Abstract

We developed a simulation tool for investigating the evolution of early metabolism, allowing us to speculate on the formation of metabolic pathways from catalyzed chemical reactions and on the development of their characteristic properties. Our model consists of a protocellular entity with a simple RNA-based genetic system and an evolving metabolism of catalytically active ribozymes that manipulate a rich underlying chemistry. Ensuring an almost open-ended and fairly realistic simulation is crucial for understanding the first steps in metabolic evolution. We show here how our simulation tool can be helpful in arguing for or against hypotheses on the evolution of metabolic pathways. We demonstrate that seemingly mutually exclusive hypotheses may well be compatible when we take into account that different processes dominate different phases in the evolution of a metabolic system. Our results suggest that forward evolution shapes metabolic network in the very early steps of evolution. In later and more complex stages, enzyme recruitment supersedes forward evolution, keeping a core set of pathways from the early phase.

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Author notes

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Contact author.

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Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany. E-mail: alexander@bioinf.uni-leipzig.de (A.U.); studla@bioinf.uni-leipzig.de (P.F.S.)

Image and Signal Processing Group, Department of Computer Science, University of Leipzig, Johannisgasse 26, PF 100920 D-04009 Leipzig, Germany. E-mail: rohrschneider@informatik.uni-leipzig.de (M.R.); scheuermann@informatik.uni-leipzig.de (G.S.)

Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, D-04103 Leipzig, Germany. E-mail: stadler@mis.mpg.de. Fraunhofer Institut für Zelltherapie und Immunologie, Perlickstraße 1, D-04103 Leipzig, Germany. Center for Non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg, Denmark. The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501.

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Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria. E-mail: studla@tbi.univie.ac.at (P.F.S.); xtof@univie.ac.at (C.F.)