Evolution of metabolic networks

A computational frame-work

Christoph Flamm, Alexander Ullrich, Heinz Ekker, Martin Mann, Daniel Högerl, Markus Rohrschneider, Sebastian Sauer, Gerik Scheuermann, Konstantin Klemm, Ivo L. Hofacker, Peter F. Stadler

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

Background: The metabolic architectures of extant organisms share many key pathways such as the citric acid cycle, glycolysis, or the biosynthesis of most amino acids. Several competing hypotheses for the evolutionary mechanisms that shape metabolic networks have been discussed in the literature, each of which finds support from comparative analysis of extant genomes. Alternatively, the principles of metabolic evolution can be studied by direct computer simulation. This requires, however, an explicit implementation of all pertinent components: a universe of chemical reactions upon which the metabolism is built, an explicit representation of the enzymes that implement the metabolism, a genetic system that encodes these enzymes, and a fitness function that can be selected for. Results: We describe here a simulation environment that implements all these components in a simplified way so that large-scale evolutionary studies are feasible. We employ an artificial chemistry that views chemical reactions as graph rewriting operations and utilizes a toy-version of quantum chemistry to derive thermodynamic parameters. Minimalist organisms with simple string-encoded genomes produce model ribozymes whose catalytic activity is determined by an ad hoc mapping between their secondary structure and the transition state graphs that they stabilize. Fitness is computed utilizing the ideas of metabolic flux analysis. We present an implementation of the complete system and first simulation results. Conclusions: The simulation system presented here allows coherent investigations into the evolutionary mechanisms of the first steps of metabolic evolution using a self-consistent toy universe.

Original languageEnglish
Article number4
JournalJournal of Systems Chemistry
Volume1
DOIs
Publication statusPublished - 2013
Externally publishedYes

Fingerprint

Play and Playthings
Metabolic Networks and Pathways
Metabolism
Chemical reactions
Enzymes
Genes
Metabolic Flux Analysis
Genome
Quantum chemistry
Catalytic RNA
Citric Acid Cycle
Biosynthesis
Glycolysis
Thermodynamics
Computer Simulation
Amino acids
Catalyst activity
Fluxes
Amino Acids
Computer simulation

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Chemical Engineering(all)

Cite this

Flamm, C., Ullrich, A., Ekker, H., Mann, M., Högerl, D., Rohrschneider, M., ... Stadler, P. F. (2013). Evolution of metabolic networks: A computational frame-work. Journal of Systems Chemistry, 1, [4]. https://doi.org/10.1186/1759-2208-1-4

Evolution of metabolic networks : A computational frame-work. / Flamm, Christoph; Ullrich, Alexander; Ekker, Heinz; Mann, Martin; Högerl, Daniel; Rohrschneider, Markus; Sauer, Sebastian; Scheuermann, Gerik; Klemm, Konstantin; Hofacker, Ivo L.; Stadler, Peter F.

In: Journal of Systems Chemistry, Vol. 1, 4, 2013.

Research output: Contribution to journalArticle

Flamm, C, Ullrich, A, Ekker, H, Mann, M, Högerl, D, Rohrschneider, M, Sauer, S, Scheuermann, G, Klemm, K, Hofacker, IL & Stadler, PF 2013, 'Evolution of metabolic networks: A computational frame-work', Journal of Systems Chemistry, vol. 1, 4. https://doi.org/10.1186/1759-2208-1-4
Flamm C, Ullrich A, Ekker H, Mann M, Högerl D, Rohrschneider M et al. Evolution of metabolic networks: A computational frame-work. Journal of Systems Chemistry. 2013;1. 4. https://doi.org/10.1186/1759-2208-1-4
Flamm, Christoph ; Ullrich, Alexander ; Ekker, Heinz ; Mann, Martin ; Högerl, Daniel ; Rohrschneider, Markus ; Sauer, Sebastian ; Scheuermann, Gerik ; Klemm, Konstantin ; Hofacker, Ivo L. ; Stadler, Peter F. / Evolution of metabolic networks : A computational frame-work. In: Journal of Systems Chemistry. 2013 ; Vol. 1.
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