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Regulation of Gene Expression in Plants pp 148–188Cite as

Control of Gene Expression by mRNA Transport and Turnover

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Abstract

Newly synthesized mRNA is neither naked nor static. Transcription is coupled to the assembly of mRNPs (messenger ribonucleoprotein particles) so that RNA-binding factors which are recruited to active transcription sites are available for immediate construction of the mRNP complex. These factors specify the processing, export, subcellular location, and stability of the mRNA. Assembly of the mRNP proceeds in an orderly fashion beginning with the association of the cap-binding protein complex. This step is followed by the splicing-dependent assembly of proteins at the exon junctions of intron-containing genes and the addition of adaptor proteins to facilitate RNA export. In this way it can be said that transcription is physically and functionally coupled to the pre-mRNA processing events that lead to the final, export-competent mRNP. The relationships among these processes are summarized in Figure 6.1.

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References

  • Aguilera, A., 2005, Cotranscriptional mRNP assembly: from the DNA to the nuclear pore, Curr. Opin. Cell Biol. 17:242–250.

    PubMed  CAS  Google Scholar 

  • Allmang, C., Petfalski, E., Podtelejnikov, A., Mann, M., Tollervey, D., and Mitchell, P., 1999, The yeast exosome and human PM-Scl are related complexes of 3′→5′ exonucleases, Genes Dev. 13:2148–2158.

    PubMed  CAS  Google Scholar 

  • Amiri, A., Keiper, B.D., Kawasaki, I., Fan, Y., Kohara, Y., Rhoads, R.E., and Strome, S., 2001, An isoform of eIF4E is a component of germ granules and is required for spermatogenesis in C. elegans, Development 128:3899–3912.

    PubMed  CAS  Google Scholar 

  • Anantharaman, V., and Aravind, L., 2004, Novel conserved domains in proteins with predicted roles in eukaryotic cell-cycle regulation, decapping and RNA stability, BMC Genomics 5:45.

    PubMed  Google Scholar 

  • Anderson, P., and Kedersha, N., 2002, Stressful initiations, J. Cell Sci. 115:3227–3234.

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Anderson, J.S.J., and Parker, R., 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.

    PubMed  CAS  Google Scholar 

  • Arciga-Reys, L., Wootton, L., Kieffer, M., and Davies, B., 2006, UPF1 is required for nonsense-mediated mRNA decay (NMD) and RNAi in Arabidopsis, Plant J. 47:480–489.

    Google Scholar 

  • Atlas, R., Behar, L., Elliott, E., and Ginzburg, I., 2004, The insulin-like growth factor mRNA binding-protein IMP-1 and the Ras-regulatory protein G3BP associate with tau mRNA and HuD protein in differentiated P19 neuronal cells, J. Neurochem. 89:613–626.

    PubMed  CAS  Google Scholar 

  • Bailey-Serres, J., 1999, Selective translation of cytoplasmic mRNAs in plants. TRENDS Plant Sci. 4:142–148.

    PubMed  Google Scholar 

  • Bashkirov, V.I., Scherthan, H., Solinger, J.A., Buerstedde, J.M., and Heyer, W.D., 1997, A mouse cytoplasmic exoribonuclease (mXRN1p) with preference for G4 tetraplex substrates, J. Cell Biol. 136:761–773.

    PubMed  CAS  Google Scholar 

  • Belostotsky, D.A., 2003, Unexpected complexity of poly(A)-binding protein gene families in flowering plants. Three conserved lineages that are at least 200 million years old and possible auto-and cross-regulation, Genetics 163:311–319.

    PubMed  CAS  Google Scholar 

  • Belostotsky, D.A., and Meagher, R.B., 1993, Differential organ-specific expression of three poly(A)-binding-protein genes from Arabidopsis thaliana, Proc. Natl. Acad. Sci. USA 90:6686–6690.

    PubMed  CAS  Google Scholar 

  • Belostotsky, D.A., and Meagher, R.B., 1996, A pollen-, ovule-, and early embryospecific poly(A) binding protein from Arabidopsis complements essential function in yeast, Plant Cell 8:1261–1275.

    PubMed  CAS  Google Scholar 

  • Bertrand, E., Chartrand, P., Schaefer, M., Shenoy, S.M., Singer, R.H., and Long, R.M., 1998, Localization of ASH1 mRNA particles in living yeast, Mol. Cell 2:437–445.

    PubMed  CAS  Google Scholar 

  • Bhat, S., Tang, L., Krueger, A.D., Smith, C.L., Ford, S.R., Dickey, L.F., and Petracek, M.E., 2004, the Fed-1 (CAUU)4 element is a 5′ UTR dark-responsive mRNA instability element that functions independently of dark-induced polyribosome dissociation, Plant Mol. Biol. 56:761–773.

    PubMed  CAS  Google Scholar 

  • Bhattacharyya, S.N., Habermacher, R., Martine, U., Closs, E., and Filipowicz, W., 2006, Relief of microRNA-mediated translational repression in human cells subjected to stress, Cell 125:1111–1124.

    PubMed  CAS  Google Scholar 

  • Binder, R., Horowitz, J.A., Basilion, J.P., Koeller, D.M., Klausner, R.D., and Harford, J.B., 1994, Evidence that the pathway of transferrin receptor mRNA degradation involves an endonucleolytic cleavage within the 3 UTR and does not involve poly(A) tail shortening, EMBO J. 13:1969–1980.

    PubMed  CAS  Google Scholar 

  • Boeck, R., Tarun, Jr., S., Rieger, M., Deardorff, J.A., Müller-Auer, S., and Sachs, A.B., 1996, The yeast Pan2 protein is required for poly(A)-binding proteinstimulated poly(A)-nuclease activity, J. Biol. Chem., 271:432–438.

    PubMed  CAS  Google Scholar 

  • Boudonck, K., Dolan, L., and Shaw, P.J., 1999, The movement of coiled bodies visualized in living plant cells by the green fluorescent protein, Mol. Biol. Cell 10: 2297–2307.

    PubMed  CAS  Google Scholar 

  • Bouget, F.-Y., Gerttula, S., and Quatrano, R.S., 1996, Localization of actin mRNA during the establishment of cell polarity and early cell divisions in Fucus embryos, Plant Cell 8:189–201.

    PubMed  CAS  Google Scholar 

  • Bousquet-Antonelli, C., Presutti, C., and Tollervey, D., 2000, Identification of a regulated pathway for nuclear pre-mRNA turnover, Cell 102:765–775.

    PubMed  CAS  Google Scholar 

  • Bravo, J., Aguilar-Henonin, L., Olmedo, G., and Guzmán, P., 2005, four distinct classes of proteins as interaction partners of the PABC domain of Arabidopsis thaliana poly(A)-binding proteins, Mol. Gen. Genomics 272:651–665.

    CAS  Google Scholar 

  • Brendza, R.P., Serbus, L.R., Duffy, J.B., and Saxton, W.M., 2000, A function for kinesin I in the posterior transport of oskar mRNA and Staufen protein, Science 289:2120–2122.

    PubMed  CAS  Google Scholar 

  • Brumbaugh, K.M., Otterness, D.M., Geisen, C., Oliveira, V., Brognard, J., Li, X., Lejeune, F., Tibbetts, R.S., Maquat, L.E., and Abraham, R.T., 2004, The mRNA surveillance protein hSMG-1 functions in genotoxic stress response pathways in mammalian cells, Mol. Cell 14:585–598.

    PubMed  CAS  Google Scholar 

  • Bruno, I., and Wilkinson, M.F., 2006, P-bodies react to stress and nonsense, Cell 125:1036–1038.

    PubMed  CAS  Google Scholar 

  • Bubunenko, M., Kress, T.L., Vempati, U.D., Mowry, K.L., and King, M.L., 2002, A consensus RNA signal that directs germ layer determinants to the vegetal cortex of Xenopus oocytes, Dev. Biol. 248:82–92.

    PubMed  CAS  Google Scholar 

  • Cairrao, F., Arraiano, C., and Newbury, S., 2005, Drosophila gene tazman, an orthologue of the yeast exosome component Rrp44p/Dis3, is differentially expressed during development, Dev. Dyn. 232:733–737.

    PubMed  CAS  Google Scholar 

  • Chamot, D., and Kuhlemeier, C., 1992, Differential expression of genes encoding the hypusine-containing translation initiation factor, eIF-5A, in tobacco, Nucl. Acids Res. 20:665–669.

    PubMed  CAS  Google Scholar 

  • Chan, S.W., Henderson, I.R., and Jacobsen, S.E., 2005, Gardening the genome: DNA methylation in Arabidopsis thaliana, Nat. Rev. Genet. 6:351–360.

    PubMed  CAS  Google Scholar 

  • Chekanova, J.A., and Belostotsky, D.A., 2003, evidence that poly(A) binding protein has an evolutionarily conserved function in facilitating mRNA biogenesis and export, RNA 9:1476–1490.

    PubMed  CAS  Google Scholar 

  • Chekanova, J.A., Dutko, J.A., Mian, I.S., and Belostotsky, D.A., 2002, Arabidopsis thaliana exosome subunit AtRrp4p is a hydrolytic 3′→5′ exonuclease containing S1 and KH RNA-binding domains, Nucl. Acids Res. 30:695–700.

    PubMed  CAS  Google Scholar 

  • Chekanova, J.A., Shaw, R.J., and Belostotsky, D.A., 2001, Analysis of an essential requirement for the poly(A) binding protein function using cross-species complementation, Curr. Biol. 11:1207–1214.

    PubMed  CAS  Google Scholar 

  • Chekanova, J.A., Shaw, R.J., wills, M.A., and Belostotsky, D.A., 2000, Poly(A) tail-dependent exonuclease AtRrp41p from Arabidopsis thaliana rescues 5.8 S rRNA processing and mRNA decay defects of the yeast ski6 mutant and is found in an exosome-sized complex in plant and yeast cells, J. Biol. Chem. 275: 33158–33166.

    PubMed  CAS  Google Scholar 

  • Chen, C.Y., and 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.

    PubMed  CAS  Google Scholar 

  • Chen, X., 2004, A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development, Science 303:2022–2025.

    PubMed  CAS  Google Scholar 

  • Cheng, J., and Maquat, L.E., 1993, Nonsense codons can reduce the abundance of nuclear mRNA without affecting the abundance of pre-mRNA or the half-life of cytoplasmic mRNA, Mol. Cell. Biol. 13:1892–1902.

    PubMed  CAS  Google Scholar 

  • Choi, S.-B., Wang, C., Muench, D.G., Ozawa, K., Franceschi, V.R., Wu, Y., and Okita, T.W., 2000, Messenger RNA targeting of rice seed storage proteins to specific ER subdomains, Nature 407:765–767.

    PubMed  CAS  Google Scholar 

  • Chuong, S.D.X., Good, A.G., Taylor, G.J., Freeman, M.C., Moorhead, G.B.G., and Muench, D.G., 2004, Large-scale identification of tubulin-binding proteins provides insight on subcellular trafficking, metabolic channeling, and signaling in plant cells, Mol. Cell. Proteomics 3:970–983.

    PubMed  CAS  Google Scholar 

  • Ciaudo, C., Bourdet, A., Cohen-Tannoudji, M., Dietz, H.C., Rougeulle, C., and Avner, P., 2006, Nuclear mRNA degradation pathway(s) are implicated in Xist regulation and X chromosome inactivation, PLoS Genet. 2:874–881.

    CAS  Google Scholar 

  • Cioce, M., and Lamond, A.I., 2005, Cajal bodies: a long history of discovery, Annu. Rev. Cell. Dev. Biol. 21:105–131.

    PubMed  CAS  Google Scholar 

  • Colon-Ramos, D.A., Salisbury, J.L., Senders, M.A., Shenoy, S.M., Singer, R.H., and Garcia-Blanco, M.A., 2003, Asymmetric distribution of nuclear pore complexes and the cytoplasmic localization of beta2-tubulin mRNA in Chlamydomonas reinhardtii, Dev. Cell 4:941–952.

    PubMed  CAS  Google Scholar 

  • Costanzo, M.C., Crawford, M.E., Hirschman, J.E., Kranz, J.E., Olsen, P.. et al., 2001, YPD, PombePD and WormPD: Model organism volumes of the BioKnowledge library, an integrated resource for protein information, Nucl. Acids Res. 29:75–79.

    PubMed  CAS  Google Scholar 

  • Cougot, N., Babajko, S., and Seraphin, B., 2004, Cytoplasmic foci are sites of mRNA decay in human cells, J. Cell Biol. 165:31–40.

    PubMed  CAS  Google Scholar 

  • Couttet, P., Fromont-Racine, M., Steel, D., Pictet, R., and Grange, T., 1997, Messenger RNA deadenylation precedes decapping in mammalian cells, Proc. Nat. Acad. Sci. USA 94:5628–5633.

    PubMed  CAS  Google Scholar 

  • Crofts, A.J., Washida, H., Okita, T.W., Ogawa, M., Kumamaru, T., and Satoh, H., 2004, Targeting of proteins to endoplasmic reticulum-derived compartments in plants: The importance of RNA localization, Plant Physiol. 136:3414–3419.

    PubMed  CAS  Google Scholar 

  • Crofts, A.J., Washida, H., Okita, T.W., Satoh, M., Ogawa, M., Kumamaru, T., and Satoh, H., 2005, The role of mRNA and protein sorting in seed storage protein synthesis, transport, and deposition, Biochem. Cell Biol. 83:728–737.

    PubMed  CAS  Google Scholar 

  • Davis, B.M., McCurrach, M.E., Taneja, K.L., Singer, R.H., and Housman, D.E., 1997, Expansion of a CUG trinucleotide repeat in the 3′ untranslated region of myotonic dystrophy protein kinase transcripts results in nuclear retention of transcripts, Proc. Natl. Acad. Sci USA 94:7388–7393.

    PubMed  CAS  Google Scholar 

  • Dietz, H., 1998. Polishing the cutting edge of gems, Nat. Genet. 20:321–322.

    PubMed  CAS  Google Scholar 

  • Docquier, S., Tillemans, V., Deltour, R., and Motte, P., 2004, Nuclear bodies and compartmentalization of pre-mRNA splicing factors in higher plants, Chromosoma 112:255–266.

    PubMed  CAS  Google Scholar 

  • Doench, J.G., Petersen, C.P., and Sharp, P.A., 2003, siRNAs can function as miRNAs, Genes Dev. 17:438–442.

    PubMed  CAS  Google Scholar 

  • Doma, M.K., and Parker, R., 2006, Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation, Nature 440:561–564.

    PubMed  CAS  Google Scholar 

  • Dunyak, D.S., Everdeen, D.S., Albanese, J.G., and Quinn, C.L., 2002, Deletion of individual mRNA capping genes is unexpectedly not lethal to Candida albicans and results in modified mRNA cap structures, Eukaryotic Cell 1:1010–1020.

    PubMed  CAS  Google Scholar 

  • Eystathioy, T., Jakymiw, A., Chan, E.K., Seraphin, B., Cougot, N., and Fritzler, M.J., 2003, The GW182 protein colocalizes with mRNA degradation associated proteins hDcp1 and hLSm4 in cytoplasmic GW bodies, RNA 9:1171–1173.

    PubMed  CAS  Google Scholar 

  • Fagard, M., Boutet, S., Morel, J.-B., Bellini, C., and Vaucheret, H., 2000, AGO1, QDE-2, and RDE-1 are related proteins required for post-transcriptional gene silencing in plants, quelling in fungi, and RNA interference in animals, Proc. Nat. Acad. Sci. USA 97:11650–11654.

    PubMed  CAS  Google Scholar 

  • Farina, K.L., and Singer, R.H., 2002, The nuclear connection in RNA transport and localization, Trends Cell Biol. 12:466–472.

    PubMed  CAS  Google Scholar 

  • Fechir, M., Linker, K., Pautz, A., Hubrich, T., Forstermann, U., Rodriguez-Pascual, F., and Kleinert, H., 2005, Tristetraprolin regulates the expression of the human inducible nitric-oxide synthase gene, Mol. Pharmacol. 67:2148–2161.

    PubMed  CAS  Google Scholar 

  • Ferraiuolo, M.A., Basak, S., Dostie, J., Murray, E.L., Schoenberg, D.R., and Sonenberg, N., 2005, A role for the eIF4E-binding protein 4E-T in P-body formation and mRNA decay, J. Cell Biol. 170:913–924.

    PubMed  CAS  Google Scholar 

  • Forrest, K.M., and Gavis, E.R., 2003, Live imaging of endogenous RNA reveals a diffusion and entrapment mechanism for nanos mRNA localization in Drosophila, Curr. Biol. 13:1159–1168.

    PubMed  CAS  Google Scholar 

  • Frischmeyer, P.A., van Hoof, A., O’Donnell, K., Guerrerio, A.L., Parker, R., and Dietz, H.C., 2002, Mechanism that eliminates transcripts lacking termination codons, Science 295:2258–2261.

    PubMed  CAS  Google Scholar 

  • Fu, D., and Collins, K., 2006, Human telomerase and Cajal body ribonucleoproteins share a unique specificity of Sm protein association, Genes Dev. 20:531–536.

    PubMed  CAS  Google Scholar 

  • Gall, J.G., Bellini, M., Wu, Z., and Murphy, C., 1999, Assembly of the nuclear transcription and processing machinery: Cajal bodies (coiled bodies) and transcriptosomes, Mol. Biol. Cell 10:4385–4402.

    PubMed  CAS  Google Scholar 

  • Gallouzi, I.E., Brennan, C.M., Stenberg, M.G., Swanson, M.S., Eversole, A., Maizels, N., and Steitz, J.A., 2000, HuR binding to cytoplasmic mRNA is perturbed by heat shock, Proc. Natl. Acad. Sci. USA 97:3073–3078.

    PubMed  CAS  Google Scholar 

  • Gatfield, D., and Izaurralde, E., 2002, REF1/Aly and the additional exon junction complex proteins are dispensable for nuclear mRNA export, J. Cell. Biol. 159:579–588.

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Graham, A.C., Kiss, D.L., and Andrulis, E.D., 2006, Differential distribution of exosome subunits at the nuclear lamina and in cytoplasmic foci, Mol. Biol Cell 17:1399–1409.

    PubMed  CAS  Google Scholar 

  • Gueneau de Novoa, P., and Williams, K.P., 2004, The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts, Nucl. Acids Res. 32:D104–D108.

    PubMed  CAS  Google Scholar 

  • Hammell, C.M., Gross, S., Zenklusen, D., Heath, C.V., Stutz, F., Moore, C., and Cole, C.N., 2002, Coupling of termination, 3′ processing, and mRNA export, Mol. Cell. Biol. 22:6441–6457.

    PubMed  CAS  Google Scholar 

  • Hanauske-Abel, H.M., Slowinska, B., Zagulska, S., Wilson, R.C., Staiano-Coico, L., Hanauske, A.-R., McCaffrey, T., and Szabo, P., 1995, Detection of a sub-set of polysomal mRNAs associated with modulation of hypusine formation at the G1-S boundary: Proposal of a role for eIF-5A in onset of DNA replication, FEBS Lett. 366:92–98.

    PubMed  CAS  Google Scholar 

  • Han, Y., Yu, J., Guo, F., and Watkins, S.C., 2006, Polysomes are associated with microtubules in fertilized eggs of Chinese pine (Pinus tabulaeformis), Protoplasma 227:223–227.

    PubMed  Google Scholar 

  • Hannon, G.J., 2002, RNA interference, Nature 418:244–251.

    PubMed  CAS  Google Scholar 

  • Hector, R.E., Nykamp, K.R., Dheur, S., Anderson, J.T., Non, P.J., Urbinati, C.R., Wilson, S.M., Minvielle-Sebastiz, L., and Swanson, M.S., 2002, Dual requirement for yeast hnRNP Nab2p in mRNA poly(A) tail length control and nuclear export, EMBO J. 21:1800–1810.

    PubMed  CAS  Google Scholar 

  • Hilleren, P., McCarthy, T., Rosbash, M., Parker, R., and Jensen, T.H., 2001, Quality control of mRNA 3′ end processing is linked to the nuclear exosome, Nature 413:538–542.

    PubMed  CAS  Google Scholar 

  • Hilson, P., Carroll, K.L., and Masson, P.H., 1993, Molecular characterization of PAB2, a member of the multigene family coding for poly(A)-binding proteins in Arabidopsis thaliana, Plant Physiol. 103:525–533.

    PubMed  CAS  Google Scholar 

  • Hollien, J., and Weissman, J. S., 2006, Decay of endoplasmic reticulum-localized mRNAs during the unfolded protein response, Science 313:104–107.

    PubMed  CAS  Google Scholar 

  • Hori, H., and Watanabe, Y., 2005, UPF3 suppresses aberrant spliced mRNA in Arabidopsis, Plant J. 43:530–540.

    PubMed  CAS  Google Scholar 

  • Hua, Y., and Zhou, J., 2004, Survival motor neuron protein facilitates assembly of stress granules, FEBS Lett. 572:69–74.

    PubMed  CAS  Google Scholar 

  • Huang, Y., and Steitz, J.A., 2001, Splicing factors SRp20 and 9G8 promote the nucleocytoplasmic export of mRNA, Mol. Cell 7:899–905.

    PubMed  CAS  Google Scholar 

  • Huttelmaier, S., Zenklusen, D., Lederer, M., Dictenberg, J., Lorenz, M., Meng, X., Bassell, G.J., Condeelis, J., and Singer, R.H., 2005, Spatial regulation of beta-actin translation by Src-dependent phosphorylation of ZBP1, Nature 438:512–515.

    PubMed  Google Scholar 

  • Inada, T., and Aiba, H., 2005, Translation of aberrant mRNAs lacking a termination codon or with a shortened 3′-UTR is repressed after initiation in yeast, EMBO J. 24:1584–1595.

    PubMed  CAS  Google Scholar 

  • Ingelfinger, D., Amdt-Jovin, D.J., Luhrmann, R., and Achsel, T., 2002, The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrn1 in distinct cytoplasmic foci, RNA 8:1489–1501.

    PubMed  CAS  Google Scholar 

  • Isshiki, M., Yamamoto, Y., Satoh, H., and Shimamoto, K., 2001, Nonsense-mediated decay of mutant waxy mRNA in rice, Plant Physiol. 125:1388–1395.

    PubMed  CAS  Google Scholar 

  • Jabri, E., 2005, P-bodies take a RISC, Nat. Struct. Mol. Biol. 12:564.

    PubMed  CAS  Google Scholar 

  • Jackson, R.J., 2005, Alternative mechanisms of initiating translation of mammalian mRNAs, Biochem. Soc. Trans. 33:1231–1241.

    PubMed  CAS  Google Scholar 

  • Jacob, Y., Seif, E., Paquet, P-O., and Lang, B.F., 2004, Loss of the mRNA-like region in mitochondrial tmRNAs of jakobids, RNA 10:605–614.

    PubMed  CAS  Google Scholar 

  • Jacobson, A., 2004, Regulation of mRNA decay: decapping goes solo, Mol. Cell. 12:1–2.

    Google Scholar 

  • Jady, B.E., Darzacq, X., Tucker, K.E., Matera, A.G., Bertrand, E., and Kiss, T., 2003, Modification of Sm small nuclear RNAs occurs in the nucleoplasmic Cajal body following import from the cytoplasm, EMBO J. 22:1878–1888.

    PubMed  CAS  Google Scholar 

  • Jang, S.Y., 2006, Internal initiation: IRES elements of picornaviruses and hepatitis c virus, Virus Res. 119:2–15.

    PubMed  CAS  Google Scholar 

  • Januschke, J., Gervais, L., Dass, S., Kaltschmidt, J.A., Lopec-Schier, H., Johnston, D.S., Brand, A.H., Roth, S., and Guichet, A., 2002, Polar transport in the Drosophila oocyte requires dynein and kinesin I cooperation, Curr. Biol. 12:1971–1981.

    PubMed  CAS  Google Scholar 

  • Jiang, Y., Xu, X-S., and Russell, J.E., 2006, A nucleolin-binding 3′ untranslated region element stabilizes β-globin mRNA in vivo, Mol. Cell. Biol. 26:2419–2429.

    PubMed  CAS  Google Scholar 

  • Jing, Q., Huang, S., Guth, S., Zarubin, T., Motoyama, A., Chen, J., Di Padova, F., Lin, S-C., Gram, H., and Han, J., 2005, Involvement of microRNA in AU-rich element-mediated mRNA instability, Cell 120:623–634.

    PubMed  CAS  Google Scholar 

  • Johnson, A.W., and Kolodner, R.D., 1995, Synthetic lethality of sep1 (xrn1) ski2 and sep1 (xrn1) ski3 mutants of Saccharomyces cerevisiae is independent of killer virus and suggests a general role for these genes in translation control, Mol Cell Biol, 15:2719–2727.

    PubMed  CAS  Google Scholar 

  • Jones-Rhoades, M.W., Bartel, D.P., and Bartel, B., 2006, MicroRNAs and their regulatory roles in plants, Ann. Rev. Plant Biol. 57:19–53.

    CAS  Google Scholar 

  • Joseph, B., Orlian, M., and Furneaux, H., 1998, p21 mRNA contains a conserved element in its 3′-untranslated region that is bound by Elav-like mRNA-stabilizing proteins, J. Biol. Chem. 273:20511–20516.

    PubMed  CAS  Google Scholar 

  • Kalyna, M., Lopato, S., and Barta, A., 2003, Ectopic expression of atRSZ33 reveals its function in splicing and causes pleiotropic changes in development, Mol. Biol. Cell 14:3565–3577.

    PubMed  CAS  Google Scholar 

  • Kao, T.H., and Tsukamoto, T., 2004, The molecular and genetic bases of S-Rnase-based self-incompatibility, Plant Cell 16:Suppl:S72–S83.

    PubMed  CAS  Google Scholar 

  • Kedersha, N., and Anderson, P., 2002, Stress granules: sites of mRNA triage that regulate mRNA stability and translatability, Biochem. Soc. Trans. 30:963–969.

    PubMed  CAS  Google Scholar 

  • Kedersha, N., Chen, S., Gilks, N., Li, W., Miller, I.J., Stahl, J., and Anderson, P., 2002, Evidence that ternary complex (eIF2-GTP-tRNA(i)(Met))-deficient preinitiation complexes are core constituents of mammalian stress granules, Mol. Biol. Cell 13:195–210.

    PubMed  CAS  Google Scholar 

  • Kedersha, N.L., Gupta, M., Li, W., Miller, I., and Anderson, P., 1999, RNA-binding proteins TIA-1 and TIAR link the phosphorylation of eIF-2a to the assembly of mammalian stress granules, J. Cell Biol. 147:1431–1441.

    PubMed  CAS  Google Scholar 

  • Kedersha, N., Stoecklin, G., Ayodele, M., Yacono, P., Lykke-Andersen, J., Fritzler, M.J., Scheuner, D., Kaufman, R.J., Golan, D.E., and Anderson, P., 2005, Stress granules and processing bodies are dynamically linked sites of mRNP remodeling, J. Cell Biol. 169:871–884.

    PubMed  CAS  Google Scholar 

  • Keene, J.D., and Tenenbaum, S.A., 2002, Eukaryotic mRNPs may represent posttranscriptional operons, Mol. Cell 9:1161–1167.

    PubMed  CAS  Google Scholar 

  • Keiler, K.C., Waller, P.R., and Sauer, R.T., 1996, Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA, Science 271:990–993.

    PubMed  CAS  Google Scholar 

  • Kessler, M.M., Henry, M.F., Shen, E., Zhao, J., Gross, S., Silver, P.A., and Moore, C.L., 1997, Hrp1, a sequence-specific RNA-binding protein that shuttles between the nucleus and the cytoplasm, is required for mRNA 3′-end formation in yeast, Genes Dev. 11:2545–2556.

    PubMed  CAS  Google Scholar 

  • Kindler, S., Wang, H., Richter, D., and Tiedge, H., 2005, RNA transport and local control of translation, Annu. Rev. Cell Dev. Biol. 21:223–245.

    PubMed  CAS  Google Scholar 

  • Klyachko, N.L., 2005, The cytoskeleton and intracellular motility in plants, Russian J. Plant Physiol. 52:786–795.

    Google Scholar 

  • Korner, C.G., Wormington, M., Muckenthaler, M., Schneider, S., Dehlin, E. and Wahle, E., 1998, The deadenylating nuclease (DAN) is involved in poly(A) tail removal during the meiotic maturation of Xenopus oocytes, EMBO J. 17:5427–5437.

    PubMed  CAS  Google Scholar 

  • Kosik, K.S., and Krichevsky, A.M., 2002, The message and the messenger: delivering RNA in neurons, Sci. STKE. 126:pe16.

    Google Scholar 

  • Kozak, M., 2005, A second look at cellular mRNA sequences said to function as internal ribosome entry sites, Nucl. Acids Res. 33:6593–6602.

    PubMed  CAS  Google Scholar 

  • Krichevsky, A.M., and Kosik, K.S., 2001, Neuronal RNA granules: a link between RNA localization and stimulation-dependent translation, Neuron, 32:683–696.

    PubMed  CAS  Google Scholar 

  • Lai, W.S., Carballo, E., Strum, J.R., Kennington, E.A., Phillips, R.S. and Blackshear, P.J., 1999, Evidence that tristetraprolin binds to AU-rich elements and promotes the deadenylation and destabilization of tumor necrosis factor alpha mRNA, Mol. Cell. Biol. 19:4311–4323.

    PubMed  CAS  Google Scholar 

  • Lall, S., Piano, F., and Davis, R.E., 2005, Caenorhabditis elegans decapping proteins: localization and functional analysis of Dcp1, Dcp2, and DcpS during embryogenesis, Mol. Biol. Cell 16:5880–5890.

    PubMed  CAS  Google Scholar 

  • Lawrence, C.J., Morris, N.R., Meagher, R.B., and Dawe, R.K., 2001, Dyneins have run their course in plant lineage, Traffic, 2:362–363.

    PubMed  CAS  Google Scholar 

  • Lazar, G., Schaal, T., Maniatis, T., and Goodman, H.M., 1995, Identification of a plant serine-arginine-rich protein similar to the mammalian splicing factor SF2/ASF, Proc. Natl. Acad. Sci. USA 92:7672–7676.

    PubMed  CAS  Google Scholar 

  • Leatherman, J.L., and Jongens, T.A., 2003, Transcriptional silencing and translational control: key features of early germline development, Bioessays, 25:326–335.

    PubMed  CAS  Google Scholar 

  • Lee, T.I., Causton, H.C., Holstege, F.C., Shen, W.C., Hannett, N., Jennings, E.G., Winston, F., Green, M.R., Young, R.A., 2000, Redundant roles for the TFIID and SAGA complexes in global transcription, Nature 405:701–704.

    PubMed  CAS  Google Scholar 

  • Lee, Y.R.J. and Liu, B., 2004, Cytoskeletal motors in Arabidopsis. Sixty-one kinesins and seventeen myosins, Plant Physiol. 136:3877–3883.

    PubMed  CAS  Google Scholar 

  • Le Hir, H., Gatfield, D., Izaurralde, E., and Moore, M.J., 2001, The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay, EMBO J. 20:4987–4997.

    PubMed  Google Scholar 

  • Le Hir, H., Izaurralde, E., Maquat, L.E., and Moore, M.J., 2000a, The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions, EMBO J. 19:6860–6869.

    PubMed  Google Scholar 

  • Le Hir, H., Moore, M.J., and Maquat, L.E., 2000b, Pre-mRNA splicing alters mRNP composition: evidence for stable association of proteins at exon-exon junctions, Genes Dev. 14:1098–1108.

    PubMed  Google Scholar 

  • Lei, E.P., Krebber, H., and Silver, P.A., 2001, Messenger RNAs are recruited for nuclear export during transcription, Genes Dev. 15:1771–1782.

    PubMed  CAS  Google Scholar 

  • Lejeune, F., Ishigaki, Y., Li, X., and Maquat, L.E., 2002, The exon junction complex is detected on CBP80-bound but not eIF4E-bound mRNA in mammalian cells: dynamics of mRNP remodeling, EMBO J, 21:3536–3545.

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Lemaire, R., Prasad, J., Kashima, T., Gustafson, J., Manley, J.L., and Lafyatis, R., 2002, Stability of a PKCI-1-related mRNA is controlled by the splicing factor ASF/SF2: a novel function for SR proteins, Genes Dev. 16:594–607.

    PubMed  CAS  Google Scholar 

  • Li, C.F., Pontes, O., El-Shami, M., Henderson, I.R., Bematavichute, Y.V., Chan, S.WL., Lagrange, T., Pikaard, C.S., and Jacobsen, S.E., 2006, An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana, Cell 126:93–106.

    PubMed  CAS  Google Scholar 

  • Lieb, B., Carl, M., Hock, R., Gebauer, D., and Scheer, U., 1998, Identification of a novel mRNA-associated protein in oocytes of Pleurodeles waltl and Xenopus laevis, Exp. Cell Res. 245:272–281.

    PubMed  CAS  Google Scholar 

  • Linder, P., and Stutz, F., 2001, mRNA export: traveling with DEAD box proteins, Curr. Biol. 11:R961–R963.

    PubMed  CAS  Google Scholar 

  • Liu, J., Valencia-Sanchez, M.A., Hannon, G.J., and Parker, R., 2005, MicroRNAdependent localization of targeted mRNAs to mammalian P-bodies, Nat. Cell Biol. 7:719–723.

    PubMed  CAS  Google Scholar 

  • Long, R.M., and McNally, M.T., 2003, mRNA decay:X (XRN1) marks the spot. Mol. Cell. 11:1126–1128.

    PubMed  CAS  Google Scholar 

  • Lopato, S., Gattoni, R., Fabini, G., Stevenin, J., and Barta, A., 1999, A novel family of plant splicing factors with Zn knuckle motif: examination of RNA binding and splicing activities, Plant Mol. Biol. 39:761–773.

    PubMed  CAS  Google Scholar 

  • Lopato, S., Mayeda, A., Krainer, A.R., and Barta, A., 1996, Pre-mRNA splicing in plants: characterization of Ser/Arg splicing factors, Proc. Natl. Acad. Sci. USA 93:3074–3079.

    PubMed  CAS  Google Scholar 

  • Lorković, Z.J., and Barta, A., 2002, Genome analysis: RNA recognition motif (RRM) and K homology (KH) domain RNA-binding proteins from the flowering plant Arabidopsis thaliana, Nucl. Acids Res. 30:623–635.

    PubMed  Google Scholar 

  • Losson, R., and Lacroute, F., 1979, Interference of nonsense mutations with eukaryotic messenger mRNA stability, Proc. Natl. Acad. Sci. USA 76:5134–5137.

    PubMed  CAS  Google Scholar 

  • Mangus, D.A., Evans, M.C., and Jacobson, A., 2003, Poly(A)-binding proteins: multifunctional scaffolds for the post-transcriptional control of gene expression, Genome Biol. 4:223.1–223.14.

    Google Scholar 

  • Maniatis, R., and Reed, R., 2002, An extensive network of coupling among gene expression machines, Nature 416:499–506.

    PubMed  CAS  Google Scholar 

  • Mansfield, S.G., and Briarty, L.G., 1991, Early embryogenesis in Arabidopsis thaliana. II. The developing embryo, Can. J. of Bot. 69:461–476.

    Google Scholar 

  • Maquat, L.E., and Li, X., 2001, Mammalian heat shock p70 and histone H4 transcripts, which derive from naturally intronless genes, are immune to nonsense-mediated decay, RNA 7:445–456.

    PubMed  CAS  Google Scholar 

  • Maquat, L.E., 2004, Nonsense-mediated mRNA decay: Splicing, translation and mRNP dynamics. Nat. Rev. Mol. Cell Biol. 5:89–99.

    PubMed  CAS  Google Scholar 

  • Marshall, N.F., Peng, J., Xie, Z., and Price, D.H., 1996, Control of RNA polymerase II elongation potential by a novel carboxyl-terminal domain kinase, J. Biol. Chem. 271:27176–27183.

    PubMed  CAS  Google Scholar 

  • Matera, A.G., 1999, Nuclear bodies: multifaceted subdomains of the interchromatin space, Trends Cell Biol. 9:302–309.

    PubMed  CAS  Google Scholar 

  • Mehlin, H., Daneholt, B., and Skoglund, U., 1992, Translocation of a specific premessenger ribo-nucleoprotein particle through the nuclear pore studies with electron microscope tomography, Cell, 69:605–613.

    PubMed  CAS  Google Scholar 

  • Mendell, J.T., Sharifi, N.A., Meyers, J.L., Martinez-Murillo, F., and Dietz, H.C., 2004, Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise, Nat. Genet. 36:1073–1078.

    PubMed  CAS  Google Scholar 

  • Mignone, F., Gissi, C., Liuni, S., and Pesole, G., 2002, Untranslated regions of mRNAs, Genome Biology 3:0004.1–0004.10.

    Google Scholar 

  • Millard, S.S., Vidal, A., Markus, M., and Koff, A., 2000, A U-rich element in the 5′ untranslated region is necessary for the translation of p27 mRNA, Mol. Cell. Biol. 20:6947–6959.

    Google Scholar 

  • Misteli, T., 2000, Cell biology of transcription and pre-mRNA splicing: nuclear architecture meets nuclear function, J. Cell Sci. 113:1841–1849.

    PubMed  CAS  Google Scholar 

  • Mitchell, P., and Tollervey, D., 2003, An NMD pathway in yeast involving accelerated de-adenylation and exosome-mediated 3′–5′ degradation, Mol. Cell 11:1405–1413.

    PubMed  CAS  Google Scholar 

  • Mitrovich, Q.M., and Anderson, P., 2005, mRNA surveillance of expressed pseudogenes in C. elegans, Curr. Biol. 15:963–967.

    PubMed  CAS  Google Scholar 

  • Moore, M., 2005, From birth to death: The complex lives of eukaryotic mRNAs, Science, 309:1514–1518.

    PubMed  CAS  Google Scholar 

  • Moreno Diaz de la Espina, S., Sanchez-Pina, M.A., Risueño, M.C., Medina, F.J., and Fernández-Gómez, M.E., 1980, The role of plant coiled bodies in the nuclear RNA metabolism, Electron Microsc. 2:240–241.

    Google Scholar 

  • Moriarty, P.M., Reddy, C.C., and Maquat, L.E., 1998, Selenium deficiency reduces the abundance of mRNA for Se-dependent glutathione peroxidase 1 by a UGA-dependent mechanism likely to be nonsense codon-mediated decay of cytoplasmic mRNA, Mol. Cell. Biol. 18:2932–2939.

    PubMed  CAS  Google Scholar 

  • Moteki, S., and Price, D., 2002, Functional coupling of capping and transcription of mRNA, Mol. Cell 10:599–609.

    PubMed  CAS  Google Scholar 

  • Muhlrad, D., and Parker, R., 1999, Aberrant mRNAs with extended 3′ UTRs are substrates for rapid degradation by mRNA surveillance, RNA 5:1299–1307.

    PubMed  CAS  Google Scholar 

  • Mukherjee, D., Gao, M., O’Connor, J.P., Raijmakers, R., Pruijn, G., Lutz, C.S., and Wilusz, J., 2002, The mammalian exosome mediates the efficient degradation of mRNAs that contain AU-rich elements, EMBO J. 21:165–174.

    PubMed  CAS  Google Scholar 

  • Nagai, K., Oubridge, C., Ito, N., Avis, J., and Evans, P., 1995, The RNP domain — a sequence-specific RNA-binding domain involved in processing and transport of RNA, Trends Biochem. Sci. 20:235–240.

    PubMed  CAS  Google Scholar 

  • Navarro, R., and Blackwell, T.K., 2005, Requirement for P granules and meiosis for accumulation of the germline RNA helicase CGH-1, Genesis 42:172–180.

    PubMed  CAS  Google Scholar 

  • Neugebauer, K.M., 2002, On the importance of being co-transcriptional, J. Cell Sci. 115;3865-3871.

    Google Scholar 

  • Nott, A., Le Hir, H., and Moore, M.J., 2004, Splicing enhances translation in mammalian cells: an additional function of the exon junction complex, Genes Dev. 18:210–222.

    PubMed  CAS  Google Scholar 

  • Nover, L., K.-D., Scharf, and Neumann, D., 1983. Formation of cytoplasmic heat shock granules in tomato cell cultures and leaves, Mol. Cell. Biol. 3:1648–1655.

    PubMed  CAS  Google Scholar 

  • Nover, L., and Scharf, K.D., 1984, Synthesis, modification and structural binding of heat-shock proteins in tomato cell cultures, Eur. J. Biochem. 139:303–313.

    PubMed  CAS  Google Scholar 

  • Nover, L., Scharf, K.-D., and Neumann, D., 1989, Cytoplasmic heat shock granules are formed from precursor particles and are associated with a specific set of mRNAs, Mol. Cell. Biol. 9:1298–1308.

    PubMed  CAS  Google Scholar 

  • Okita, T.W., and Choi, S-B., 2002, mRNA localization in plants: targeting to the cell’s cortical region and beyond, Curr. Opin. Plant Biol. 5:553–559.

    PubMed  CAS  Google Scholar 

  • Okita, T.W., and Rogers, J.C., 1996, Compartmentation of proteins in the endomem-brane system of plant cells, Ann. Rev. Plant Physiol. & Plant Mol. Biol. 47:327–350.

    CAS  Google Scholar 

  • Oliveira, C.C., and McCarthy, J.E., 1995, The relationship between eukaryotic translation and mRNA stability: A short upstream open reading frame strongly inhibits translational initiation and greatly accelerates mRNA degradation in the yeast Saccharomyces cerevisiae, J. Biol. Chem. 270:8936–8943.

    PubMed  CAS  Google Scholar 

  • Onouchi, H., Nagami, Y., Haraguchi, Y., Nakamoto, M., Nishimura, Y., Sakurai, R., Nagao, N., Kawasake, D., Kadokura, Y., and Naito, S., 2005, Nascent peptide-mediated translation elongation arrest coupled with mRNA degradation in the CGS1 gene of Arabidopsis, Genes Dev. 19:1799–1810.

    PubMed  CAS  Google Scholar 

  • Orban, T.I., and Izaurralde, E., 2005, Decay of mRNAs targeted by RISC requires XRN1, the Ski complex and the exosome, RNA 11:459–469.

    PubMed  CAS  Google Scholar 

  • Ortega, J.L., Moguel-Esponda, S., Potenza, C., Conklin, C.F., Quintana, A., and Sengupta-Gopalan, C., 2006, The 3′ untranslated region of a soybean cytosolic glutamine synthetase (GS1) affects transcript stability and protein accumulation in transgenic alfalfa, Plant J. 45:832–846.

    PubMed  CAS  Google Scholar 

  • Palacios, I.M., 2002, RNA processing: splicing and the cytoplasmic localization of mRNA, Curr. Biol. 12:R50–R52.

    PubMed  CAS  Google Scholar 

  • Palanivelu, R., Belostotsky, D.A., and Meagher, R.B., 2000a. Arabidopsis thaliana poly (A) binding protein 2 (PAB2) functions in yeast translational and mRNA decay processes, Plant J. 22:187–198.

    PubMed  CAS  Google Scholar 

  • Palanivelu, R., Belostotsky, D.A., Meagher, R.B., 2000b, Conserved expression of Arabidopsis thaliana poly (A) binding protein 2 (PAB2) in distinct vegetative and reproductive tissues, Plant J. 22:199–210.

    PubMed  CAS  Google Scholar 

  • Park, J-W., Faure-Rabasse, S., Robinson, M.A., Desvoyes, B., and Scholthof, H.B., 2004, The multifunctional plant viral suppressor of gene silencing P19 interacts with itself and an RNA binding host protein, Virology 323:49–58.

    PubMed  CAS  Google Scholar 

  • Pelletier, J., and Sonenberg, N., 1988, Internal initiation translation of eukaryotic mRNA directed by a sequence derived from poliovirus RNA, Nature, 334:320–325.

    PubMed  CAS  Google Scholar 

  • Pendle, A.F., Clark, G.P., Boon, R., Lewandowska, D., Lam, Y.W., Andersen, J., Mann, M., Lamond, A.I., Brown, J.W., and Shaw, P.J., 2005, Proteomic analysis of the Arabidopsis nuclelolus suggests novel nucleolar functions, Mol. Biol. Cell 16:260–269.

    PubMed  CAS  Google Scholar 

  • Phillips, K., Kedersha, N., Shen, L., Blackshear, P.J., and Anderson, P., 2004. Arthritis suppressor genes TIA-1 and TTP dampen the expression of tumor necrosis factor α, cyclooxygenase 2, and inflammatory arthritis, Proc. Natl. Acad. Sci. USA 101:2011–2016.

    PubMed  CAS  Google Scholar 

  • Pillai, R.S., Bhattacharyya, S.N., Artus, C.G., Zoller, T., Cougot, N., Basyuk, E., Bertrand, E., and Filipowicz, W., 2005, Inhibition of translational initiation by Let-7 microRNA in human cells, Science 309:1573–1576.

    PubMed  CAS  Google Scholar 

  • Ping, Y-H., and Rana, T.M., 2001, DSIF and NELF interact with RNA polymerase II elongation complex and HIV-1 Tat stimulates P-TEFb-mediated phosphorylation of RNA polymerase II and DSIF during transcription elongation, J. Biol. Chem 276: 12951–12958.

    PubMed  CAS  Google Scholar 

  • Pisarev, A.V., Shirokikh, N.E., and Hellen, C.U., 2005, Translation initiation by factor-independent binding of eukaryotic ribosomes to internal ribosomal entry sites, Comptes Rendus. Biol. 328:589–605.

    CAS  Google Scholar 

  • Raghavan, A., Robison, R.L., McNabb, J., Miller, C.R., Williams, D.A., and Bohjanen, P.R., 2001, HuA and tristetraprolin are induced following T cell activation and display distinct but overlapping RNA binding specificities, J. Biol. Chem. 276:47958–47965.

    PubMed  CAS  Google Scholar 

  • Reddy, A.S.N., 2004, Plant serine/arginine-rich proteins and their role in pre-mRNA splicing, TRENDS in Plant Sci. 9:541–547.

    CAS  Google Scholar 

  • Reddy, A.S.N., and Day, I.S., 2001, Kinesins in the Arabidopsis genome: a comparative analysis among eukaryotes, BMC Genomics, 2:2.

    PubMed  CAS  Google Scholar 

  • Reinhart, B.J., Slack, F.J., Basson, M., Pasquinelli, A.E., Bettinger, J.C., Rougvie, A.E., Horvita, H.R., and Ruvkun, G., 2000, The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans, Nature 403:901–906.

    PubMed  CAS  Google Scholar 

  • Reverdatto, S.V., Dutko, J.A., Chekanova, J.A., Hamilton, D.A., and Belostotsky, D.A., 2006, mRNA deadenylation by PARN is essential for embryogenesis in higher plants, RNA 10:1200–1214.

    Google Scholar 

  • Ridley, S.P., Sommer, S.S., and Wickner, R.B., 1984, Superkiller mutations in Saccharomyces cerevisiae suppress exclusion of M2 double-stranded RNA by L-A-HN and confer cold sensitivity in the presence of M and L-A-HN, Mol Cell Biol. 4:761–770.

    PubMed  CAS  Google Scholar 

  • Rogers, N.D., Wang, Z., and Kiledjian, M., 2002, Characterization and purification of a mammalian endoribonuclease specific for the globin mRNA, J. Biol. Chem. 277:2597–2604.

    Google Scholar 

  • Rodriguez, C.M., Freire, M.A., Camilleri, C., and Robaglia, C., 1998, The Arabidopsis thaliana cDNAs coding for eIF4E and eIF(iso)4E are not functionally equivalent for yeast complementation and are differentially expressed during plant development, Plant J. 13:465–474.

    PubMed  CAS  Google Scholar 

  • Rosorius, O., Reichart, B., Kratzer, F., Heger, P., Dabauvalle, M.C., and Hauber, J., 1999, Nuclear pore localization and nucleocytoplasmic transport of eIF5A: evidence for direct interaction with the export receptor CRM1, J. Cell Sci. 112: 2369–2380.

    PubMed  CAS  Google Scholar 

  • Sachs, A.B., Davis, R.W., and Kornberg, R.D., 1987, A single domain of yeast poly(A)-binding protein is necessary and sufficient for RNA binding and cell viability, Mol. Cell Biol. 7:3268–3276.

    PubMed  CAS  Google Scholar 

  • Sanford, J.R., Gray, N.K., Beckmann, K., and Cáceres, J.F., 2004, A novel role for shuttling SR proteins in mRNA translation, Genes Dev. 18:755–768.

    PubMed  CAS  Google Scholar 

  • Saxena, S., Jonsson, Z.O., and Dutta, A., 2003, Small RNAs with imperfect match to endogenous mRNA repress translationzzz: Implications for off-target activity of small inhibitory RNA in mammalian cells, J. Biol. Chem. 278:44312–44319.

    PubMed  CAS  Google Scholar 

  • Scharf, K.D., Heider, H., Hohfeld, I., Lyck, R., Schmidt, E., and Nover, L., 1998, The tomato Hsf system: HsfA2 needs interaction with HsfA1 for efficient nuclear import and may be localized in cytoplasmic heat stress granules, Mol. Cell. Biol. 18:2240–2251.

    PubMed  CAS  Google Scholar 

  • Schisa, J.A., Pitt, J.N., and Priess, J.R., 2001, Analysis of RNA associated with P granules in germ cells of C. elegans adults, Development 128:1287–1298.

    PubMed  CAS  Google Scholar 

  • Schulz, R., and Jensen, W.A., 1968. Capsella embryogenesis: the egg, zygote and young embryo, Amer. J. Bot. 55:807–819.

    Google Scholar 

  • Schwab, R., Palatnik, J.F., Riester, M., Schommer, C., Schmid, M., and Weigel, D., 2005, Specific effects of microRNAs on the plant transcriptome, Dev. Cell 8:517–527.

    PubMed  CAS  Google Scholar 

  • Sen, G.L., and Blau, H.M., 2005, Argonaute 2/RISC resides in sites of mammalian mRNA decay known as cytoplasmic bodies, Nat. Cell Biol. 7:633–636.

    PubMed  CAS  Google Scholar 

  • Shaw, P.J., Beven, A.F., Leader, D.J., and Brown, J.W.S., 1998, Localization and processing from a polycistronic precursor of novel snoRNAs in maize, J. Cell Sci. 111:2121–2128.

    PubMed  Google Scholar 

  • Shaw, P.J., and Brown, J.W., 2004, Plant nuclear bodies, Curr. Opin. Plant Biol. 7:614–620.

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Shuman, S., 2000, Structure, mechanism, and evolution of the mRNA capping apparatus, Prog. Nucleic Acid Res. Mol. Biol. 66:1–40.

    CAS  Google Scholar 

  • Sigrist, S.J., Thiel, P.R., Reiff, D.F., Lachance, P.E., Lasko, P., and Schuster, C.M., 2000, Postsynaptic translation affects the efficacy and morphology of neuromuscular junctions, Nature 405:1062–1065.

    PubMed  CAS  Google Scholar 

  • Singer, R.H., 1993, RNA zipcodes for cytoplasmic addresses, Curr. Biol. 3:719-721.

    PubMed  CAS  Google Scholar 

  • Siomi, H., Matunis, M.J., Michael, W.M., and Dreyfuss, G., 1993, The premessenger RNA-binding K-protein contains a novel evolutionarily conserved motif, Nucl. Acids Res. 21:1193–1198.

    PubMed  CAS  Google Scholar 

  • Sleeman, J.E., and Lamond, A.I., 1999, Newly assembled snRNPs associate with coiled bodies before speckles, suggesting a nuclear snRNP maturation pathway, Curr. Biol. 9:1065–1074.

    PubMed  CAS  Google Scholar 

  • Smart, F.M., Edelman, G.M., and Vanderklish, P.W., 2003, BDNF induces translocation of initiation factor 4E to mRNA granules: evidence for a role of synaptic microfilaments and integrins, Proc. Natl. Acad. Sci. USA 100:14403–14408.

    PubMed  CAS  Google Scholar 

  • Souter, M., and Lindsey, K., 2000, Polarity and signaling in plant embryogenesis, J. Exp. Bot. 51:971–983.

    PubMed  CAS  Google Scholar 

  • Stevens, A., 2001, 5′-exoribonuclease 1:XRN1, Methods Enzymol. 342:251–259.

    PubMed  CAS  Google Scholar 

  • St. Johnston, D., Brown, N.H., Gall, J.G., and Jantsch, M., 1992, A conserved double-stranded RNA-binding domain, Proc. Natl. Acad. Sci. USA 89:10979–10983.

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Stoecklin, G., Stubbs, T., Kedersha, N., Blackwell, T.K., and Anderson, P., 2004, MK2-induced tristetraprolin:14-3-3 complexes prevent stress granule association and ARE-mRNA decay, EMBO J. 23:1313–1324.

    PubMed  CAS  Google Scholar 

  • Storozhenko, S., Inze, D., Van Montagu, M., and Kushnir, S., 2001. Arabidopsis coactivator ALY-like proteins, DIP1 and DIP2, interact physically with the DNA-binding domain of the Zn-finger poly (ADP-ribose) polymerase, J. Exp. Bot. 52:1375–1380.

    PubMed  CAS  Google Scholar 

  • Strasser, K., and Hurt, E., 2000, Yra1p, a conserved nuclear RNA-binding protein, interacts directly with Mex67p and is required for mRNA export, EMBO J. 19:410–420

    PubMed  CAS  Google Scholar 

  • Stuger, R., Ranostaj, S., Materna, T., and Forreiter, C., 1999, Messenger RNAbinding properties of nonpolysomal ribonucleoproteins from heat-stressed tomato cells, Plant Physiol. 120:23–32.

    PubMed  CAS  Google Scholar 

  • Subramanian, A.R., 1983, Structure and functions of ribosomal protein S1, Prog. Nucl. Acid Res. Mol. Biol. 28:101–142.

    CAS  Google Scholar 

  • Sudarsan, N., Barrick, J.E., and Breaker, R.R., 2003, Metabolite-binding RNA domains are present in the genes of eukaryotes, RNA 9:644–647.

    PubMed  CAS  Google Scholar 

  • Sunohara, R., Jojima, K., Tagami, H., Inada, T., and Aiba, H., 2004, Ribosome stalling during translation elongation induces cleavage of mRNA being translated in Escherichia coli, J. Biol. Chem. 279:15368–15375.

    PubMed  CAS  Google Scholar 

  • Tekotte, H., and Davis, I., 2002, Intracellular mRNA localization: motors move messages, Trends Genet. 18:636–642.

    PubMed  CAS  Google Scholar 

  • Thakurta, A.G., Ho Yoon, J., and Dhar, R., 2002. Schizosaccharomyces pombe spPABP, a homologue of Saccharomyces cerevisiae Pab1p, is a non-essential, shuttling protein that facilitates mRNA export, Yeast 19:803–810.

    PubMed  Google Scholar 

  • Thomas, M.G., Tosar, L.J., Loschi, M., Pasquini, J.M., Correale, J., Kindler, S., and Boccaccio, G.L., 2005, Staufen recruitment into stress granules does not affect early mRNA transport in oligodendrocytes, Mol. Biol. Cell 16:405–420.

    PubMed  CAS  Google Scholar 

  • Thompson, J.E., Hopkins, M.T., Taylor, C., and Wang, T-W., 2004, Regulation of senescence by eukaryotic translation initiation factor 5A: implications for plant growth and development, TRENDS Plant Sci. 9:174–179.

    PubMed  CAS  Google Scholar 

  • Timchenko, N.A., Welm, A.L., Lu, X., and Timchenko, L.T., 1999, CUG repeat binding protein (CUGBP1) interacts with the 5 region of C/EBP mRNA and regulates translation of C/EBP isoforms, Nucl. Acids Res. 27:4517–4525.

    PubMed  CAS  Google Scholar 

  • Tourriere, H., Chebli, K., Zekri, L., Courselaud, B., Blanchard, J.M., Bertrand, E., and Tazi, J., 2003, The RasGAP-associated endoribonuclease G3BP assembles stress granules, J. Cell Biol. 160:823–831.

    PubMed  CAS  Google Scholar 

  • Uhrig, J.F., Canto, T., Marshall, D., and MacFarlane, S.A., 2004, Relocalization of nuclear ALY proteins to the cytoplasm by the tomato bushy stunt virus P19 pathogenicity protein, Plant Physiol. 135:2411–2423.

    PubMed  CAS  Google Scholar 

  • Van De Bor, V., and Davis, I., 2004, mRNA localization gets more complex, Curr. Opin. Cell Biol. 16:300–307.

    PubMed  Google Scholar 

  • van Hoof, A., Frischmeyer, P.A., Dietz, H.C., and Parker, R., 2002, Exosome-mediated recognition and degradation of mRNAs lacking a termination codon, Science 295:2262–2264.

    PubMed  Google Scholar 

  • van Hoof, A., and Green, P.J., 1996, Premature nonsense codons decrease the stability of phytohemagglutinin mRNA in a position-dependent manner, Plant J. 10:415–424.

    PubMed  Google Scholar 

  • Vinciguerra, P., and Stutz, F., 2004, mRNA export: an assembly line from genes to nuclear pores, Curr. Opin. Cell Biol. 16:285–292.

    PubMed  CAS  Google Scholar 

  • Voelker, T.A., Moreno, J., and Chrispeels, M.J., 1990, Expression analysis of a pseudogene in transgenic tobacco: a frameshift mutation prevents mRNA accumulation, Plant Cell 2:255–261.

    PubMed  CAS  Google Scholar 

  • Volpe, T.A., Kidner, C., Hall, I.M., Teng, G., Grewal, S.I., and Martienssen, R.A., 2002, Regulation of heterochromatic silencing and histone He lysine-9 methylation by RNAi, Science 297:1833–1837.

    PubMed  CAS  Google Scholar 

  • Wang, T-W., Lu, L., Wang, D., and Thompson, J.E., 2001, Isolation and characterization of senescence-induced cDNAs encoding deoxyhypusine synthase and eukaryotic translation initiation factor 5A from tomato, J. Biol. Chem. 276:17541–17549.

    PubMed  CAS  Google Scholar 

  • Weischenfeldt, J., Lykke-Andersen, J., and Porse, B., 2005, Messenger RNA surveillance: Neutralizing natural nonsense, Curr. Biol. 15:R559–R562.

    PubMed  CAS  Google Scholar 

  • Wickens, M., Bernstein, D.S., Kimble, J., and Parker, R., 2002, A PUF family portrait: 3′ UTR regulation as a way of life, Trends Genet. 18:150–157.

    PubMed  CAS  Google Scholar 

  • Wiegand, H.L., Lu, S., and Cullen, B.R., 2003, Exon junction complexes mediate the enhancing effect of splicing on mRNA expression, Proc. Natl. Acad. Sci. USA 100:11327–11332.

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Wilkie, G.S., and Davis, I., 2001. Drosophila wingless and pair-rule transcripts localize apically by dynein-mediated transport of RNA particles, Cell 105:209–219.

    PubMed  CAS  Google Scholar 

  • Williams, K.P., 2002, Descent of a split RNA, Nucl. Acids Res. 30:2025–2030.

    PubMed  CAS  Google Scholar 

  • Wilusz, C.J., and Wilusz, J., 2004, Bringing the role of mRNA decay in the control of gene expression into focus, TRENDS in Genet. 20:491–497.

    CAS  Google Scholar 

  • Winkler, W., Nahvi, A., and Breaker, R.R., 2002, Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression, Nature 419:952–956.

    PubMed  CAS  Google Scholar 

  • Yamamoto, Y., Sunohara, T., Jojima, K., Inada, T., and Aiba, H., 2003, SsrA-mediated trans-translation plays a role in mRNA quality control by facilitating degradation of truncated mRNAs, RNA 9:408–418.

    PubMed  CAS  Google Scholar 

  • Yekta, S., Shih, I.H., and Bartel, D.P., 2004, MicroRNA-directed cleavage of HOXB8 mRNA, Science 304:594–596.

    PubMed  CAS  Google Scholar 

  • Zhang, S., Ruiz-Echevarria, M.J., Quan, Y., and Peltz, S.W., 1995, Identification and characterization of a sequence motif involved in nonsense-mediated mRNA decay, Mol. Cell. Biol. 15:2231–2244.

    PubMed  CAS  Google Scholar 

  • Zhang, J., Sun, X., Qian, Y., LaDuca, J.P., and Maquat, L.E., 1998, At least one intron is required for the nonsense-mediated decay of triosephosphate isomerase mRNA: a possible link between nuclear splicing and cytoplasmic translation, Mol. Cell. Biol. 18:5272–5283.

    PubMed  CAS  Google Scholar 

  • Zhou, J.P., Yand, Z.J., Feng, J., Chi, S.H., Liu, C., and Ren, Z.L., 2006, [Cloning and analysis of a gene encoding wheat translation initiation factor, eIF5A], Yi Chuan 28:571–577 [article in Chinese].

    PubMed  CAS  Google Scholar 

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  1. Appalachian Fruit Research Station, USDA-ARS, 2217 Wiltshire Road, Kearneysville, WV, 25430, USA

    Carole L. Bassett

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    Carole L. Bassett

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Bassett, C.L. (2007). Control of Gene Expression by mRNA Transport and Turnover. In: Bassett, C.L. (eds) Regulation of Gene Expression in Plants. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-35640-2_6

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