Maturation of selected human mitochondrial tRNAs requires deadenylation
- University of Cambridge, United Kingdom
Abstract
Human mitochondria contain a genome (mtDNA) that encodes essential subunits of the oxidative phosphorylation system. Expression of mtDNA entails multi-step maturation of precursor RNA. In other systems, the RNA life cycle involves surveillance mechanisms, however, the details of RNA quality control have not been extensively characterised in human mitochondria. Using a mitochondrial ribosome profiling and mitochondrial poly(A)-tail RNA sequencing (MPAT-Seq) assay we identify the poly(A)-specific exoribonuclease PDE12 as a major factor for the quality control of mitochondrial non-coding RNAs. The lack of PDE12 results in a spurious polyadenylation of the 3' ends of the mitochondrial (mt-) rRNA and mt-tRNA. While the aberrant adenylation of 16S mt-rRNA did not affect the integrity of the mitoribosome, spurious poly(A) additions to mt-tRNA led to reduced levels of aminoacylated pool of certain mt-tRNAs and mitoribosome stalling at the corresponding codons. Therefore, our data uncover a new, deadenylation-dependent mtRNA maturation pathway in human mitochondria.
Data availability
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Analysis of mitochondrial gene expression with Ribosome ProfilingPublicly available at ArrayExpress (accession no. E-MTAB-5519).
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Application of next generation sequencing approaches to assess effects of PDE12 knockout on the mitochondrial transcriptomePublicly available at the NCBI Gene Expression Omnibus (accession no: GSE95351).
Article and author information
Author details
Funding
Medical Research Council (MC_U105697135)
- Sarah F Pearce
- Joanna Rorbach
- Lindsey Van Haute
- Aaron R D'Souza
- Pedro Rebelo-Guiomar
- Christopher A Powell
- Michal Minczuk
Wellcome (106207)
- Ian Brierley
- Andrew E Firth
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Timothy W Nilsen, Case Western Reserve University, United States
Version history
- Received: April 7, 2017
- Accepted: July 21, 2017
- Accepted Manuscript published: July 26, 2017 (version 1)
- Version of Record published: August 4, 2017 (version 2)
Copyright
© 2017, Pearce et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Maturation of selected human mitochondrial tRNAs requires deadenylation
eLife 6:e27596.
https://doi.org/10.7554/eLife.27596
Further reading
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Recent findings indicate that the translation elongation rate influences mRNA stability. One of the factors that has been implicated in this link between mRNA decay and translation speed is the yeast DEAD-box helicase Dhh1p. Here, we demonstrated that the human ortholog of Dhh1p, DDX6, triggers the deadenylation-dependent decay of inefficiently translated mRNAs in human cells. DDX6 interacts with the ribosome through the Phe-Asp-Phe (FDF) motif in its RecA2 domain. Furthermore, RecA2-mediated interactions and ATPase activity are both required for DDX6 to destabilize inefficiently translated mRNAs. Using ribosome profiling and RNA sequencing, we identified two classes of endogenous mRNAs that are regulated in a DDX6-dependent manner. The identified targets are either translationally regulated or regulated at the steady-state-level and either exhibit signatures of poor overall translation or of locally reduced ribosome translocation rates. Transferring the identified sequence stretches into a reporter mRNA caused translation- and DDX6-dependent degradation of the reporter mRNA. In summary, these results identify DDX6 as a crucial regulator of mRNA translation and decay triggered by slow ribosome movement and provide insights into the mechanism by which DDX6 destabilizes inefficiently translated mRNAs.
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