The repeated exposure to rising pH starts costly regulation programs and reduces production performance in Corynebacterium glutamicum

Large-scale bioprocesses often exhibit performance losses compared to laboratory-scale operations because of environmental heterogeneities, such as pH, oxygen, and nutrient gradients. Among these, pH fluctuations represent a critical challenge in maintaining performance. In this study, the aminobenzoate-producing Corynebacterium glutamicum AB01 was cultivated in a two-compartment scale-down reactor (STR-PFR) designed to mimic realistic short-term alkaline pH fluctuations in large-scale bioreactors (ΔpH = +0.3). Cellular responses were investigated at multiple levels, including process performance metrics, intracellular energy charge, and transcriptomic profiling. The results revealed that repeated pH shifts reduced product yield and glucose uptake while increasing non-growth-associated maintenance demands (+38%). Differential gene expression indicated the activation of stress defense and protein quality control mechanisms, reflecting a metabolic trade-off between stress tolerance and biosynthetic efficiency. Transcript analysis revealed a strong induction of stress-related regulators (Crp/Fnr-, MarR-, IclR-, and PadR-family regulators), activation of DNA repair functions (RecR, HNH endonucleases, and DEAD-box helicases), and coordinated remodeling of translation, including the reduced expression of ribosomal proteins and aminoacyl-tRNA synthetases. Importantly, the integration of energetic cost analysis with transcriptomic data enabled the identification of nonessential, high-cost stress-responsive functions as rational targets for strain optimization under industrially relevant dynamic pH conditions. These findings provide mechanistic insights into how C. glutamicum reallocates resources under dynamic pH conditions, contributing to the design of more robust strains for large-scale industrial applications. • The exposure to fluctuating alkaline pH in scale-down systems determines lower process metrics and deteriorates the internal energy status of an aminobenzoate C. glutamicum producer strain. • The cells activate a basal adaptation mechanism to an alkaline environment and an acute response triggered by dynamic pH shifts. • The overall response to the pH shift increases the non-growth-associated maintenance up to about +38%. • Many genes or clusters, such as musEFGK2I , were defined as putative optimal targets for gene deletion to reduce the cellular maintenance and thus increase the availability of energy for aminobenzoate biosynthesis.