Abstract
S6 kinases (S6Ks) are mechanistic target of rapamycin substrates that participate in cell growth control. S6Ks phosphorylate ribosomal protein S6 (rpS6) and additional proteins involved in the translational machinery, although the functional roles of these modifications remain elusive. Here we analyze the S6K-dependent transcriptional and translational regulation of gene expression by comparing whole-genome microarray of total and polysomal mouse liver RNA after feeding. We show that tissue lacking S6Ks 1 and 2 (S6K1 and S6K2), displays a defect in the ribosome biogenesis (RiBi) transcriptional program after feeding. Over 75% of RiBi factors are controlled by S6K, including Nop56, Nop14, Gar1, Rrp9, Rrp15, Rrp12 and Pwp2 nucleolar proteins. Importantly, the reduced activity of RiBi transcriptional promoters in S6K1;S6K2−/− cells is also observed in rpS6 knock-in mutants that cannot be phosphorylated. As ribosomal protein synthesis is not affected by these mutations, our data reveal a distinct and specific aspect of RiBi under the control of rpS6 kinase activity, that is, the RiBi transcriptional program.
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References
Kozma SC, Ferrari S, Bassand P, Siegmann M, Totty N, Thomas G . Cloning of the mitogen-activated S6 kinase from rat liver reveals an enzyme of the second messenger subfamily. Proc Natl Acad Sci USA 1990; 87: 7365–7369.
Grove JR, Banerjee P, Balasubramanyam A, Coffer PJ, Price DJ, Avruch J et al. Cloning and expression of two human p70 S6 kinase polypeptides differing only at their amino termini. Mol Cell Biol 1991; 11: 5541–5550.
Shima H, Pende M, Chen Y, Fumagalli S, Thomas G, Kozma SC . Disruption of the p70(s6k)/p85(s6k) gene reveals a small mouse phenotype and a new functional S6 kinase. EMBO J 1998; 17: 6649–6659.
Pende M, Um SH, Mieulet V, Sticker M, Goss VL, Mestan J et al. S6K1(−/−)/S6K2(−/−) mice exhibit perinatal lethality and rapamycin-sensitive 5′-terminal oligopyrimidine mRNA translation and reveal a mitogen-activated protein kinase-dependent S6 kinase pathway. Mol Cell Biol 2004; 24: 3112–3124.
Thomas G, Siegmann M, Kubler AM, Gordon J, Jimenez dA . Regulation of 40S ribosomal protein S6 phosphorylation in Swiss mouse 3T3 cells. Cell 1980; 19: 1015–1023.
Krieg J, Hofsteenge J, Thomas G . Identification of the 40 S ribosomal protein S6 phosphorylation sites induced by cycloheximide. J Biol Chem 1988; 263: 11473–11477.
Isotani S, Hara K, Tokunaga C, Inoue H, Avruch J, Yonezawa K . Immunopurified mammalian target of rapamycin phosphorylates and activates p70 S6 kinase alpha in vitro. J Biol Chem 1999; 274: 34493–34498.
Laplante M, Sabatini DM . mTOR signaling. Cold Spring Harb Perspect Biol 2011; 4: pii a011593.
Montagne J, Stewart MJ, Stocker H, Hafen E, Kozma SC, Thomas G . Drosophila S6 kinase: a regulator of cell size. Science 1999; 285: 2126–2129.
Pende M, Kozma SC, Jaquet M, Oorschot V, Burcelin R, Marchand-Brustel Y et al. Hypoinsulinaemia, glucose intolerance and diminished beta-cell size in S6K1-deficient mice. Nature 2000; 408: 994–997.
Shahbazian D, Roux PP, Mieulet V, Cohen MS, Raught B, Taunton J et al. The mTOR/PI3K and MAPK pathways converge on eIF4B to control its phosphorylation and activity. EMBO J 2006; 25: 2781–2791.
Wang X, Li W, Williams M, Terada N, Alessi DR, Proud CG . Regulation of elongation factor 2 kinase by p90(RSK1) and p70 S6 kinase. EMBO J 2001; 20: 4370–4379.
Holz MK, Ballif BA, Gygi SP, Blenis J . mTOR and S6K1 mediate assembly of the translation preinitiation complex through dynamic protein interchange and ordered phosphorylation events. Cell 2005; 123: 569–580.
Mieulet V, Roceri M, Espeillac C, Sotiropoulos A, Ohanna M, Oorschot V et al. S6 kinase inactivation impairs growth and translational target phosphorylation in muscle cells maintaining proper regulation of protein turnover. Am J Physiol Cell Physiol 2007; 293: C712–C722.
Choo AY, Yoon SO, Kim SG, Roux PP, Blenis J . Rapamycin differentially inhibits S6Ks and 4E-BP1 to mediate cell-type-specific repression of mRNA translation. Proc Natl Acad Sci USA 2008; 105: 17414–17419.
Thoreen CC, Kang SA, Chang JW, Liu Q, Zhang J, Gao Y et al. An ATP-competitive mTOR inhibitor reveals rapamycin-insensitive functions of mTORC1. J Biol Chem 2009; 284: 8023–8032.
Thoreen CC, Chantranupong L, Keys HR, Wang T, Gray NS, Sabatini DM . A unifying model for mTORC1-mediated regulation of mRNA translation. Nature 2012; 485: 109–113.
Hsieh AC, Liu Y, Edlind MP, Ingolia NT, Janes MR, Sher A et al. The translational landscape of mTOR signalling steers cancer initiation and metastasis. Nature 2012; 485: 55–61.
Powley IR, Kondrashov A, Young LA, Dobbyn HC, Hill K, Cannell IG et al. Translational reprogramming following UVB irradiation is mediated by DNA-PKcs and allows selective recruitment to the polysomes of mRNAs encoding DNA repair enzymes. Genes Dev 2009; 23: 1207–1220.
Patursky-Polischuk I, Stolovich-Rain M, Hausner-Hanochi M, Kasir J, Cybulski N, Avruch J et al. The TSC-mTOR pathway mediates translational activation of TOP mRNAs by insulin largely in a raptor- or rictor-independent manner. Mol Cell Biol 2008; 29: 640–649.
Lempiainen H, Shore D . Growth control and ribosome biogenesis. Curr Opin Cell Biol 2009; 21: 855–863.
Kiss T, Fayet-Lebaron E, Jady BE . Box H/ACA small ribonucleoproteins. Mol Cell 2010; 37: 597–606.
Girard JP, Lehtonen H, Caizergues-Ferrer M, Amalric F, Tollervey D, Lapeyre B . GAR1 is an essential small nucleolar RNP protein required for pre-rRNA processing in yeast. EMBO J 1992; 11: 673–682.
Liu PC, Thiele DJ . Novel stress-responsive genes EMG1 and NOP14 encode conserved, interacting proteins required for 40S ribosome biogenesis. Mol Biol Cell 2001; 12: 3644–3657.
Venema J, Vos HR, Faber AW, van Venrooij WJ, Raue HA . Yeast Rrp9p is an evolutionarily conserved U3 snoRNP protein essential for early pre-rRNA processing cleavages and requires box C for its association. RNA 2000; 6: 1660–1671.
Bernstein KA, Granneman S, Lee AV, Manickam S, Baserga SJ . Comprehensive mutational analysis of yeast DEXD/H box RNA helicases involved in large ribosomal subunit biogenesis. Mol Cell Biol 2006; 26: 1195–1208.
Dosil M, Bustelo XR . Functional characterization of Pwp2, a WD family protein essential for the assembly of the 90 S pre-ribosomal particle. J Biol Chem 2004; 279: 37385–37397.
Gautier T, Berges T, Tollervey D, Hurt E . Nucleolar KKE/D repeat proteins Nop56p and Nop58p interact with Nop1p and are required for ribosome biogenesis. Mol Cell Biol 1997; 17: 7088–7098.
De Marchis ML, Giorgi A, Schinina ME, Bozzoni I, Fatica A . Rrp15p a novel component of pre-ribosomal particles required for 60S ribosome subunit maturation. RNA 2005; 11: 495–502.
Ohanna M, Sobering AK, Lapointe T, Lorenzo L, Praud C, Petroulakis E et al. Atrophy of S6K1(−/−) skeletal muscle cells reveals distinct mTOR effectors for cell cycle and size control. Nat Cell Biol 2005; 7: 286–294.
Ma XM, Yoon SO, Richardson CJ, Julich K, Blenis J . SKAR links pre-mRNA splicing to mTOR/S6K1-mediated enhanced translation efficiency of spliced mRNAs. Cell 2008; 133: 303–313.
Dibble CC, Asara JM, Manning BD . Characterization of Rictor phosphorylation sites reveals direct regulation of mTOR complex 2 by S6K1. Mol Cell Biol 2009; 29: 5657–5670.
Tremblay F, Brule S, Hee US, Li Y, Masuda K, Roden M et al. Identification of IRS-1 Ser-1101 as a target of S6K1 in nutrient- and obesity-induced insulin resistance. Proc Natl Acad Sci USA 2007; 104: 14056–14061.
Ruvinsky I, Sharon N, Lerer T, Cohen H, Stolovich-Rain M, Nir T et al. Ribosomal protein S6 phosphorylation is a determinant of cell size and glucose homeostasis. Genes Dev 2005; 19: 2199–2211.
Huber A, French SL, Tekotte H, Yerlikaya S, Stahl M, Perepelkina MP et al. Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L. EMBO J 2011; 30: 3052–3064.
Yoon A, Peng G, Brandenburger Y, Zollo O, Xu W, Rego E et al. Impaired control of IRES-mediated translation in X-linked dyskeratosis congenita. Science 2006; 312: 902–906.
Ge J, Rudnick DA, He J, Crimmins DL, Ladenson JH, Bessler M et al. Dyskerin ablation in mouse liver inhibits rRNA processing and cell division. Mol Cell Biol 2010; 30: 413–422.
Espeillac C, Mitchell C, Celton-Morizur S, Chauvin C, Koka V, Gillet C et al. S6 kinase 1 is required for rapamycin-sensitive liver proliferation after mouse hepatectomy. J Clin Invest 2011; 121: 2821–2832.
Jorgensen P, Nishikawa JL, Breitkreutz BJ, Tyers M . Systematic identification of pathways that couple cell growth and division in yeast. Science 2002; 297: 395–400.
Jorgensen P, Rupes I, Sharom JR, Schneper L, Broach JR, Tyers M . A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size. Genes Dev 2004; 18: 2491–2505.
Guertin DA, Guntur KV, Bell GW, Thoreen CC, Sabatini DM . Functional genomics identifies TOR-regulated genes that control growth and division. Curr Biol 2006; 16: 958–970.
Urban J, Soulard A, Huber A, Lippman S, Mukhopadhyay D, Deloche O et al. Sch9 is a major target of TORC1 in Saccharomyces cerevisiae. Mol Cell 2007; 26: 663–674.
Hannan KM, Brandenburger Y, Jenkins A, Sharkey K, Cavanaugh A, Rothblum L et al. mTOR-dependent regulation of ribosomal gene transcription requires S6K1 and is mediated by phosphorylation of the carboxy-terminal activation domain of the nucleolar transcription factor UBF. Mol Cell Biol 2003; 23: 8862–8877.
Mayer C, Zhao J, Yuan X, Grummt I . mTOR-dependent activation of the transcription factor TIF-IA links rRNA synthesis to nutrient availability. Genes Dev 2004; 18: 423–434.
Lempiainen H, Uotila A, Urban J, Dohnal I, Ammerer G, Loewith R et al. Sfp1 interaction with TORC1 and Mrs6 reveals feedback regulation on TOR signaling. Mol Cell 2009; 33: 704–716.
Iadevaia V, Zhang Z, Jan E, Proud CG . mTOR signaling regulates the processing of pre-rRNA in human cells. Nucleic Acids Res 2011; 40: 2527–2539.
Mariappan MM, D'Silva K, Lee MJ, Sataranatarajan K, Barnes JL, Choudhury GG et al. Ribosomal biogenesis induction by high glucose requires activation of upstream binding factor in kidney glomerular epithelial cells. Am J Physiol Renal Physiol 2011; 300: F219–F230.
De S, Brogna S . Are ribosomal proteins present at transcription sites on or off ribosomal subunits? Biochem Soc Trans 2010; 38: 1543–1547.
Malygin AA, Parakhnevitch NM, Ivanov AV, Eperon IC, Karpova GG . Human ribosomal protein S13 regulates expression of its own gene at the splicing step by a feedback mechanism. Nucleic Acids Res 2007; 35: 6414–6423.
Dai MS, Sun XX, Lu H . Ribosomal protein L11 associates with c-Myc at 5 S rRNA and tRNA genes and regulates their expression. J Biol Chem 2010; 285: 12587–12594.
De S, Varsally W, Falciani F, Brogna S . Ribosomal proteins' association with transcription sites peaks at tRNA genes in Schizosaccharomyces pombe. RNA 2011; 17: 1713–1726.
Chomczynski P, Sacchi N . Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 1987; 162: 156–159.
Acknowledgements
We thank the Novartis Foundation and George Thomas laboratory for the use of S6K mutant mice. We are grateful to the members of INSERM-U845 for support, and to Stefano Fumagalli and Olivier Jean-Jean for helpful discussions and sharing reagents. We thank Sophie Berissi, Ana Diaz and Sylvie Fabrega for excellent technical support. We thank Pfizer for the generous gift of Temsirolimus. This work was supported by grants to MP from the European Research Council, from Fondation de la Recherche Medicale, from Fondation Schlumberger pour l’Education et la Recherche and from ANR and by grants to OM from the US-Israel Binational Science Foundation (2009054), Israel Cancer Research Fund and Ministry of Health. CC received a fellowship from the Coddim Ile de France.
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Chauvin, C., Koka, V., Nouschi, A. et al. Ribosomal protein S6 kinase activity controls the ribosome biogenesis transcriptional program. Oncogene 33, 474–483 (2014). https://doi.org/10.1038/onc.2012.606
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DOI: https://doi.org/10.1038/onc.2012.606
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