Engineering ATP homeostasis to enhance robustness and productivity in microbial cell factories

Adenosine triphosphate (ATP) is the primary energy currency of microbial cells and a system-wide signal coordinating metabolism, gene expression and cellular physiology. Yet, ATP homeostasis is often treated implicitly in strain and process engineering. This review presents an ATP-centered framework for microbial cell factory design, integrating mechanistic interpretation, quantitative measurement, computational modeling and engineering strategies. ATP homeostasis is maintained through a dynamic balance between ATP-generating and ATP-consuming processes. ATP is mainly generated by substrate-level phosphorylation and oxidative phosphorylation, and consumed by biosynthesis, transport, maintenance, stress protection, and protein quality control. Beyond energy supply, the adenylate pool regulates transcription through ATP-dependent initiation and regulatory factors, translation through nucleotide availability and ribosome activity, proteostasis through ATP-dependent chaperones and proteases, and metabolism through allosteric control. We critically assess ATP measurement approaches, including luciferase-based assays, chromatography and mass spectrometry, and genetically encoded biosensors. ATP-explicit modeling frameworks are discussed for quantifying ATP supply and demand and guiding rational engineering. ATP-centered engineering strategies are organized by their effects on ATP supply, consumption and allocation, including optimizing ATP yield and energy-conversion efficiency, minimization of nonproductive expenditure, dynamic control of ATP homeostasis, enhancement of ATP turnover, attenuation of ATP-dependent feedback inhibition, and implementation of synthetic ATP-regeneration modules and orthogonal energy systems. Strategy selection depends on pathway ATP balance, cellular state and industrial process. ATP engineering should therefore optimize, rather than simply maximize or minimize, ATP generation, consumption and allocation. Together, integrating ATP sensing, mechanistic modeling, and ATP-explicit engineering can support energy-aware design of robust, high-performing microbial cell factories.