A single-nucleotide change in the Kozak sequence enhances protein expression

Abstract

In vitro-transcribed messenger RNA (IVT mRNA) has emerged as a versatile protein expression platform with broad clinical potential. Current optimization strategies for IVT mRNA focus on untranslated regions (UTRs), mRNA stability, and codon usage, often guided by massively parallel screening and machine learning approaches. In contrast, the Kozak sequence, a key determinant of translation initiation, is often inconsistently incorporated into synthetic 5' UTR design, and its contribution to translation efficiency remains poorly defined. Here, we systematically varied the Kozak sequence across diverse UTR contexts and performed combinatorial optimization using synthetic, established, and viral UTRs to identify design principles for enhanced translation. We show that a single-nucleotide deviation from the consensus Kozak sequence consistently enhances protein expression across UTR contexts and coding sequences. This effect is conserved across in vitro and in vivo models, highlighting the generalizability of the optimized Kozak sequence. These findings redefine the role of the Kozak sequence in synthetic mRNA design and demonstrate its substantial contribution to translation efficiency when optimized, enabling improved mRNA-based therapeutics.