RNA thermometers as temperature-dependent tools for enhanced recombinant protein production in precision fermentation

Abstract

Precision fermentation is a key technology for the future sustainable production of food proteins, bulk ingredients, and high-value recombinant products. However, process efficiency is often limited by the coupling of biomass formation and recombinant protein synthesis, leading to substantial carbon losses into non-recyclable biomass. Particularly for cost-sensitive bulk products such as food proteins, economically viable production requires highly efficient and dynamically controllable bioprocesses. RNA thermometers (RNATs) offer a promising inducer-free strategy for temperature-dependent control of recombinant protein production and dynamic bioprocess regulation, with the potential to improve carbon efficiency and product yields. In this study, a fluorescent reporter protein (EmGFP) under the control of a fourU (4U) RNA thermometer was evaluated in E. coli BL21 across a temperature range of 25–40 °C. Temperature-dependent regulation enabled maximal recombinant protein production at 35 °C, resulting in a 2.6-fold higher specific productivity compared to the derepressed control. The strongest RNAT-mediated regulatory effect was observed at 35.5 °C, highlighting the relevance of precise temperature control for recombinant protein production. Evaluation of altered carbon partitioning revealed a substantially increased carbon allocation toward product formation, while carbon partitioning into biomass and CO2 remained largely unchanged. Furthermore, the product-per-acetate yield increased more than threefold at induction temperature, indicating controllable carbon partitioning and reveals potential for decoupling approaches of biomass formation from recombinant protein production. This study demonstrates the successful implementation of an RNAT-controlled recombinant expression system enabling temperature-dependent regulation of protein production in E. coli. Quantitative analysis revealed controllable carbon partitioning toward recombinant protein synthesis and defined target temperatures for future process induction and switching. In contrast to conventional inducer-based systems, RNAT-mediated regulation enables dynamic control without chemical additives, supporting more resource-efficient bioprocess operation. However, fully exploiting RNAT-based process control will require advanced model-based strategies integrating temperature and feeding regimes, particularly for cost-sensitive precision fermentation processes such as food protein production. Overall, RNATs represent promising molecular control elements for future high-efficiency precision fermentation processes.