P bodies and the control of mRNA translation and degradation.

Recent results indicate that many untranslating mRNAs in somatic eukaryotic cells assemble into related mRNPs that accumulate in specific cytoplasmic foci referred to as P bodies. Transcripts associated with P body components can either be degraded or return to translation. Moreover, P bodies are also biochemically and functionally related to some maternal and neuronal mRNA granules. This suggests an emerging model of cytoplasmic mRNA function in which the rates of translation and degradation of mRNAs are influenced by a dynamic equilibrium between polysomes and the mRNPs seen in P bodies. Moreover, some mRNA-specific regulatory factors, including miRNAs and RISC, appear to repress translation and promote decay by recruiting P body components to individual mRNAs.

[1]  K. Oegema,et al.  A complex containing the Sm protein CAR-1 and the RNA helicase CGH-1 is required for embryonic cytokinesis in Caenorhabditis elegans , 2005, The Journal of cell biology.

[2]  T. Rana,et al.  Human Retroviral Host Restriction Factors APOBEC3G and APOBEC3F Localize to mRNA Processing Bodies , 2006, PLoS pathogens.

[3]  E. Chan,et al.  Disruption of GW bodies impairs mammalian RNA interference , 2005, Nature Cell Biology.

[4]  M. Gorospe,et al.  Translational Repression by RNA-Binding Protein TIAR , 2006, Molecular and Cellular Biology.

[5]  C. Beckham,et al.  Virus-like particles of the Ty3 retrotransposon assemble in association with P-body components. , 2006, RNA.

[6]  A. Sachs,et al.  Loss of Translational Control in Yeast Compromised for the Major mRNA Decay Pathway , 2004, Molecular and Cellular Biology.

[7]  Tom R. Mayo,et al.  ARE‐mRNA degradation requires the 5′–3′ decay pathway , 2006, EMBO reports.

[8]  F. He,et al.  Identification of a novel component of the nonsense-mediated mRNA decay pathway by use of an interacting protein screen. , 1995, Genes & development.

[9]  M. Wickens,et al.  PUF proteins bind Pop2p to regulate messenger RNAs , 2006, Nature Structural &Molecular Biology.

[10]  Gregory J. Hannon,et al.  MicroRNA-dependent localization of targeted mRNAs to mammalian P-bodies , 2005, Nature Cell Biology.

[11]  P. Lambin,et al.  Gene expression during acute and prolonged hypoxia is regulated by distinct mechanisms of translational control , 2006, The EMBO journal.

[12]  M. Ladomery,et al.  Xp54, the Xenopus homologue of human RNA helicase p54, is an integral component of stored mRNP particles in oocytes. , 1997, Nucleic acids research.

[13]  H. Blau,et al.  Argonaute 2/RISC resides in sites of mammalian mRNA decay known as cytoplasmic bodies , 2005, Nature Cell Biology.

[14]  P. Bork,et al.  deadenylase and DCP 1 : DCP 2 decapping complexes mRNA degradation by miRNAs and GW 182 requires both CCR 4 : NOT Material , 2006 .

[15]  Roy Parker,et al.  Decapping and Decay of Messenger RNA Occur in Cytoplasmic Processing Bodies , 2003 .

[16]  Randal J. Kaufman,et al.  Stress granules and processing bodies are dynamically linked sites of mRNP remodeling , 2005, The Journal of cell biology.

[17]  E. Izaurralde,et al.  SMG7 acts as a molecular link between mRNA surveillance and mRNA decay. , 2004, Molecular cell.

[18]  J. Rader,et al.  Human papillomaviruses target the double-stranded RNA protein kinase pathway. , 2006, The Journal of general virology.

[19]  A. Jacobson,et al.  A faux 3′-UTR promotes aberrant termination and triggers nonsense- mediated mRNA decay , 2004, Nature.

[20]  J. Lykke-Andersen Identification of a Human Decapping Complex Associated with hUpf Proteins in Nonsense-Mediated Decay , 2002, Molecular and Cellular Biology.

[21]  Min Han,et al.  The developmental timing regulator AIN-1 interacts with miRISCs and may target the argonaute protein ALG-1 to cytoplasmic P bodies in C. elegans. , 2005, Molecular cell.

[22]  Pierre Baldi,et al.  Retroviruses and yeast retrotransposons use overlapping sets of host genes. , 2005, Genome research.

[23]  D. A. Smillie,et al.  RNA helicase p54 (DDX6) is a shuttling protein involved in nuclear assembly of stored mRNP particles. , 2002, Journal of cell science.

[24]  S. Mohammed,et al.  Quantitative proteomics identifies Gemin5, a scaffolding protein involved in ribonucleoprotein assembly, as a novel partner for eukaryotic initiation factor 4E. , 2006, Journal of proteome research.

[25]  K. Bloch,et al.  Ge-1 is a central component of the mammalian cytoplasmic mRNA processing body. , 2005, RNA.

[26]  P. Anderson,et al.  TIA‐1 is a translational silencer that selectively regulates the expression of TNF‐α , 2000 .

[27]  Roy Parker,et al.  Movement of Eukaryotic mRNAs Between Polysomes and Cytoplasmic Processing Bodies , 2005, Science.

[28]  N. Sonenberg,et al.  A role for the eIF4E-binding protein 4E-T in P-body formation and mRNA decay , 2005, The Journal of cell biology.

[29]  B. Séraphin,et al.  The GW182 protein colocalizes with mRNA degradation associated proteins hDcp1 and hLSm4 in cytoplasmic GW bodies. , 2003, RNA.

[30]  K. Weis,et al.  The DEAD box protein Dhh1 stimulates the decapping enzyme Dcp1 , 2002, The EMBO journal.

[31]  K. Chébli,et al.  The RasGAP-associated endoribonuclease G3BP assembles stress granules , 2003, The Journal of cell biology.

[32]  Jun O. Liu,et al.  Eukaryotic Initiation Factor 2α-independent Pathway of Stress Granule Induction by the Natural Product Pateamine A* , 2006, Journal of Biological Chemistry.

[33]  J. Gall,et al.  Subnuclear organelles: new insights into form and function. , 2006, Trends in cell biology.

[34]  Roy Parker,et al.  Targeting of Aberrant mRNAs to Cytoplasmic Processing Bodies , 2006, Cell.

[35]  J. Lykke-Andersen,et al.  Multiple processing body factors and the ARE binding protein TTP activate mRNA decapping. , 2005, Molecular cell.

[36]  Jeongsik Yong,et al.  Why do cells need an assembly machine for RNA-protein complexes? , 2004, Trends in cell biology.

[37]  Kaleb M. Pauley,et al.  Formation of GW bodies is a consequence of microRNA genesis , 2006, EMBO reports.

[38]  Jean-Marie Buerstedde,et al.  A Mouse Cytoplasmic Exoribonuclease (mXRN1p) with Preference for G4 Tetraplex Substrates , 1997, The Journal of cell biology.

[39]  R. Parker,et al.  Processing bodies require RNA for assembly and contain nontranslating mRNAs. , 2005, RNA.

[40]  R. Parker,et al.  Differential effects of translational inhibition in cis and in trans on the decay of the unstable yeast MFA2 mRNA. , 1994, The Journal of biological chemistry.

[41]  Y. Kohara,et al.  cgh-1, a conserved predicted RNA helicase required for gametogenesis and protection from physiological germline apoptosis in C. elegans. , 2001, Development.

[42]  Li-Ting Jang,et al.  Determinants of Rbp1p Localization in Specific Cytoplasmic mRNA-processing Foci, P-bodies* , 2006, Journal of Biological Chemistry.

[43]  B. Séraphin,et al.  Human Dcp2: a catalytically active mRNA decapping enzyme located in specific cytoplasmic structures , 2002, The EMBO journal.

[44]  H. Mitsui,et al.  Dhh1p, a putative RNA helicase, associates with the general transcription factors Pop2p and Ccr4p from Saccharomyces cerevisiae. , 1998, Genetics.

[45]  A. Pasquinelli,et al.  Regulation by let-7 and lin-4 miRNAs Results in Target mRNA Degradation , 2005, Cell.

[46]  R. Parker,et al.  The DEAD box helicase, Dhh1p, functions in mRNA decapping and interacts with both the decapping and deadenylase complexes. , 2001, RNA.

[47]  D. Melamed,et al.  The RNA polymerase II subunit Rpb4p mediates decay of a specific class of mRNAs. , 2005, Genes & development.

[48]  G. Lyons,et al.  CAR-1, a protein that localizes with the mRNA decapping component DCAP-1, is required for cytokinesis and ER organization in Caenorhabditis elegans embryos. , 2005, Molecular biology of the cell.

[49]  S. Lall,et al.  Caenorhabditis elegans decapping proteins: localization and functional analysis of Dcp1, Dcp2, and DcpS during embryogenesis. , 2005, Molecular biology of the cell.

[50]  L. Maquat Nonsense-mediated mRNA decay: splicing, translation and mRNP dynamics , 2004, Nature Reviews Molecular Cell Biology.

[51]  T. Rana,et al.  Translation Repression in Human Cells by MicroRNA-Induced Gene Silencing Requires RCK/p54 , 2006, PLoS biology.

[52]  A. Nakamura,et al.  Drosophila cup is an eIF4E binding protein that associates with Bruno and regulates oskar mRNA translation in oogenesis. , 2004, Developmental cell.

[53]  Haiwei Song,et al.  The enzymes and control of eukaryotic mRNA turnover , 2004, Nature Structural &Molecular Biology.

[54]  J. Pelletier,et al.  Inhibition of ribosome recruitment induces stress granule formation independently of eukaryotic initiation factor 2alpha phosphorylation. , 2006, Molecular biology of the cell.

[55]  T. Dunckley,et al.  Sbp1p Affects Translational Repression and Decapping in Saccharomyces cerevisiae , 2006, Molecular and Cellular Biology.

[56]  D. Weil,et al.  The translational regulator CPEB1 provides a link between dcp1 bodies and stress granules , 2005, Journal of Cell Science.

[57]  P. Boag,et al.  A conserved RNA-protein complex component involved in physiological germline apoptosis regulation in C. elegans , 2005, Development.

[58]  S. Peltz,et al.  Interrelationships of the pathways of mRNA decay and translation in eukaryotic cells. , 1996, Annual review of biochemistry.

[59]  R. Lührmann,et al.  The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci. , 2002, RNA.

[60]  R. Parker,et al.  Premature translational termination triggers mRNA decapping , 1994, Nature.

[61]  P. Anderson,et al.  Stress granule assembly is mediated by prion-like aggregation of TIA-1. , 2004, Molecular biology of the cell.

[62]  N. Sonenberg,et al.  Regulation of cap-dependent translation by eIF4E inhibitory proteins , 2005, Nature.

[63]  R. Ozawa,et al.  A comprehensive two-hybrid analysis to explore the yeast protein interactome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[64]  P. Anderson,et al.  Stressful initiations. , 2002, Journal of cell science.

[65]  Geppino Falco,et al.  Identification and Functional Outcome of mRNAs Associated with RNA-Binding Protein TIA-1 , 2005, Molecular and Cellular Biology.

[66]  R. Levine,et al.  Staufen- and FMRP-Containing Neuronal RNPs Are Structurally and Functionally Related to Somatic P Bodies , 2006, Neuron.

[67]  K. Bloch,et al.  RNA-associated protein 55 (RAP55) localizes to mRNA processing bodies and stress granules. , 2006, RNA.

[68]  N. Malys,et al.  Dcs2, a novel stress-induced modulator of m7GpppX pyrophosphatase activity that locates to P bodies. , 2006, Journal of molecular biology.

[69]  Gary D Bader,et al.  Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.

[70]  R. Parker,et al.  Identification of Edc3p as an enhancer of mRNA decapping in Saccharomyces cerevisiae. , 2004, Genetics.

[71]  W. Filipowicz,et al.  Relief of microRNA-Mediated Translational Repression in Human Cells Subjected to Stress , 2006, Cell.

[72]  Shih-Jung Fan,et al.  Drosophila decapping protein 1, dDcp1, is a component of the oskar mRNP complex and directs its posterior localization in the oocyte. , 2006, Developmental cell.

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

[74]  Paolo Sassone-Corsi,et al.  The chromatoid body of male germ cells: similarity with processing bodies and presence of Dicer and microRNA pathway components. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[75]  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.

[76]  Roy Parker,et al.  General Translational Repression by Activators of mRNA Decapping , 2005, Cell.

[77]  Elmar Wahle,et al.  Messenger RNA Turnover in Eukaryotes: Pathways and Enzymes , 2004, Critical reviews in biochemistry and molecular biology.

[78]  J. Yates,et al.  A role for the P-body component GW182 in microRNA function , 2005, Nature Cell Biology.

[79]  R. Heintzmann,et al.  A role for eIF4E and eIF4E-transporter in targeting mRNPs to mammalian processing bodies. , 2005, RNA.

[80]  P. Bork,et al.  Proteome survey reveals modularity of the yeast cell machinery , 2006, Nature.

[81]  W. Filipowicz,et al.  Inhibition of Translational Initiation by Let-7 MicroRNA in Human Cells , 2005, Science.

[82]  N. Standart,et al.  A conserved role of a DEAD box helicase in mRNA masking. , 2001, RNA.

[83]  Sean R. Collins,et al.  Global landscape of protein complexes in the yeast Saccharomyces cerevisiae , 2006, Nature.

[84]  Isabelle Behm-Ansmant,et al.  A crucial role for GW182 and the DCP1:DCP2 decapping complex in miRNA-mediated gene silencing. , 2005, RNA.

[85]  Me31B silences translation of oocyte-localizing RNAs through the formation of cytoplasmic RNP complex during Drosophila oogenesis. , 2001, Development.

[86]  T. Tuschl,et al.  Identification of Novel Argonaute-Associated Proteins , 2005, Current Biology.

[87]  B. Séraphin,et al.  Cytoplasmic foci are sites of mRNA decay in human cells , 2004, The Journal of cell biology.

[88]  E. Izaurralde,et al.  P bodies: at the crossroads of post-transcriptional pathways , 2007, Nature Reviews Molecular Cell Biology.

[89]  R. Parker,et al.  The yeast EDC1 mRNA undergoes deadenylation‐independent decapping stimulated by Not2p, Not4p, and Not5p , 2005, The EMBO journal.

[90]  Roy Parker,et al.  Eukaryotic mRNA decapping. , 2004, Annual review of biochemistry.

[91]  Circe W. Tsui,et al.  Functional genomics reveals relationships between the retrovirus-like Ty1 element and its host Saccharomyces cerevisiae. , 2003, Genetics.

[92]  R. Parker,et al.  Recognition of yeast mRNAs as "nonsense containing" leads to both inhibition of mRNA translation and mRNA degradation: implications for the control of mRNA decapping. , 1999, Molecular biology of the cell.