015-0009-7 Text en © Sousa et al.; licensee Springer. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.
spellingShingle Research Article
Sousa, Filipa L
Hordijk, Wim
Steel, Mike
Martin, William F
Autocatalytic sets in E. coli metabolism
title Autocatalytic sets in E. coli metabolism
title_full Autocatalytic sets in E. coli metabolism
title_fullStr Autocatalytic sets in E. coli metabolism
title_full_unstemmed Autocatalytic sets in E. coli metabolism
title_short Autocatalytic sets in E. coli metabolism
title_sort autocatalytic sets in e. coli metabolism
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4429071/
https://www.ncbi.nlm.nih.gov/pubmed/25995773
http://dx.doi.org/10.1186/s13322-015-0009-7
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