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A unifying model for mTORC1-mediated regulation of mRNA translation

Abstract

The mTOR complex 1 (mTORC1) kinase nucleates a pathway that promotes cell growth and proliferation and is the target of rapamycin, a drug with many clinical uses1. mTORC1 regulates messenger RNA translation, but the overall translational program is poorly defined and no unifying model exists to explain how mTORC1 differentially controls the translation of specific mRNAs. Here we use high-resolution transcriptome-scale ribosome profiling to monitor translation in mouse cells acutely treated with the mTOR inhibitor Torin 1, which, unlike rapamycin, fully inhibits mTORC1 (ref. 2). Our data reveal a surprisingly simple model of the mRNA features and mechanisms that confer mTORC1-dependent translation control. The subset of mRNAs that are specifically regulated by mTORC1 consists almost entirely of transcripts with established 5′ terminal oligopyrimidine (TOP) motifs, or, like Hsp90ab1 and Ybx1, with previously unrecognized TOP or related TOP-like motifs that we identified. We find no evidence to support proposals that mTORC1 preferentially regulates mRNAs with increased 5′ untranslated region length or complexity3. mTORC1 phosphorylates a myriad of translational regulators, but how it controls TOP mRNA translation is unknown4. Remarkably, loss of just the 4E-BP family of translational repressors, arguably the best characterized mTORC1 substrates, is sufficient to render TOP and TOP-like mRNA translation resistant to Torin 1. The 4E-BPs inhibit translation initiation by interfering with the interaction between the cap-binding protein eIF4E and eIF4G1. Loss of this interaction diminishes the capacity of eIF4E to bind TOP and TOP-like mRNAs much more than other mRNAs, explaining why mTOR inhibition selectively suppresses their translation. Our results clarify the translational program controlled by mTORC1 and identify 4E-BPs and eIF4G1 as its master effectors.

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Figure 1: Profile of mTOR-regulated translation.
Figure 2: Translation of TOP and TOP-like mRNAs is hypersensitive to mTOR inhibition.
Figure 3: mTOR regulates general protein synthesis and TOP mRNA translation through the 4E-BPs.
Figure 4: Destabilization of the eIF4E–eIF4G1 interaction dissociates TOP mRNAs from eIF4E and inhibits their translation.

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Primary accessions

Gene Expression Omnibus

Data deposits

Small RNA sequencing data were deposited in the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo) under accession number GSE36892.

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Acknowledgements

We thank members of the Gray and Sabatini laboratories for helpful discussions, H. Guo, S. Hawthorne, G. Brar, J. Damon, C. Miller and W. Gilbert for advice and N. Sonenberg for providing 4EBP1/2 wild-type and double-knockout MEFs. This work was supported by the National Institutes of Health (CA103866 and CA129105 to D.M.S.), Department of Defense (W81XWH-07-0448 to D.M.S.), the W.M. Keck Foundation (D.M.S.), LAM Foundation (D.M.S.), Dana Farber Cancer Institute (N.S.G., C.C.T.), and fellowship support from the American Cancer Society (C.C.T.), and the National Science Foundation (L.C. and T.W.). D.M.S. is an investigator of the Howard Hughes Medical Institute.

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Authors

Contributions

C.C.T. and D.M.S. conceived the project. C.C.T. designed and performed most experiments and data analyses with input from D.M.S. and N.S.G. L.C. and H.R.K. assisted with experiments and T.W. with sequence analysis. C.C.T. and D.M.S. wrote and edited the manuscript with input from N.S.G.

Corresponding authors

Correspondence to Nathanael S. Gray or David M. Sabatini.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Figures

This file contains Supplementary Figures 1-9. (PDF 1636 kb)

Supplementary Table 1

In this table we see changes in translational efficiency, ribosome density (RD) and total transcript levels of 4840 robustly detected mRNAs for WT and DKO cells treated with Torin1 for 2 h. (XLS 871 kb)

Supplementary Table 2

In this table we see Torin1-dependent translational regulation of selected functional classes of mRNAs. (XLS 78 kb)

Supplementary Table 3

In this table we see TOP and TOP-like annotations for 43 mRNAs not previously known to encode a TOP motif and which are amongst the 100 transcripts whose translation is most suppressed by mTOR inhibition. (XLS 24 kb)

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Thoreen, C., Chantranupong, L., Keys, H. et al. A unifying model for mTORC1-mediated regulation of mRNA translation. Nature 485, 109–113 (2012). https://doi.org/10.1038/nature11083

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