Hanson, G. | bioRxiv Science

bioRxiv2018

Codon usage and amino acid identity are major determinants of mRNA stability in humans

mRNA degradation is a critical, yet poorly understood, aspect of gene expression. Previous studies demonstrate that codon content acts as a major determinant of mRNA stability in model organisms. In humans, the importance of open reading frame (ORF)-mediated regulation remains unclear. Here, we globally analyzed mRNA stability for both endogenous and human ORFeome collection mRNAs in human cells. Consistent with previous studies, we observed that synonymous codon usage impacts human mRNA decay. Unexpectedly, amino acid identity also acts as a driver of translation-dependent decay, meaning that primary protein sequence dictates overall mRNA levels and, consequently, protein abundance. Both codon usage and amino acid identity affect translational elongation rate to varying degrees in distinct organisms, with the net result being sensed by mRNA degradation machinery. In humans, interplay between ORF- and UTR-mediated control of mRNA stability may be critical to offset this fundamental relationship between protein sequence and mRNA abundance.

molecular biology↗

bioRxiv2018

Translation elongation and mRNA stability are coupled through the ribosomal A-site

Messenger RNA (mRNA) degradation plays a critical role in regulating transcript levels in eukaryotic cells. Previous work by us and others has shown that codon identity exerts a powerful influence on mRNA stability. In Saccharomyces cerevisiae, studies using a handful of reporter mRNAs show that optimal codons increase translation elongation rate, which in turn increase mRNA stability. However, a direct link between elongation rate and mRNA stability has not been established across the entire yeast transcriptome. In addition, there is evidence from work in higher eukaryotes that amino acid identity influences mRNA stability, raising the question as to whether the impact of translation elongation on mRNA decay is at the level of tRNA decoding, amino acid incorporation, or some combination of each. To address these questions, we performed ribosome profiling of wildtype yeast. In good agreement with other studies, our data showed faster codon-specific elongation over optimal codons and faster transcript-level elongation correlating with transcript optimality. At both the codon-level and transcript-level, faster elongation correlated with increased mRNA stability. These findings were reinforced by showing increased translation efficiency and kinetics for a panel of 11 HIS3 reporter mRNAs of increasing codon optimality. While we did observe that elongation measured by ribosome profiling is composed of both amino acid identity and synonymous codon effects, further analyses of these data establish that A-site tRNA decoding rather than other steps of translation elongation is driving mRNA decay in yeast.

molecular biology↗