Elementary vectors and autocatalytic sets for computational models of cellular growth

Abstract

Traditional (genome-scale) metabolic models of cellular growth involve an approximate biomass "reaction", which specifies biomass composition in terms of precursor metabolites (such as amino acids and nucleotides). On the one hand, biomass composition is often not known exactly and may vary drastically between conditions and strains. On the other hand, the predictions of computational models crucially depend on biomass. Also elementary flux modes (EFMs), which generate the flux cone, depend on the biomass reaction. To better understand cellular phenotypes across growth conditions, we introduce and analyze new classes of elementary vectors for comprehensive (next-generation) metabolic models, involving explicit synthesis reactions for all macromolecules. Elementary growth modes (EGMs) are given by stoichiometry and generate the growth cone. Unlike EFMs, they are not support-minimal, in general, but cannot be decomposed "without cancellations". In models with additional (capacity) constraints, elementary growth vectors (EGVs) generate a growth polyhedron and depend also on growth rate. However, EGMs/EGVs do not depend on the biomass composition. In fact, they cover all possible biomass compositions and can be seen as unbiased versions of elementary flux modes/vectors (EFMs/EFVs) used in traditional models. To relate the new concepts to other branches of theory, we consider autocatalytic sets of reactions. Further, we illustrate our results in a small model of a self-fabricating cell, involving glucose and ammonium uptake, amino acid and lipid synthesis, and the expression of all enzymes and the ribosome itself. In particular, we study the variation of biomass composition as a function of growth rate. In agreement with experimental data, low nitrogen uptake correlates with high carbon (lipid) storage. Author summaryNext-generation, genome-scale metabolic models allow to study the reallocation of cellular resources upon changing environmental conditions, by not only modeling flux distributions, but also expression profiles of the catalyzing proteome. In particular, they do no longer assume a fixed biomass composition. Methods to identify optimal solutions in such comprehensive models exist, however, an unbiased understanding of all feasible allocations is missing so far. Here we develop new concepts, called elementary growth modes and vectors, that provide a generalized definition of minimal pathways, thereby extending classical elementary flux modes (used in traditional models with a fixed biomass composition). The new concepts provide an understanding of all possible flux distributions and of all possible biomass compositions. In other words, elementary growth modes and vectors are the unique functional units in any comprehensive model of cellular growth. As an example, we show that lipid accumulation upon nitrogen starvation is a consequence of resource allocation and does not require active regulation. Our work puts current approaches on a theoretical basis and allows to seamlessly transfer existing workflows (e.g. for the design of cell factories) to next-generation metabolic models.