Decapping factor Dcp2 controls mRNA abundance and translation to adjust metabolism and filamentation to nutrient availability
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, United States
- Saint Louis University, United States
- State University of New York, United States
- Wayne State University, United States
Abstract
Degradation of most yeast mRNAs involves decapping by Dcp1/Dcp2. DEAD-box protein Dhh1 has been implicated as an activator of decapping, in coupling codon non-optimality to enhanced degradation, and as a translational repressor, but its functions in cells are incompletely understood. RNA-Seq analyses coupled with CAGE sequencing of all capped mRNAs revealed increased abundance of hundreds of mRNAs in dcp2Δ cells that appears to result directly from impaired decapping rather than elevated transcription. Interestingly, only a subset of mRNAs requires Dhh1 for targeting by Dcp2, and also generally requires the other decapping activators Pat1, Edc3 or Scd6; whereas most of the remaining transcripts utilize NMD factors for Dcp2-mediated turnover. Neither inefficient translation initiation nor stalled elongation appears to be a major driver of Dhh1-enhanced mRNA degradation. Surprisingly, ribosome profiling revealed that dcp2Δ confers widespread changes in relative translational efficiencies (TEs) that generally favor well-translated mRNAs. Because ribosome biogenesis is reduced while capped mRNA abundance is increased by dcp2&Delta, we propose that an increased ratio of mRNA to ribosomes increases competition among mRNAs for limiting ribosomes to favor efficiently translated mRNAs in dcp2Δ cells. Interestingly, genes involved in respiration or utilization of alternative carbon or nitrogen sources are up-regulated, and both mitochondrial function and cell filamentation are elevated in dcp2Δ cells, suggesting that decapping sculpts gene expression post-transcriptionally to fine-tune metabolic pathways and morphological transitions according to nutrient availability.
Data availability
Sequencing data have been deposited in GEO under accession codes GSE220578. All other data generated or analysed during this study are included in the manuscript and supporting files; Source Data files have been provided for all figures.
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Ribosome profiling of dhh1∆ yeastNCBI Gene Expression Omnibus, GSE87892.
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Genome-wilde identification of decapping substrates in the yeast Saccharomyces cervisiaeNCBI Gene Expression Omnibus, GSE107841.
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A High Resolution Profile of NMD Substrates in YeastNCBI Gene Expression Omnibus, GSE86428.
Article and author information
Author details
Funding
National Heart, Lung, and Blood Institute (HL117880)
- Miriam L Greenberg
National Heart, Lung, and Blood Institute (HL117880)
- Chisom Onu
National Institute of General Medical Sciences (GM098629)
- Matthew D Vandermeulen
National Institute of General Medical Sciences (GM098629)
- Paul J Cullen
National Science Foundation (1951332)
- Xiao Niu
National Science Foundation (1951332)
- Zhenguo Lin
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
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Decapping factor Dcp2 controls mRNA abundance and translation to adjust metabolism and filamentation to nutrient availability
eLife 12:e85545.
https://doi.org/10.7554/eLife.85545
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Type II nuclear receptors (T2NRs) require heterodimerization with a common partner, the retinoid X receptor (RXR), to bind cognate DNA recognition sites in chromatin. Based on previous biochemical and overexpression studies, binding of T2NRs to chromatin is proposed to be regulated by competition for a limiting pool of the core RXR subunit. However, this mechanism has not yet been tested for endogenous proteins in live cells. Using single-molecule tracking (SMT) and proximity-assisted photoactivation (PAPA), we monitored interactions between endogenously tagged RXR and retinoic acid receptor (RAR) in live cells. Unexpectedly, we find that higher expression of RAR, but not RXR, increases heterodimerization and chromatin binding in U2OS cells. This surprising finding indicates the limiting factor is not RXR but likely its cadre of obligate dimer binding partners. SMT and PAPA thus provide a direct way to probe which components are functionally limiting within a complex TF interaction network providing new insights into mechanisms of gene regulation in vivo with implications for drug development targeting nuclear receptors.
