Amino Acid Misincorporation Propensities Revealed through Systematic Amino Acid Starvation

Elevated amino acid misincorporation levels during protein translation can cause disease and adversely impact biopharmaceutical product quality. Our previous work, along with that of others, identified numerous low-level unintended sequence variants. However, because of the limited analytical detection efficiency, we believed that these observations represented only a fraction of biologically relevant outcomes. Because amino acid misincorporation can be exacerbated by amino acid starvation, we believed that a more comprehensive set of sequence variants could be derived through systematic starvation. Our goals for this study were therefore (1) to systematically characterize misincorporation patterns under amino acid starvation and (2) to elucidate the major misincorporation mechanisms and propensities for cultured mammalian cells. To the best of our knowledge, this is the first study to use controlled systematic starvation to maximize the observation of unique sequence variants to provide a more holistic perspective of amino acid misincorporation. Our findings bridge the two prevailing lines of research and propose that both base mismatches during codon recognition (especially G/U and wobble mismatches) and misacylation are common and major amino acid misincorporation mechanisms. This proposal is also supported by the observation of mechanistic additivity between the base mismatch and misacylation mechanisms. In addition, we observed significant overlap in misincorporation mechanisms and propensities among cell lines and organisms. Lastly, we explored factors that can lead to codon-associated misincorporation behavior.