Poster abstracts
Poster number 22 submitted by Ying Hsin Chen
The DEAD-box helicase Dhh1p couples translation elongation to mRNA decay
Ying-Hsin Chen (Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106 ), Sophie Martin (Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106 ), Aditya Radhakrishnan (Program in Molecular Biophysics, Johns Hopkins University School of Medicine), Najwa Al Husaini (Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106 ), Rachel Green (Program in Molecular Biophysics, Johns Hopkins University School of Medicine), Jeff Coller (Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106 )
Abstract:
mRNA decay controls the steady-state levels of mRNAs. In eukaryotic cells, the major pathway of mRNA decay initiated with 3’ deadenylation, followed by 5’ decapping and exonucleolytic digestion in a 5’ to 3’ direction. Our labs recently measured the global decay rate of mRNA and investigated the correlation between mRNA half-lives and codon usage based upon the classical translational efficiency (cTE) scale. We found that mRNA stability correlates well with codon usage. The transcripts with a higher ratio of optimal codons are more stable compared to those composed with non-optimal codons. We also demonstrate that codon optimality impacts ribosome translocation. How is translation elongation coupled to mRNA decay is the subject of our current work.
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 in our lab have shown that endogenous Dhh1p can associate with slowly moving ribosomes. In current study we demonstrate that DHH1 is a sensor of codon optimality- consolidating an mRNA into decay if elongation rate is slow. First, we find that mRNAs whose translation elongation rate is slowed by inclusion of non-optimal codons are specifically degraded in a DHH1-dependent manner. We find that these effects on the mRNA decay are sensitive to the concentration of DHH1 in the cell and the number of slowly moving ribosomes on an mRNA. Second, using a tethering system, we find that DHH1 saturates an mRNA with ribosomes when bound. Third, over-expression of DHH1 leads to the accumulation of ribosomes specifically on mRNAs with low codon optimality in ribosome profiling experiments. Finally, biochemical pull-downs show that DHH1 is preferentially associated with mRNAs with suboptimal codon choice.
These findings are consistent with a model that Dhh1p can bind on transcripts with slower translational elongation rate and act to promote mRNA decay.
References:
1. Vladimir Presnyak, N. A.-H., Ying-Hsin Chen, Sophie Martin, Nathan, Morris, N. K., Sara Olson, David Weinberg, Kristian E. Baker, Brenton R. & Graveley, a. J. C. Codon optimality is a major determinant of mRNA stability. Cell (2015).
2. Sweet, T., Kovalak, C. & Coller, J. The DEAD-box protein Dhh1 promotes decapping by slowing ribosome movement. PLoS Biol (2012).
Keywords: DHH1, codon optimality, mRNA decay