Design principles of autocatalytic cycles constrain enzyme kinetics and force over-expression at flux branch points

A set of chemical reactions that require a metabolite to synthesize more of that metabolite is an autocatalytic cycle. Such metabolic designs must meet specific conditions to support stable fluxes, hence avoiding depletion of intermediate metabolites. Here we show that most of the reactions in central carbon metabolism are part of compact autocatalytic cycles. As such, they are subjected to constraints that may seem irrational: the enzymes of branch reactions out of the cycle must be overexpressed and the affinity of these enzymes to their substrates must be relatively low. We use recent quantitative proteomics and fluxomics measurements to show that the above conditions hold for all functioning cycles in central carbon metabolism of E.coli. This work demonstrates that the topology of a metabolic network can shape kinetic parameters of enzymes and lead to apparently reduced enzyme efficiency. Introduction An essential trait of a living system is its ability to reproduce. This fundamental ability makes all living systems autocatalytic by definition. It then follows that any essential component of a living system is autocatalytic, as it is required for reproduction, that leads to duplication of that component. Specifically, the metabolic system of any living organism, composed of the intermediate metabolites and enzymes catalyzing its reactions, is autocatalytic as a whole and must enable both the excess production of each of its metabolites, as well as the production of all the precursor molecules needed in order for the translation-transcription machinery to synthesize new copies of its enzymes. Autocatalytic systems have an inherent potential to be unstable as their operation changes the amount of their components. Even though the whole metabolic system of an organism is part of the autocatalytic process of reproduction, this does not imply that it is composed of smaller autocatalytic components. The metabolic system is composed of two classes of components, enzymes and metabolites. Clearly, the metabolic system by itself is not autocatalytic with respect to enzymes, as it lacks the transcription-translation machinery needed to produce them. Regarding metabolites, it 1 . CC-BY-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/074641 doi: bioRxiv preprint first posted online Sep. 11, 2016;