The importance of nonsense errors: Estimating the rates and implications of ribosome drop-off during protein synthesis

Abstract

The process of translation is both energetically costly and relatively error-prone compared to transcription and replication. Nonsense errors during translation occur when a ribosome drops off a transcript before reaching a stop codon, resulting in energetic investment in an incomplete and likely non-functional protein. Nonsense errors impose a potentially significant energy burden on the cell, making it critical to quantify their frequency and energetic cost. Here, we present a model of ribosome movement for estimating protein production, elongation, and nonsense error rates from high-throughput ribosome profiling data. Applying this model to an exemplary ribosome profiling dataset in S. cerevisiae, we find that nonsense error rates vary substantially between codons and that these types of errors place an energetic burden on cells comparable to ribosome pausing. Overall, we present multiple lines of evidence that selection against nonsense errors is a prominent force shaping protein-coding sequence evolution and codon usage bias, in particular.