Mechanistic modeling of bacterial translation initiation across growth conditions
Translation frequency in bacteria depends on how ribosomes, mRNAs, and initiation factors are allocated across growth conditions. Here, we developed a mechanistic ODE-based model of Escherichia coli translation that represents initiation, elongation, termination, and coupled auxiliary processes. Growth-dependent abundances were derived from physiological relationships and reprocessed omics data,…
Bacterial translation frequency is influenced by the allocation of ribosomes, messenger RNAs (mRNAs), and initiation factors in response to growth conditions. Researchers have created a mathematical model, based on ordinary differential equations (ODEs), to simulate Escherichia coli translation, focusing on initiation, elongation, termination, and auxiliary processes.
This model uses data from physiological relationships and reanalyzed omics data to determine the levels of these components under different growth conditions. When compared to experimental data, the model accurately predicts the frequency of translation and the number of active ribosomes in the cell. As the bacteria grow, there is a gradual shift from a situation where the formation of initiation complexes is the limiting factor to one where ribosomes become the limiting factor.
This shift is reflected in a decrease in the number of free ribosomes, while the amount of initiation factors remains largely unchanged and does not decrease. This indicates that the availability of initiation factors allows productive translation to continue even as ribosomes are increasingly utilized. Furthermore, the model shows that the overall level of ribosome loading on mRNAs remains below its maximum potential, while simulations at the level of cellular functions (COG) reveal different patterns of translation frequency in different cellular sectors.
This resource allocation framework can help explain how mRNA-ribosome interactions influence bacterial translation across various growth conditions.
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