Engineering 3'-UTR hairpin structures to modulate mRNA stability and recombinant protein production in Escherichia coli.

Engineering mRNA stability is a promising yet underexplored approach for improving recombinant protein production in bacterial systems. In this study, we evaluated the effect of synthetic 3'-UTR hairpin structures on mRNA stability and protein yield in Escherichia coli using two SUMO-fusion expression systems. Hairpin elements with defined structural features were introduced downstream of the coding sequence. In all constructs, 3'-UTR hairpins increased mRNA half-life, with stabilization ranging from approximately 2-fold to 3-fold (n = 3 biological replicates). In the SUMO-SARS-CoV-2-derived peptide system, enhanced transcript stability was accompanied by a marked increase in specific cellular fusion-protein content, reaching up to 6.8-fold relative to the control (n = 3). In the SUMO-liraglutide-derived peptide system, mRNA stabilization was also pronounced, and the increase in specific cellular fusion-protein content reached approximately 3-fold (p < 0.001, n = 6). These findings show that 3'-UTR engineering is an effective strategy for modulating mRNA stability in *E. coli*, but the quantitative relationship between transcript persistence and protein accumulation is context-dependent and likely influenced by additional factors, including translation efficiency. Overall, engineering of 3'-terminal RNA structures provides a practical tool for post-transcriptional tuning of recombinant expression systems.