TY - JOUR
T1 - Translation elongation and mRNA stability are coupled through the ribosomal A-site
AU - Hanson, Gavin
AU - Alhusaini, Najwa
AU - Morris, Nathan
AU - Sweet, Thomas
AU - Coller, Jeff
N1 - Funding Information:
We thank all members of the Coller laboratory and the laboratory of Dr. Kristian Baker for helpful comments and discussion. We also thank DaJuan Whiteside for technical assistance. This work was supported by National Institutes of Health grant GM080464 to J.C., National Institutes of Health T32 grant GM007250 for G. H., and National Institutes of Health grants R01GM118018 and R01GM125086.
Publisher Copyright:
© 2018 Hanson et al.
PY - 2018/10
Y1 - 2018/10
N2 - 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 increases mRNA stability. However, a direct relationship 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 wild-type 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 Asite tRNA decoding rather than other steps of translation elongation is driving mRNA decay in yeast.
AB - 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 increases mRNA stability. However, a direct relationship 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 wild-type 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 Asite tRNA decoding rather than other steps of translation elongation is driving mRNA decay in yeast.
KW - Codon optimality
KW - Decoding
KW - MRNA decay
KW - Translation elongation
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U2 - 10.1261/rna.066787.118
DO - 10.1261/rna.066787.118
M3 - Article
C2 - 29997263
AN - SCOPUS:85053762860
SN - 1355-8382
VL - 24
SP - 1377
EP - 1389
JO - RNA
JF - RNA
IS - 10
ER -