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bioRxiv · 10.1101/2025.07.29.667445

Entangled stoichiometric objectives shape microbial catabolism

Remeijer, M.·Bruggeman, F. J.
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Abstract

The search for fundamental relationships between energetic and biosynthetic parameters of catabolism and anabolism is a major goal in microbiology. This is complicated by the fact that ATP synthesis is required for some anabolic precursors, all building blocks, and their polymerization into macromolecules, while the synthesis of other anabolic precursors and catabolic products yields ATP. Yield parameters were classically predicted from approximate phenomenological relations between catabolic and anabolic stoichiometry. Here we compare the catabolisms of a diverse set of microbial species across conditions using genome-scale stoichiometric models. We focus on states of maximal energetic efficiency (maximal yield of biomass of the energy source) and present an unbiased method for calculating stoichiometric relations between catabolism and anabolism. We find that synthesis of charged energy-carriers and anabolic precursors by catabolism is strongly intertwined. Catabolic intermediates and reactions vary greatly, due to variation in the energy and carbon source for growth. We find that the ATP requirement for 1 gram biomass varies between 72.8 and 246.1 moles, precursor sets vary between 4 and 14 in size, and acetyl-CoA is the only common precursor across species. We conclude that the complex interplay between precursor synthesis and energy conservation of heterotrophic catabolism results from an optimal compromise between conflicting objectives. The state of maximal energetic efficiency is reached by minimizing the carbon source lost during energy catabolism due to catabolic-product formation. This choice is influenced by the need for an optimal precursor set that compromises between maximal ATP production during its formation from the carbon source and minimal ATP consumption when it is converted into building blocks. We find that the associated optimal catabolic pathways are diverse across species and conditions.

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Remeijer, M., Bruggeman, F. J.. 2025-07-30. Entangled stoichiometric objectives shape microbial catabolism. https://doi.org/10.1101/2025.07.29.667445

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