Tao, Y. F. | Search bioRxiv

bioRxiv2026

5' UTR length regulates alternative N-terminal protein isoform production in health and disease

The 5' untranslated region (5' UTR) of an mRNA is classically viewed as a regulatory region that controls the amount of protein production, but not the resulting protein sequence. Here, we demonstrate that 5' UTR length plays a direct role in alternative N-terminal protein isoform production by controlling start codon selection. We find that very short 5' UTRs enhance leaky ribosome scanning, thereby promoting the production of truncated alternative N-terminal protein isoforms. We also show that endogenous changes in 5' UTR length due to alternative transcription initiation can tune the relative abundance of alternative N-terminal isoforms from the same gene. In addition, we identify mutations in rare genetic diseases that alter 5' UTR length, including a deletion in the VHL 5' UTR in von Hippel-Lindau disease that shifts translation toward the shorter VHLp19 isoform. Together, our results implicate 5' UTR length as a determinant of alternative N-terminal isoform production and reveal an underappreciated mechanism by which noncoding changes can reshape the proteome. HighlightsO_LI5' UTR length affects the landscape of endogenous alternative N-terminal protein isoforms C_LIO_LIGeneration of an alternative truncated AKR7A2 isoform is mediated by short 5' UTR length C_LIO_LIAlternative transcription initiation modulates 5' UTR length to tune N-terminal isoform ratios C_LIO_LIPathogenic VHL 5' UTR variants perturb N-terminal isoform ratios by altering 5' UTR length C_LI

molecular biology↗

bioRxiv2025

Alternative start codon selection shapes mitochondrial function during evolution, homeostasis, and disease

Mitochondrial endosymbiosis was a pivotal event in eukaryotic evolution, requiring core proteins to adapt to function both within the mitochondria and in the host cell. Here, we systematically profile the localization of protein isoforms generated by alternate start codon selection during translation. We identify hundreds of pairs of differentially-localized protein isoforms, many of which affect mitochondrial targeting and are essential for mitochondrial function. The emergence of dual-localized mitochondrial protein isoforms coincides with mitochondrial acquisition during early eukaryotic evolution. We further reveal that eukaryotes use diverse mechanisms--such as leaky ribosome scanning, alternative transcription, and paralog duplication--to maintain the production of dual-localized isoforms. Finally, we identify multiple isoforms that are specifically dysregulated by rare disease patient mutations and demonstrate how these mutations can help explain unique clinical presentations. Together, our findings illuminate the evolutionary and pathological relevance of alternative translation initiation, offering new insights into the molecular underpinnings of mitochondrial biology.

cell biology↗