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

Linan Chen,Howard D Lipshitz,J Timothy Westwood,Craig A Smibert,John D Laver,Xiao Li,Quaid Morris,Zhiyong Yang,Najeeb U Siddiqui,Matthew Hk Cheng,Jason G Dumelie

doi:10.1186/gb-2014-15-1-r4

Abstract

BackgroundSmaug 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.ResultsTo 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.ConclusionsSmaug 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.

Highlights

Smaug is an RNA-binding protein that induces the degradation and represses the translation of mRNAs in the early Drosophila embryo
We find that Smaug regulates the expression of multiple mRNAs that are localized to the posterior of the embryo
Genes that were not expressed or were expressed at low levels in starting crude extracts were removed from further analysis and Significance Analysis of Microarrays (SAM) [38] was used to identify 339 genes whose mRNAs were significantly enriched in Smaug RNA co-immunoprecipitation (RIP) compared to control RIPs at a false discovery rate (FDR) of

Summary

Introduction

Smaug is an RNA-binding protein that induces the degradation and represses the translation of mRNAs in the early Drosophila embryo. Post-transcriptional regulatory mechanisms that function in the cytoplasm to control mRNA translation, stability and subcellular localization play essential roles in a wide variety of biological processes. While these types of controls function in a variety of cell types, they are prevalent during early metazoan development where mRNAs synthesized from the mother’s genome direct the early stages of embryogenesis [1]. The RNA-binding protein Smaug plays a major role in mRNA destabilization in the early Drosophila embryo [9]. SRE recognition by Smaug family members is mediated by a sterile alpha motif domain, which contains a cluster of conserved basic residues that functions as an RNA-binding surface [17,19,20,21,22]

Methods

Results

Discussion

Conclusion