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Global regulation of mRNA translation and stability in the early Drosophila embryo by the Smaug RNA-binding protein

Linan Chen1, Jason G Dumelie2, Xiao Li1, Matthew HK Cheng2, Zhiyong Yang1, John D Laver1, Najeeb U Siddiqui15, J Timothy Westwood3, Quaid Morris14, Howard D Lipshitz1* and Craig A Smibert12*

Author Affiliations

1 Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, Ontario M5S 1A8, Canada

2 Department of Biochemistry, University of Toronto, 1 King’s College Circle, Toronto, Ontario M5S 1A8, Canada

3 Department of Cell & Systems Biology and Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada

4 Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, 160 College Street, Toronto, Ontario M5S 3E1, Canada

5 Current address: Program in Developmental & Stem Cell Biology, Hospital for Sick Children Research Institute, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada

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Genome Biology 2014, 15:R4  doi:10.1186/gb-2014-15-1-r4

Published: 7 January 2014

Abstract

Background

Smaug is an RNA-binding protein that induces the degradation and represses the translation of mRNAs in the early Drosophila embryo. Smaug has two identified direct target mRNAs that it differentially regulates: nanos and Hsp83. Smaug represses the translation of nanos mRNA but has only a modest effect on its stability, whereas it destabilizes Hsp83 mRNA but has no detectable effect on Hsp83 translation. Smaug is required to destabilize more than one thousand mRNAs in the early embryo, but whether these transcripts represent direct targets of Smaug is unclear and the extent of Smaug-mediated translational repression is unknown.

Results

To gain a panoramic view of Smaug function in the early embryo, we identified mRNAs that are bound to Smaug using RNA co-immunoprecipitation followed by hybridization to DNA microarrays. We also identified mRNAs that are translationally repressed by Smaug using polysome gradients and microarrays. Comparison of the bound mRNAs to those that are translationally repressed by Smaug and those that require Smaug for their degradation suggests that a large fraction of Smaug’s target mRNAs are both translationally repressed and degraded by Smaug. Smaug directly regulates components of the TRiC/CCT chaperonin, the proteasome regulatory particle and lipid droplets, as well as many metabolic enzymes, including several glycolytic enzymes.

Conclusions

Smaug plays a direct and global role in regulating the translation and stability of a large fraction of the mRNAs in the early Drosophila embryo, and has unanticipated functions in control of protein folding and degradation, lipid droplet function and metabolism.