Dual Role of 3′ UTR Length in Modulating Translation Termination Efficiency

The 3′ untranslated region of mRNAs are involved in post-transcriptional control, influencing mRNA stability, localization, and translation efficiency through its interaction with various proteins and RNAs. While eukaryotic 3′ UTRs are typically several hundred nucleotides long, certain protozoan species possess remarkably short 3′ UTRs and have evolved alternative genetic codes where canonical stop codons are reassigned to sense codons. This suggests a potential link between 3′ UTR architecture and the efficiency of translation termination. In this study, we investigate how the length and secondary structure of the 3′ UTR modulate translation termination efficiency across different species. We demonstrate that shortening of structured 3′ UTRs confer a translational advantage for mRNAs bearing UAA stop codons. Using purified pre-termination complexes, we show that 3′ UTR secondary structures enhance the termination rate by facilitating the spatial proximity of PABP (bound to the poly(A) tail) to eRF3a on the ribosome. Furthermore, we found that the termination rate at UGA stop codons is highly sensitive to 3′ UTR length when assayed with both human and ciliate release factors. Our investigation of stop codon reassignment underscores the primary role of release factor recognition efficiency in this process. Collectively, our findings reveal a dual regulatory mechanism: while long, structured 3′ UTRs can sterically hinder stop codon recognition, they simultaneously promote eRF3a–PABP interactions that facilitate the recruitment of release factors to the ribosome. This work establishes 3′ UTR length as a key cis-regulatory factor fine-tuning the fundamental process of translation termination.