Poster abstracts
Poster number 24 submitted by Ying Hsin Chen
The DEAD-box helicase Dhh1p monitors translational elongation rate to simulate mRNA decay
Ying-Hsin Chen (Center for RNA Molecular Biology, Case Western Reserve University, Cleveland), Sophie Martin (Center for RNA Molecular Biology, Case Western Reserve University, Cleveland), Vladimir Presnyak (Center for RNA Molecular Biology, Case Western Reserve University, Cleveland), Najwa Al Husaini (Center for RNA Molecular Biology, Case Western Reserve University, Cleveland), Jeff Coller (Center for RNA Molecular Biology, Case Western Reserve University, Cleveland)
Abstract:
mRNA decay is a cellular process that controls the steady-state levels of mRNAs. Every mRNA has a different half-life. In eukaryotic cells, the major pathway of mRNA decay initiates with digestion of the 3’ poly (A) tail (deadenylation), followed by removal of the 5’ cap (decapping) and exonucleolytic digestion in a 5’ to 3’ direction. Previous work in our lab indicated that mRNA decay occurs co-translationally and the insertion of rare codons in a PGK1 reporter, which slowed the elongation rate, resulted in destabilization of the mRNA (Hu et al, 2009). To understand how translational elongation affects the mRNA decay rate, we globally measured mRNA decay rates and investigated the correlation between mRNA half-life and codon usage.
We found that mRNA stability correlates well with codon usage and that transcripts with a higher ratio of optimal codons are more stable than transcripts with a higher ratio of non-optimal codons. As a way to verify that codon usage affects mRNA stability, we designed two synthetic synonymous reporters that encoded the same amino acid sequence but that were comprised of either all optimal or all non-optimal codons. We found that the reporter that consisted of all optimal codons had a longer half-life than the reporter that consisted of all non-optimal codons. Optimal codons are translated faster and more accurately by the ribosome, while non-optimal codons slow down translational elongation rate. Our data strongly suggest that translational elongation rate impacts mRNA stability. We also found that deletion of decay factors including DCP2, PAT1, LSM1, and CCR4 increased the half-lives of both the optimal and non-optimal reporters, while deletion of DHH1 only stabilized the non-optimal reporter. The DEAD-box helicase Dhh1p is a highly abundant enzyme (>50,000 per cell), far exceeding the levels of all other mRNA decay factors in yeast. Previous results from our lab have shown that endogenous Dhh1p can associate with slowly moving ribosomes (Sweet et al, 2012). We therefore propose that Dhh1p senses slowly translocating ribosomes on transcripts and drives these transcripts into decay.
References:
1. Hu, W., Sweet, T. J., Chamnongpol, S., Baker, K. E. & Coller, J. Co-translational mRNA decay in Saccharomyces cerevisiae. Nature 461, 225-229, doi:10.1038/nature08265 (2009).
2. Sweet, T., Kovalak, C. & Coller, J. The DEAD-box protein Dhh1 promotes decapping by slowing ribosome movement. PLoS Biol 10, e1001342, doi:10.1371/journal.pbio.1001342 (2012).
Keywords: DHH1, translational elongation, mRNA decay