An Engineered Halotolerant Chimeric T7 RNA Polymerase for High-Yield, Low-Immunogenicity Synthesis of RNA via Simple Batch Transcription

Abstract

The rapid advancement of mRNA therapeutics has imposed stringent requirements on both the quality and scalability of in vitro transcription (IVT) products. However, the accumulation of double-stranded RNA (dsRNA) byproducts and 3-terminal heterogeneity during T7 RNA polymerase (T7 RNAP)-mediated transcription can robustly trigger deleterious innate immune responses and compromise translation efficiency. Existing enzyme engineering strategies frequently struggle to reconcile the trade-offs between salt tolerance, volumetric productivity, and product purity. Here, we report a novel engineering strategy for halotolerant T7 RNAP by fusing optimized mutant polymerases with diverse DNA-binding domains (e.g., Sso7d, MC1). This approach orchestrated the development of a series of chimeric T7 RNAP mutants designed to bolster catalytic activity and template selectivity under high-salt conditions while concurrently suppressing RNA-dependent RNA polymerase (RdRP) activity. Our lead chimeric mutants exhibited exceptional salt tolerance and processivity in the presence of up to 270 mM NaCl. Notably, these mutants significantly diminished dsRNA formation to less than 0.001%, while markedly improving transcript integrity and 3 homogeneity, thereby facilitating superior translation efficiency for both linear mRNA and circular RNA (circRNA). Crucially, this heightened salt tolerance does not necessitate a trade-off in RNA yield, affording broader flexibility for downstream process optimization. In an enzymatic circRNA synthesis system, these mutants enabled a non-fed-batch configuration with high initial rNTP concentrations (15 mM each), resulting in a 50% increase in yield and achieving an unprecedented titer of 15 mg/mL. This research provides a robust enzymological solution that harmonizes quality and productivity for the industrial-scale manufacturing of high-concentration, low-immunogenicity RNA.