Augmentation of nonsense mediated decay by rapamycin

RNA surveillance by the Nonsense Mediated Decay (NMD) pathway eliminates potentially deleterious transcripts containing Premature Termination Codons (PTCs). The transition from a pioneering round of translation to steady state translation is hypothesized to be a major checkpoint in this process. One hallmark of mRNAs licensed for translation is the exchange of 7-methylguanosine cap binding proteins. However, mRNAs undergoing steady state translation are also NMD substrates, raising mechanistic questions about the NMD checkpoint. To test the role of cap binding proteins in NMD, we modulated the protein composition of cytoplasmic messenger ribonucleoprotein particles (mRNPs) with the naturally occurring macrolide rapamycin. We demonstrate that despite well-documented attenuation of cap-dependent mRNA translation, rapamycin can augment NMD. Rapamycin-treatment significantly reduces the levels of endogenous and exogenous PTC-containing mRNA isoforms in a dose- and UPF1- dependent manner. PTC-containing transcripts exhibit a shorter half-life upon rapamacyin-treatment as compared to non-PTC isoforms. Rapamycin also causes depletion of PTC-containing mRNA isoforms from polyribosomes, suggesting that actively translating ribosomes can transition between low and high NMD states. Importantly, mRNPs show depletion of eIF4E and retention of the nuclear Cap Binding Complex (CBC) in rapamycin-treated cells. Our data demonstrate that rapamycin potentiates pioneer-like mRNP context thereby decreasing NMD evasion.

[1]  M. Hentze,et al.  A network of SMG-8, SMG-9 and SMG-1 C-terminal insertion domain regulates UPF1 substrate recruitment and phosphorylation , 2015, Nucleic acids research.

[2]  J. Lykke-Andersen,et al.  Identification of elements in human long 3′ UTRs that inhibit nonsense-mediated decay , 2015, RNA.

[3]  L. Maquat,et al.  Attenuation of nonsense-mediated mRNA decay facilitates the response to chemotherapeutics , 2015, Nature Communications.

[4]  L. Delavaine,et al.  Identification and characterization of novel factors that act in the nonsense-mediated mRNA decay pathway in nematodes, flies and mammals , 2014, EMBO reports.

[5]  O. Mühlemann,et al.  Eukaryotic Initiation Factor 4G Suppresses Nonsense-Mediated mRNA Decay by Two Genetically Separable Mechanisms , 2014, PloS one.

[6]  M. Valasek,et al.  The UPF1 RNA Surveillance Gene is Commonly Mutated in Pancreatic Adenosquamous Carcinoma , 2014, Nature Medicine.

[7]  M. Wilkinson,et al.  Posttranscriptional control of the stem cell and neurogenic programs by the nonsense-mediated RNA decay pathway. , 2014, Cell reports.

[8]  L. Maquat,et al.  Organizing principles of mammalian nonsense-mediated mRNA decay. , 2013, Annual review of genetics.

[9]  C. Burge,et al.  Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay , 2013, Genome research.

[10]  Sang Gyun Kim,et al.  Nutrient regulation of the mTOR Complex 1 signaling pathway , 2013, Molecules and cells.

[11]  O. Mühlemann,et al.  eIF4E-bound mRNPs are substrates for nonsense-mediated mRNA decay in mammalian cells , 2013, Nature Structural &Molecular Biology.

[12]  J. Lykke-Andersen,et al.  Nonsense-mediated mRNA decay occurs during eIF4F-dependent translation in human cells , 2013, Nature Structural &Molecular Biology.

[13]  Allan Jacobson,et al.  NMD: a multifaceted response to premature translational termination , 2012, Nature Reviews Molecular Cell Biology.

[14]  D. Sabatini,et al.  mTOR Signaling in Growth Control and Disease , 2012, Cell.

[15]  Nicholas T. Ingolia,et al.  The translational landscape of mTOR signalling steers cancer initiation and metastasis , 2012, Nature.

[16]  E. Stone,et al.  RNA homeostasis governed by cell type-specific and branched feedback loops acting on NMD. , 2011, Molecular cell.

[17]  Lawrence B. Gardner,et al.  Nonsense-Mediated RNA Decay Regulation by Cellular Stress: Implications for Tumorigenesis , 2010, Molecular Cancer Research.

[18]  Wenqian Hu,et al.  Nonsense-mediated mRNA decapping occurs on polyribosomes in Saccharomyces cerevisiae , 2010, Nature Structural &Molecular Biology.

[19]  L. Partridge,et al.  Mechanisms of Life Span Extension by Rapamycin in the Fruit Fly Drosophila melanogaster , 2010, Cell metabolism.

[20]  L. Maquat,et al.  Remodeling of the pioneer translation initiation complex involves translation and the karyopherin importin beta. , 2009, Genes & development.

[21]  Wenqian Hu,et al.  Co-translational mRNA decay in Saccharomyces cerevisiae , 2009, Nature.

[22]  Marco Pahor,et al.  Rapamycin fed late in life extends lifespan in genetically heterogeneous mice , 2009, Nature.

[23]  Matthew Mort,et al.  A meta‐analysis of nonsense mutations causing human genetic disease , 2008, Human mutation.

[24]  A. Gingras,et al.  Control of eIF4E cellular localization by eIF4E-binding proteins, 4E-BPs. , 2008, RNA.

[25]  O. Mühlemann,et al.  Posttranscriptional Gene Regulation by Spatial Rearrangement of the 3′ Untranslated Region , 2008, PLoS biology.

[26]  L. Maquat,et al.  Efficiency of the pioneer round of translation affects the cellular site of nonsense-mediated mRNA decay. , 2008, Molecular cell.

[27]  S. Brenner,et al.  Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements , 2007, Nature.

[28]  Tyson A. Clark,et al.  Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. , 2007, Genes & development.

[29]  M. Wiznerowicz,et al.  KRAB Can Repress Lentivirus Proviral Transcription Independently of Integration Site* , 2006, Journal of Biological Chemistry.

[30]  M. Hentze,et al.  A chemiluminescence-based reporter system to monitor nonsense-mediated mRNA decay. , 2006, Biochemical and biophysical research communications.

[31]  G. Dreyfuss,et al.  Binding of a novel SMG-1-Upf1-eRF1-eRF3 complex (SURF) to the exon junction complex triggers Upf1 phosphorylation and nonsense-mediated mRNA decay. , 2006, Genes & development.

[32]  L. Maquat,et al.  CBP80 promotes interaction of Upf1 with Upf2 during nonsense-mediated mRNA decay in mammalian cells , 2005, Nature Structural &Molecular Biology.

[33]  L. Maquat,et al.  The pioneer translation initiation complex is functionally distinct from but structurally overlaps with the steady-state translation initiation complex. , 2004, Genes & development.

[34]  Elisa Izaurralde,et al.  The structural basis for the interaction between nonsense-mediated mRNA decay factors UPF2 and UPF3 , 2004, Nature Structural &Molecular Biology.

[35]  K. Anders,et al.  Phosphorylation of hUPF1 induces formation of mRNA surveillance complexes containing hSMG-5 and hSMG-7. , 2003, Molecular cell.

[36]  L. Maquat,et al.  Nonsense-mediated mRNA decay in mammalian cells involves decapping, deadenylating, and exonucleolytic activities. , 2003, Molecular cell.

[37]  G. Dreyfuss,et al.  Translation Is Required to Remove Y14 from mRNAs in the Cytoplasm , 2002, Current Biology.

[38]  L. Maquat,et al.  The exon junction complex is detected on CBP80‐bound but not eIF4E‐bound mRNA in mammalian cells: dynamics of mRNP remodeling , 2002, The EMBO journal.

[39]  L. Maquat,et al.  Evidence for a Pioneer Round of mRNA Translation mRNAs Subject to Nonsense-Mediated Decay in Mammalian Cells Are Bound by CBP80 and CBP20 , 2001, Cell.

[40]  H. Dietz,et al.  A strategy for disease gene identification through nonsense-mediated mRNA decay inhibition , 2001, Nature Biotechnology.

[41]  A. Gingras,et al.  Regulation of translation initiation by FRAP/mTOR. , 2001, Genes & development.

[42]  J. Steitz,et al.  Human Upf Proteins Target an mRNA for Nonsense-Mediated Decay When Bound Downstream of a Termination Codon , 2000, Cell.

[43]  H. Le Hir,et al.  The spliceosome deposits multiple proteins 20–24 nucleotides upstream of mRNA exon–exon junctions , 2000, The EMBO journal.

[44]  N. Sonenberg,et al.  A novel shuttling protein, 4E‐T, mediates the nuclear import of the mRNA 5′ cap‐binding protein, eIF4E , 2000, The EMBO journal.

[45]  L. Maquat,et al.  Evidence to implicate translation by ribosomes in the mechanism by which nonsense codons reduce the nuclear level of human triosephosphate isomerase mRNA. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[46]  S. Peltz,et al.  The product of the yeast UPF1 gene is required for rapid turnover of mRNAs containing a premature translational termination codon. , 1991, Genes & development.

[47]  Pecht,et al.  Cold Spring Harbor Symposia on Quantitative Biology , 2005, Protoplasma.

[48]  L. Maquat,et al.  Evidence that phosphorylation of human Upfl protein varies with intracellular location and is mediated by a wortmannin-sensitive and rapamycin-sensitive PI 3-kinase-related kinase signaling pathway. , 2001, RNA.

[49]  L. Maquat,et al.  Nonsense-mediated mRNA decay: insights into mechanism from the cellular abundance of human Upf1, Upf2, Upf3, and Upf3X proteins. , 2001, Cold Spring Harbor symposia on quantitative biology.