Skip to main content
SpringerLink
Log in

The Discovery and Analysis of P Bodies

  • Chapter
  • First Online:
Book cover Ten Years of Progress in GW/P Body Research

Part of the book series: Advances in Experimental Medicine and Biology ((volume 768))

Abstract

The last decade has seen the discovery of a conserved class of cytoplasmic mRNP (messenger Ribonucleic Acid—Protein complexes) aggregates called Processing Bodies or P Bodies (Sheth and Parker 2003). They belong to a growing list of cytoplasmic mRNP aggregates, many of which are compositionally similar to P Bodies and consist of a host of translational repressors and mRNA decay factors. These aggregates have been suggested to play important roles in the regulation of gene expression through the control of translation and mRNA decay (Eulalio et al. 2007a; Parker and Sheth 2007). In this chapter, we review the experiments that led up to the discovery of P Bodies, their composition, relationship with other cellular structures and processes, and possible functions. A key theme is that P Bodies are composed of proteins functioning in translational control and mRNA degradation and thus play roles in the control of cytoplasmic mRNA.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Aizer A, Yaron S-T (2008) Intracellular trafficking and dynamics of P bodies. Prion 2:131

    Article  PubMed  Google Scholar 

  • Amrani N, Sachs MS, Jacobson A (2006) Early nonsense: mRNA decay solves a translational problem. Nat Rev Mol Cell Biol 7:415–425

    Article  PubMed  CAS  Google Scholar 

  • Anderson P, Kedersha N (2006) RNA granules. J Cell Biol 172:803–808

    Article  PubMed  CAS  Google Scholar 

  • Anderson JS, Parker RP (1998) The 3′ to 5′ degradation of yeast mRNAs is a general mechanism for mRNA turnover that requires the SKI2 DEVH box protein and 3″ to 5″ exonucleases of the exosome complex. EMBO J 17:1497–1506

    Article  PubMed  CAS  Google Scholar 

  • Andrei MA, Ingelfinger D, Heintzmann R et al (2005) A role for eIF4E and eIF4E-transporter in targeting mRNPs to mammalian processing bodies. RNA 11:717–727

    Article  PubMed  CAS  Google Scholar 

  • Baker KE, Parker R (2004) Nonsense-mediated mRNA decay: terminating erroneous gene expression. Curr Opin Cell Biol 16:293–299

    Article  PubMed  CAS  Google Scholar 

  • Balzer E, Moss EG (2007) Localization of the developmental timing regulator Lin28 to mRNP complexes, P-bodies and Stress Granules. RNA Biol 4:16–25

    Article  PubMed  CAS  Google Scholar 

  • Barbee SA, Estes PS, Cziko A-M et al (2006) Staufen- and FMRP-containing neuronal RNPs are structurally and functionally related to somatic P bodies. Neuron 52:997–1009

    Article  PubMed  CAS  Google Scholar 

  • Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297

    Article  PubMed  CAS  Google Scholar 

  • Bashkirov VI, Scherthan H, Solinger JA et al (1997) A mouse cytoplasmic exoribonuclease (mXRN1p) with preference for G4 tetraplex substrates. J Cell Biol 136:761–773

    Article  PubMed  CAS  Google Scholar 

  • Beckham CJ, Parker R (2008) P bodies, Stress Granules, and viral life cycles. Cell Host Microbe 3:206–212

    Article  PubMed  CAS  Google Scholar 

  • Beckham CJ, Hilliker A, Cziko A-M et al (2008) The DEAD-box RNA helicase Ded1p affects and accumulates in Saccharomyces cerevisiae P-bodies. Mol Biol Cell 19:984–993

    Article  PubMed  CAS  Google Scholar 

  • Beelman C, Parker R (1994) Differential effects of translational inhibition in cis and in trans on the decay of the unstable yeast MFA2 mRNA. J Biol Chem 269:9687–9692

    PubMed  CAS  Google Scholar 

  • Behm-Ansmant I, Rehwinkel J, Doerks T (2006) mRNA degradation by miRNAs and GW182 requires both CCR4: NOT deadenylase and DCP1: DCP2 decapping complexes. Genes Dev 20:1885–1898

    Article  PubMed  CAS  Google Scholar 

  • Bhattacharyya SN, Habermacher R, Martine U et al (2006) Relief of microRNA-mediated translational repression in human cells subjected to stress. Cell 125:1111–1124

    Article  PubMed  CAS  Google Scholar 

  • Bouveret E, Rigaut G, Shevchenko A et al (2000) A Sm-like protein complex that participates in mRNA degradation. EMBO J 19:1661–1671

    Article  PubMed  CAS  Google Scholar 

  • Brahms H, Meheus L, de Brabandere V et al (2001) Symmetrical dimethylation of arginine residues in spliceosomal Sm protein B/B′ and the Sm-like protein LSm4, and their interaction with the SMN protein. RNA 7:1531–1542

    Article  PubMed  CAS  Google Scholar 

  • Brengues M, Parker R (2007) Accumulation of polyadenylated mRNA, Pab1p, eIF4E, and eIF4G with P-bodies in Saccharomyces cerevisiae. Mol Biol Cell 18:2592–2602

    Article  PubMed  CAS  Google Scholar 

  • Brengues M, Teixeira D, Parker R (2005) Movement of eukaryotic mRNAs between polysomes and cytoplasmic processing bodies. Science 310:486–489

    Article  PubMed  CAS  Google Scholar 

  • Buchan JR, Parker R (2009) Eukaryotic Stress Granules: the ins and outs of translation. Mol Cell 36:932–941

    Article  PubMed  CAS  Google Scholar 

  • Buchan JR, Muhlrad D, Parker R (2008) P bodies promote Stress Granule assembly in Saccharomyces cerevisiae. J Cell Biol 183:441–455

    Article  PubMed  CAS  Google Scholar 

  • Buchan JR, Nissan T, Parker R, Elsevier B. V., Amsterdam (2010) Chapter 25 - Analyzing P-Bodies and Stress Granules in Saccharomyces cerevisiae. Guide to Yeast Genetics: Functional Genomics, Proteomics, and Other Systems Analysis, 2nd edn, vol 470. pp 619–640

    Google Scholar 

  • Buchan JR, Yoon J-H, Parker R (2011) Stress-specific composition, assembly and kinetics of Stress Granules in Saccharomyces cerevisiae. J Cell Sci 124:228–239

    Article  PubMed  CAS  Google Scholar 

  • Buchet-Poyau K, Courchet J, Le Hir H et al (2007) Identification and characterization of human Mex-3 proteins, a novel family of evolutionarily conserved RNA-binding proteins differentially localized to processing bodies. Nucleic Acids Res 35:1289–1300

    Article  PubMed  CAS  Google Scholar 

  • Cao D, Parker R (2003) Computational modeling and experimental analysis of nonsense-mediated decay in yeast. Cell 113:533–545

    Article  PubMed  CAS  Google Scholar 

  • Chang W, Zaarour RF, Reck-Peterson S et al (2008) Myo2p, a class V myosin in budding yeast, associates with a large ribonucleic acid-protein complex that contains mRNAs and subunits of the RNA-processing body. RNA 14:491–502

    Article  PubMed  CAS  Google Scholar 

  • Chen C-YA, Shyu A-B (2003) Rapid deadenylation triggered by a nonsense codon precedes decay of the RNA body in a mammalian cytoplasmic nonsense-mediated decay pathway. Mol Cell Biol 23:4805–4813

    Article  PubMed  CAS  Google Scholar 

  • Chowdhury A, Tharun S (2009) Activation of decapping involves binding of the mRNA and facilitation of the post-binding steps by the Lsm1-7-Pat1 complex. RNA 15:1837–1848

    Article  PubMed  CAS  Google Scholar 

  • Chu C-Y, Rana TM (2006) Translation repression in human cells by microRNA-induced gene silencing requires RCK/p54. PLoS Biol 4:e210

    Article  PubMed  CAS  Google Scholar 

  • Coller J, Parker R (2004) Eukaryotic mRNA decapping. Annu Rev Biochem 73:861–890

    Article  PubMed  CAS  Google Scholar 

  • Coller J, Parker R (2005) General translational repression by activators of mRNA decapping. Cell 122:875–886

    Article  PubMed  CAS  Google Scholar 

  • Coller JM, Tucker M, Sheth U et al (2001) The DEAD box helicase, Dhh1p, functions in mRNA decapping and interacts with both the decapping and deadenylase complexes. RNA 7:1717–1727

    Article  PubMed  CAS  Google Scholar 

  • Conti E, Izaurralde E (2005) Nonsense-mediated mRNA decay: molecular insights and mechanistic variations across species. Curr Opin Cell Biol 17:316–325

    Article  PubMed  CAS  Google Scholar 

  • Cougot N, Babajko S, SĂ©raphin B (2004) Cytoplasmic foci are sites of mRNA decay in human cells. J Cell Biol 165:31–40

    Article  PubMed  CAS  Google Scholar 

  • Courchet J, Buchet-Poyau K, Potemski A et al (2008) Interaction with 14-3-3 adaptors regulates the sorting of hMex-3B RNA-binding protein to distinct classes of RNA granules. J Biol Chem 283:32131–32142

    Article  PubMed  CAS  Google Scholar 

  • Couttet P, Grange T (2004) Premature termination codons enhance mRNA decapping in human cells. Nucleic Acids Res 32:488–494

    Article  PubMed  CAS  Google Scholar 

  • Decker CJ, Teixeira D, Parker R (2007) Edc3p and a glutamine/asparagine-rich domain of Lsm4p function in processing body assembly in Saccharomyces cerevisiae. J Cell Biol 179:437–449

    Article  PubMed  CAS  Google Scholar 

  • Ding L, Spencer A, Morita K, Han M (2005) The developmental timing regulator AIN-1 interacts with miRISCs and may target the argonaute protein ALG-1 to cytoplasmic P bodies in C. elegans. Mol Cell 19:437–447

    Article  PubMed  CAS  Google Scholar 

  • Durand S, Cougot N, Mahuteau-Betzer F et al (2007) Inhibition of nonsense-mediated mRNA decay (NMD) by a new chemical molecule reveals the dynamic of NMD factors in P-bodies. J Cell Biol 178:1145–1160

    Article  PubMed  CAS  Google Scholar 

  • Eulalio A, Behm-Ansmant I, Izaurralde E (2007a) P bodies: at the crossroads of post-transcriptional pathways. Nat Rev Mol Cell Biol 8:9–22

    Article  PubMed  CAS  Google Scholar 

  • Eulalio A, Behm-Ansmant I, Schweizer D, Izaurralde E (2007b) P-body formation is a consequence, not the cause, of RNA-mediated gene silencing. Mol Cell Biol 27:3970–3981

    Article  PubMed  CAS  Google Scholar 

  • Eulalio A, Rehwinkel J, Stricker M et al (2007c) Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing. Genes Dev 21:2558–2570

    Article  PubMed  CAS  Google Scholar 

  • Eulalio A, Huntzinger E, Izaurralde E (2008) GW182 interaction with Argonaute is essential for miRNA-mediated translational repression and mRNA decay. Nat Struct Mol Biol 15:346–353

    Article  PubMed  CAS  Google Scholar 

  • Eystathioy T, Jakymiw A, Chan EKL et al (2003) The GW182 protein colocalizes with mRNA degradation associated proteins hDcp1 and hLSm4 in cytoplasmic GW bodies. RNA 9:1171–1173

    Article  PubMed  CAS  Google Scholar 

  • Fasken MB, Corbett AH (2005) Process or perish: quality control in mRNA biogenesis. Nat Struct Mol Biol 12:482–488

    Article  PubMed  CAS  Google Scholar 

  • Fenger-Grøn M, Fillman C, Norrild B, Lykke-Andersen J (2005) Multiple processing body factors and the ARE binding protein TTP activate mRNA decapping. Mol Cell 20:905–915

    Article  PubMed  CAS  Google Scholar 

  • Ferraiuolo MA, Basak S, Dostie J et al (2005) A role for the eIF4E-binding protein 4E-T in P-body formation and mRNA decay. J Cell Biol 170:913–924

    Article  PubMed  CAS  Google Scholar 

  • Fierro-Monti I, Mohammed S, Matthiesen R et al (2006) Quantitative proteomics identifies Gemin5, a scaffolding protein involved in ribonucleoprotein assembly, as a novel partner for eukaryotic initiation factor 4E. J Proteome Res 5:1367–1378

    Article  PubMed  CAS  Google Scholar 

  • Franks TM, Singh G, Lykke-Andersen J (2010) Upf1 ATPase-dependent mRNP disassembly is required for completion of nonsense- mediated mRNA decay. Cell 143:938–950

    Article  PubMed  CAS  Google Scholar 

  • Fujimura K, Kano F, Murata M (2008) Identification of PCBP2, a facilitator of IRES-mediated translation, as a novel constituent of Stress Granules and processing bodies. RNA 14:425–431

    Article  PubMed  CAS  Google Scholar 

  • Gallo CM, Munro E, Rasoloson D, Merritt C, Seydoux G (2008) Processing bodies and germ granules are distinct RNA granules that interact in C. elegans embryos. Dev Biol 323:76–87

    Article  PubMed  CAS  Google Scholar 

  • Gallois-Montbrun S, Kramer B, Swanson CM et al (2007) Antiviral protein APOBEC3G localizes to ribonucleoprotein complexes found in P bodies and Stress Granules. J Virol 81:2165–2178

    Article  PubMed  CAS  Google Scholar 

  • Gatfield D, Izaurralde E (2004) Nonsense-mediated messenger RNA decay is initiated by endonucleolytic cleavage in Drosophila. Nature 429:575–578

    Article  PubMed  CAS  Google Scholar 

  • Gavin A-C, Aloy P, Grandi P et al (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440:631–636

    Article  PubMed  CAS  Google Scholar 

  • Grousl T, Ivanov P, FrĂ˝dlová I et al (2009) Robust heat shock induces eIF2alpha-phosphorylation-independent assembly of Stress Granules containing eIF3 and 40S ribosomal subunits in budding yeast, Saccharomyces cerevisiae. J Cell Sci 122:2078–2088

    Article  PubMed  CAS  Google Scholar 

  • He W, Parker R (2001) The yeast cytoplasmic LsmI/Pat1p complex protects mRNA 3′ termini from partial degradation. Genetics 158:1445–1455

    PubMed  CAS  Google Scholar 

  • Hilgers V, Teixeira D, Parker R (2006) Translation-independent inhibition of mRNA deadenylation during stress in Saccharomyces cerevisiae. RNA 12:1835–1845

    Article  PubMed  CAS  Google Scholar 

  • Hoyle NP, Castelli LM, Campbell SG et al (2007) Stress-dependent relocalization of translationally primed mRNPs to cytoplasmic granules that are kinetically and spatially distinct from P-bodies. J Cell Biol 179:65–74

    Article  PubMed  CAS  Google Scholar 

  • Huang L, Mollet S, Souquere S et al (2011) Mitochondria associate with P-bodies and modulate MicroRNA-mediated RNA interference. J Biol Chem 286:24219–24230

    Article  PubMed  CAS  Google Scholar 

  • Ingelfinger D, Arndt-Jovin DJ, LĂĽhrmann R, Achsel T (2002) The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci. RNA 8:1489–1501

    PubMed  CAS  Google Scholar 

  • Jud MC, Czerwinski MJ, Wood MP et al (2008) Large P body-like RNPs form in C. elegans oocytes in response to arrested ovulation, heat shock, osmotic stress, and anoxia and are regulated by the major sperm protein pathway. Dev Biol 318:38–51

    Article  PubMed  CAS  Google Scholar 

  • Katahira J, Miki T, Takano K et al (2007) Nuclear RNA export factor 7 is localized in processing bodies and neuronal RNA granules through interactions with shuttling hnRNPs. Nucleic Acids Res 36:616–628

    Article  PubMed  CAS  Google Scholar 

  • Kedersha NL, Gupta M, Li W et al (1999) RNA-binding proteins TIA-1 and TIAR link the phosphorylation of eIF-2 alpha to the assembly of mammalian Stress Granules. J Cell Biol 147:1431–1442

    Article  PubMed  CAS  Google Scholar 

  • Kedersha N, Stoecklin G, Ayodele M et al (2005) Stress Granules and processing bodies are dynamically linked sites of mRNP remodeling. J Cell Biol 169:871–884

    Article  PubMed  CAS  Google Scholar 

  • Kilchert C, Weidner J, Prescianotto-Baschong C, Spang A (2010) Defects in the secretory pathway and high Ca2+ induce multiple P-bodies. Mol Biol Cell 21:2624–2638

    Article  PubMed  CAS  Google Scholar 

  • Kloc M, Etkin LD (2005) RNA localization mechanisms in oocytes. J Cell Sci 118:269–282

    Article  PubMed  CAS  Google Scholar 

  • Kshirsagar M, Parker R (2004) Identification of Edc3p as an enhancer of mRNA decapping in Saccharomyces cerevisiae. Genetics 166:729–739

    Article  PubMed  CAS  Google Scholar 

  • Ladomery M, Wade E, Sommerville J (1997) Xp54, the Xenopus homologue of human RNA helicase p54, is an integral component of stored mRNP particles in oocytes. Nucleic Acids Res 25:965–973

    Article  PubMed  CAS  Google Scholar 

  • Larimer FW, Hsu CL, Maupin MK, Stevens A (1992) Characterization of the XRN1 gene encoding a 5″–>3″ exoribonuclease: sequence data and analysis of disparate protein and mRNA levels of gene-disrupted yeast cells. Gene 120:51–57

    Article  PubMed  CAS  Google Scholar 

  • Lejeune F, Li X, Maquat LE (2003) Nonsense-mediated mRNA decay in mammalian cells involves decapping, deadenylating, and exonucleolytic activities. Mol Cell 12:675–687

    Article  PubMed  CAS  Google Scholar 

  • Leung AKL, Calabrese JM, Sharp PA (2006) Quantitative analysis of Argonaute protein reveals microRNA-dependent localization to Stress Granules. Proc Natl Acad Sci U S A 103:18125–18130

    Article  PubMed  CAS  Google Scholar 

  • Lian SL, Li S, Abadal GX et al (2009) The C-terminal half of human Ago2 binds to multiple GW-rich regions of GW182 and requires GW182 to mediate silencing. RNA 15:804–813

    Article  PubMed  CAS  Google Scholar 

  • Lin M-D, Fan S-J, Hsu W-S, Chou T-B (2006) Drosophila decapping protein 1, dDcp1, is a component of the oskar mRNP complex and directs its posterior localization in the oocyte. Dev Cell 10:601–613

    Article  PubMed  CAS  Google Scholar 

  • Liu J, Valencia-Sanchez MA, Hannon GJ, Parker R (2005) MicroRNA-dependent localization of targeted mRNAs to mammalian P-bodies. Nat Cell Biol 7:719–723

    Article  PubMed  CAS  Google Scholar 

  • Loschi M, Leishman CC, Berardone N, Boccaccio GL (2009) Dynein and kinesin regulate stress-granule and P-body dynamics. J Cell Sci 122:3973–3982

    Article  PubMed  CAS  Google Scholar 

  • Lotan R, Bar-On VG, Harel-Sharvit L et al (2005) The RNA polymerase II subunit Rpb4p mediates decay of a specific class of mRNAs. Gene Dev 19:3004–3016

    Article  PubMed  CAS  Google Scholar 

  • Lykke-Andersen J (2002) Identification of a human decapping complex associated with hUpf proteins in nonsense-mediated decay. Mol Cell Biol 22:8114–8121

    Article  PubMed  CAS  Google Scholar 

  • Malys N, McCarthy JEG (2006) Dcs2, a novel stress-induced modulator of m7GpppX pyrophosphatase activity that locates to P bodies. J Mol Biol 363:370–382

    Article  PubMed  CAS  Google Scholar 

  • Meister G, Landthaler M, Peters L et al (2005) Identification of novel argonaute-associated proteins. Curr Biol 15:2149–2155

    Article  PubMed  CAS  Google Scholar 

  • Mitchell P, Tollervey D (2003) An NMD pathway in yeast involving accelerated deadenylation and exosome-mediated 3″–>5″ degradation. Mol Cell 11:1405–1413

    Article  PubMed  CAS  Google Scholar 

  • Mokas S, Mills JR, Garreau C et al (2009) Uncoupling Stress Granule assembly and translation initiation inhibition. Mol Biol Cell 20:2673–2683

    Article  PubMed  CAS  Google Scholar 

  • Mollet S, Cougot N, Wilczynska A et al (2008) Translationally repressed mRNA transiently cycles through Stress Granules during stress. Mol Biol Cell 19:4469–4479

    Article  PubMed  CAS  Google Scholar 

  • Muhlrad D, Decker CJ, Parker R (1994) Deadenylation of the unstable mRNA encoded by the yeast MFA2 gene leads to decapping followed by 5″–>3″ digestion of the transcript. Genes Dev 8:855–866

    Article  PubMed  CAS  Google Scholar 

  • Nakamura A, Amikura R, Hanyu K, Kobayashi S (2001) Me31B silences translation of oocyte-localizing RNAs through the formation of cytoplasmic RNP complex during Drosophila oogenesis. Development 128:3233–3242

    PubMed  CAS  Google Scholar 

  • Nathans R, Chu C-Y, Serquina AK et al (2009) Cellular microRNA and P bodies modulate ­host-HIV-1 interactions. Mol Cell 34:696–709

    Article  PubMed  CAS  Google Scholar 

  • Navarro RE, Shim EY, Kohara Y et al (2001) cgh-1, a conserved predicted RNA helicase required for gametogenesis and protection from physiological germline apoptosis in C. elegans. Development 128:3221–3232

    PubMed  CAS  Google Scholar 

  • Neef DW, Thiele DJ (2009) Enhancer of decapping proteins 1 and 2 are important for translation during heat stress in Saccharomyces cerevisiae. Mol Microbiol 73:1032–1042

    Article  PubMed  CAS  Google Scholar 

  • Nelson KK, Lemmon SK (1993) Suppressors of clathrin deficiency: overexpression of ubiquitin rescues lethal strains of clathrin-deficient Saccharomyces cerevisiae. Mol Cell Biol 13:521–532

    PubMed  CAS  Google Scholar 

  • Nissan T, Rajyaguru P, She M et al (2010) Decapping activators in Saccharomyces cerevisiae act by multiple mechanisms. Mol Cell 39:773–783

    Article  PubMed  CAS  Google Scholar 

  • Ohn T, Kedersha N, Hickman T et al (2008) A functional RNAi screen links O-GlcNAc modification of ribosomal proteins to Stress Granule and processing body assembly. Nat Cell Biol 10:1224–1231

    Article  PubMed  CAS  Google Scholar 

  • Ozgur S, Chekulaeva M, Stoecklin G (2010) Human Pat1b connects deadenylation with mRNA decapping and controls the assembly of processing bodies. Mol Cell Biol 30:4308–4323

    Article  PubMed  CAS  Google Scholar 

  • Parker R, Sheth U (2007) P bodies and the control of mRNA translation and degradation. Mol Cell 25:635–646

    Article  PubMed  CAS  Google Scholar 

  • Parker R, Song H (2004) The enzymes and control of eukaryotic mRNA turnover. Nat Struct Mol Biol 11:121–127

    Article  PubMed  CAS  Google Scholar 

  • Pilkington GR, Parker R (2008) Pat1 contains distinct functional domains that promote P-body assembly and activation of decapping. Mol Cell Biol 28:1298–1312

    Article  PubMed  CAS  Google Scholar 

  • Quaresma AJC, Bressan GC, Gava LM et al (2009) Human hnRNP Q re-localizes to cytoplasmic granules upon PMA, thapsigargin, arsenite and heat-shock treatments. Exp Cell Res 315:968–980

    Article  PubMed  CAS  Google Scholar 

  • Ramachandran V, Shah KH, Herman PK (2011) The cAMP-dependent protein kinase signaling pathway is a key regulator of P body foci formation. Mol Cell 43:973–981

    Article  PubMed  CAS  Google Scholar 

  • Reijns MAM, Alexander RD, Spiller MP, Beggs JD (2008) A role for Q/N-rich aggregation-prone regions in P-body localization. J Cell Sci 121:2463–2472

    Article  PubMed  CAS  Google Scholar 

  • Rendl LM, Bieman MA, Smibert CA (2008) S. cerevisiae Vts1p induces deadenylation-dependent transcript degradation and interacts with the Ccr4p-Pop2p-Not deadenylase complex. RNA 14:1328–1336

    Article  PubMed  CAS  Google Scholar 

  • Rother RP, Frank MB, Thomas PS (1992) Purification, primary structure, bacterial expression and subcellular distribution of an oocyte-specific protein in Xenopus. Eur J Biochem 206:673–683

    Article  PubMed  CAS  Google Scholar 

  • Savas JN, Makusky A, Ottosen S et al (2008) Huntington’s disease protein contributes to RNA-mediated gene silencing through association with Argonaute and P bodies. Proc Natl Acad Sci U S A 105:10820–10825

    Article  PubMed  CAS  Google Scholar 

  • Scheller N, Resa-Infante P, la Luna de S et al (2007) Identification of PatL1, a human homolog to yeast P body component Pat1. Biochim Biophys Acta 1773:1786–1792

    Google Scholar 

  • Schwartz DC, Parker R (1999) Mutations in translation initiation factors lead to increased rates of deadenylation and decapping of mRNAs in Saccharomyces cerevisiae. Mol Cell Biol 19:5247–5256

    PubMed  CAS  Google Scholar 

  • Schwartz DC, Parker R (2000) mRNA decapping in yeast requires dissociation of the cap binding protein, eukaryotic translation initiation factor 4E. Mol Cell Biol 20:7933–7942

    Article  PubMed  CAS  Google Scholar 

  • Segal SP, Dunckley T, Parker R (2006) Sbp1p affects translational repression and decapping in Saccharomyces cerevisiae. Mol Cell Biol 26:5120–5130

    Article  PubMed  CAS  Google Scholar 

  • Sheth U, Parker R (2003) Decapping and decay of messenger RNA occur in cytoplasmic processing bodies. Science 300:805–808

    Article  PubMed  CAS  Google Scholar 

  • Sheth U, Parker R (2006) Targeting of aberrant mRNAs to cytoplasmic processing bodies. Cell 125:1095–1109

    Article  PubMed  CAS  Google Scholar 

  • Squirrell JM, Eggers ZT, Luedke N et al (2006) CAR-1, a protein that localizes with the mRNA decapping component DCAP-1, is required for cytokinesis and ER organization in Caenorhabditis elegans embryos. Mol Biol Cell 17:336–344

    Article  PubMed  CAS  Google Scholar 

  • Stalder L, Muhlemann O (2009) Processing bodies are not required for mammalian nonsense-mediated mRNA decay. RNA 15:1265–1273

    Article  PubMed  CAS  Google Scholar 

  • Stoecklin G, Mayo T, Anderson P (2006) ARE-mRNA degradation requires the 5″-3″ decay ­pathway. EMBO Rep 7:72–77

    Article  PubMed  CAS  Google Scholar 

  • Stribinskis V, Ramos KS (2007) Rpm2p, a protein subunit of mitochondrial RNase P, physically and genetically interacts with cytoplasmic processing bodies. Nucleic Acids Res 35:1301–1311

    Article  PubMed  CAS  Google Scholar 

  • Sweet TJ, Boyer B, Hu W et al (2007) Microtubule disruption stimulates P-body formation. RNA 13:493–502

    Article  PubMed  CAS  Google Scholar 

  • Swetloff A, Conne B, Huarte J et al (2009) Dcp1-bodies in mouse oocytes. Mol Biol Cell 20:4951–4961

    Article  PubMed  CAS  Google Scholar 

  • Teixeira D, Parker R (2007) Analysis of P-body assembly in Saccharomyces cerevisiae. Mol Biol Cell 18:2274–2287

    Article  PubMed  CAS  Google Scholar 

  • Teixeira D, Sheth U, Valencia-Sanchez MA et al (2005) Processing bodies require RNA for ­assembly and contain nontranslating mRNAs. RNA 11:371–382

    Article  PubMed  CAS  Google Scholar 

  • Tharun S, Parker R (2001) Targeting an mRNA for decapping: displacement of translation factors and association of the Lsm1p-7p complex on deadenylated yeast mRNAs. Mol Cell 8:1075–1083

    Article  PubMed  CAS  Google Scholar 

  • Tharun S, He W, Mayes AE et al (2000) Yeast Sm-like proteins function in mRNA decapping and decay. Nature 404:515–518

    Article  PubMed  CAS  Google Scholar 

  • Tritschler F et al (2007) A divergent Sm fold in EDC3 proteins mediates DCP1 binding and P-body targeting. Mol Cell Biol 27:8600–8611

    Article  PubMed  CAS  Google Scholar 

  • Tritschler F, Braun JE, Motz C et al (2009) DCP1 forms asymmetric trimers to assemble into active mRNA decapping complexes in metazoa. Proc Natl Acad Sci U S A 106:21591–21596

    Article  PubMed  CAS  Google Scholar 

  • Tucker M, Valencia-Sanchez MA, Staples RR et al (2001) The transcription factor associated Ccr4 and Caf1 proteins are components of the major cytoplasmic mRNA deadenylase in Saccharomyces cerevisiae. Cell 104:377–386

    Article  PubMed  CAS  Google Scholar 

  • Unterholzner L, Izaurralde E (2004) SMG7 acts as a molecular link between mRNA surveillance and mRNA decay. Mol Cell 16:587–596

    Article  PubMed  CAS  Google Scholar 

  • Van Dijk E (2002) Human Dcp2: a catalytically active mRNA decapping enzyme located in specific cytoplasmic structures. EMBO J 21:6915–6924

    Article  PubMed  Google Scholar 

  • Weinmann L, Höck J, Ivacevic T et al (2009) Importin 8 is a gene silencing factor that targets argonaute proteins to distinct mRNAs. Cell 136:496–507

    Article  PubMed  CAS  Google Scholar 

  • Wichroski MJ, Robb GB, Rana TM (2006) Human retroviral host restriction factors APOBEC3G and APOBEC3F localize to mRNA processing bodies. PLoS Pathog 2:e41

    Article  PubMed  CAS  Google Scholar 

  • Wiederhold K, Passmore LA (2010) Cytoplasmic deadenylation: regulation of mRNA fate. Biochem Soc Trans 38:1531–1536

    Article  PubMed  CAS  Google Scholar 

  • Wilczynska A, Aigueperse C, Kress M, Dautry F, Weil D (2005) The translational regulator CPEB1 provides a link between dcp1 bodies and Stress Granules. J Cell Sci 118:981–992

    Article  PubMed  CAS  Google Scholar 

  • Wilhelm JE, Buszczak M, Sayles S (2005) Efficient protein trafficking requires trailer hitch, a ­component of a ribonucleoprotein complex localized to the ER in Drosophila. Dev Cell 9:675–685

    Article  PubMed  CAS  Google Scholar 

  • Yamashita A, Chang T-C, Yamashita Y et al (2005) Concerted action of poly(A) nucleases and decapping enzyme in mammalian mRNA turnover. Nat Struct Mol Biol 12:1054–1063

    Article  PubMed  CAS  Google Scholar 

  • Yang Z, Jakymiw A, Wood MR et al (2004) GW182 is critical for the stability of GW bodies expressed during the cell cycle and cell proliferation. J Cell Sci 117:5567–5578

    Article  PubMed  CAS  Google Scholar 

  • Yang W-H, Yu JH, Gulick T et al (2006) RNA-associated protein 55 (RAP55) localizes to mRNA processing bodies and Stress Granules. RNA 12:547–554

    Article  PubMed  CAS  Google Scholar 

  • Yoon J-H, Choi E-J, Parker R (2010) Dcp2 phosphorylation by Ste20 modulates Stress Granule assembly and mRNA decay in Saccharomyces cerevisiae. J Cell Biol 189:813–827

    Article  PubMed  CAS  Google Scholar 

  • Yu JH, Yang W-H, Gulick T et al (2005) Ge-1 is a central component of the mammalian cytoplasmic mRNA processing body. RNA 11:1795–1802

    Article  PubMed  CAS  Google Scholar 

  • Yu D, Tan AH-M, Hu X et al (2007) Roquin represses autoimmunity by limiting inducible T-cell co-stimulator messenger RNA. Nature 450:299–303

    Article  PubMed  CAS  Google Scholar 

  • Zeitelhofer M, Karra D, Macchi P et al (2008) Dynamic interaction between P-bodies and transport ribonucleoprotein particles in dendrites of mature hippocampal neurons. J Neurosci 28:7555–7562

    Article  PubMed  CAS  Google Scholar 

  • Zheng D, Ezzeddine N, Chen C-YA et al (2008) Deadenylation is prerequisite for P-body formation and mRNA decay in mammalian cells. J Cell Biol 182:89–101

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Molecular and Cell Biology, University of Arizona and Howard Hughes Medical Institute, Tucson, AZ, 85721, USA

    Saumya Jain & Roy Parker

  2. University of Colorado at Boulder, Boulder, CO, USA

    Saumya Jain & Roy Parker

Authors
  1. Saumya Jain
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Roy Parker
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Roy Parker .

Editor information

Editors and Affiliations

  1. College of Dentistry, Department of Oral Biology, University of Florida, Southwest Archer Road 1600, Gainesville, 32610, Florida, USA

    Edward K. L. Chan

  2. Dept. Medicine & Medical Biochemistry, University of Calgary, Hospital Drive NW., 3330, Calgary, T2N 4N1, Alberta, Canada

    Marvin J. Fritzler

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media New York

About this chapter

Cite this chapter

Jain, S., Parker, R. (2013). The Discovery and Analysis of P Bodies. In: Chan, E., Fritzler, M. (eds) Ten Years of Progress in GW/P Body Research. Advances in Experimental Medicine and Biology, vol 768. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-5107-5_3

Download citation

Publish with us

Policies and ethics

Search

Navigation