Skip to main content
Log in

mRNA Degradation Machinery in Plants

  • Review
  • Published:
Journal of Plant Biology Aims and scope Submit manuscript

Abstract

Control of gene expression is exerted by multiple steps such as transcription, mRNA processing, mRNA export, mRNA degradation, translation, and posttranslational events. Recent discovery of small RNAs has enhanced the impact of posttranscriptional regulation, in particular, alterations in mRNA stability in the regulation of gene expression. Therefore, mRNA turnover is an important process not only for setting the basal level of gene expression but also as a regulatory step. Compared to the mechanism of transcription, much less information is available regarding mRNA degradation machineries. However, in the past several years, various components involved in the mRNA degradation process have been identified in eukaryotes. In particular, progress in the plant field has revealed the involvement of mRNA turnover in a wide variety of developmental processes and hormonal responses. Here, we provide an overview of machineries involved in general mRNA degradation and mRNA surveillance systems in plants.

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

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ (2008) Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Current Biology 18(10):758–762

    PubMed  Google Scholar 

  • Allmang C, Petfalski E, Podtelejnikov A, Mann M, Tollervey D, Mitchell P (1999) The yeast exosome and human PM-Scl are related complexes of 3′ –> 5′ exonucleases. Genes Dev 13(16):2148–2158

    PubMed  Google Scholar 

  • Amrani N, Ganesan R, Kervestin S, Mangus DA, Ghosh S, Jacobson A (2004) A faux 3′-UTR promotes aberrant termination and triggers nonsense-mediated mRNA decay. Nature 432(7013):112–118

    PubMed  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(5):1497–1506

    PubMed  Google Scholar 

  • Arciga-Reyes L, Wootton L, Kieffer M, Davies B (2006) UPF1 is required for nonsense-mediated mRNA decay (NMD) and RNAi in Arabidopsis. Plant J 47(3):480–489

    PubMed  Google Scholar 

  • Beelman CA, Stevens A, Caponigro G, LaGrandeur TE, Hatfield L, Fortner DM, Parker R (1996) An essential component of the decapping enzyme required for normal rates of mRNA turnover. Nature 382(6592):642–646

    PubMed  Google Scholar 

  • Behm-Ansmant I, Gatfield D, Rehwinkel J, Hilgers V, Izaurralde E (2007) A conserved role for cytoplasmic poly(A)-binding protein 1 (PABPC1) in nonsense-mediated mRNA decay. Embo J 26(6):1591–1601

    PubMed  Google Scholar 

  • Binder BM, Walker JM, Gagne JM, Emborg TJ, Hemmann G, Bleecker AB, Vierstra RD (2007) The Arabidopsis EIN3 binding F-Box proteins EBF1 and EBF2 have distinct but overlapping roles in ethylene signaling. Plant Cell 19(2):509–523

    PubMed  Google Scholar 

  • Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, Dunoyer P, Yamamoto YY, Sieburth L, Voinnet O (2008) Widespread translational inhibition by plant miRNAs and siRNAs. Science 320(5880):1185–1190

    PubMed  Google Scholar 

  • Brown CE, Sachs AB (1998) Poly(A) tail length control in Saccharomyces cerevisiae occurs by message-specific deadenylation. Mol Cell Biol 18(11):6548–6559

    PubMed  Google Scholar 

  • Buhler M, Steiner S, Mohn F, Paillusson A, Muhlemann O (2006) EJC-independent degradation of nonsense immunoglobulin-mu mRNA depends on 3′ UTR length. Nat Struct Mol Biol 13(5):462–464

    PubMed  Google Scholar 

  • Cao D, Parker R (2003) Computational modeling and experimental analysis of nonsense-mediated decay in yeast. Cell 113(4):533–545

    PubMed  Google Scholar 

  • Chang YF, Imam JS, Wilkinson MF (2007) The nonsense-mediated decay RNA surveillance pathway. Annu Rev Biochem 76:51–74

    PubMed  Google Scholar 

  • Chekanova JA, Shaw RJ, Wills MA, Belostotsky DA (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(42):33158–33166

    PubMed  Google Scholar 

  • Chekanova JA, Dutko JA, Mian IS, Belostotsky DA (2002) Arabidopsis thaliana exosome subunit AtRrp4p is a hydrolytic 3′–>5′ exonuclease containing S1 and KH RNA-binding domains. Nucleic Acids Res 30(3):695–700

    PubMed  Google Scholar 

  • Chekanova JA, Gregory BD, Reverdatto SV, Chen H, Kumar R, Hooker T, Yazaki J, Li P, Skiba N, Peng Q, Alonso J, Brukhin V, Grossniklaus U, Ecker JR, Belostotsky DA (2007) Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome. Cell 131(7):1340–1353

    PubMed  Google Scholar 

  • Chen CY, Shyu AB (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(14):4805–4813

    PubMed  Google Scholar 

  • Chen CY, Gherzi R, Ong SE, Chan EL, Raijmakers R, Pruijn GJ, Stoecklin G, Moroni C, Mann M, Karin M (2001) AU binding proteins recruit the exosome to degrade ARE-containing mRNAs. Cell 107(4):451–464

    PubMed  Google Scholar 

  • Chen J, Chiang YC, Denis CL (2002) CCR4, a 3′–5′ poly(A) RNA and ssDNA exonuclease, is the catalytic component of the cytoplasmic deadenylase. Embo J 21(6):1414–1426

    PubMed  Google Scholar 

  • Chiba Y, Ishikawa M, Kijima F, Tyson RH, Kim J, Yamamoto A, Nambara E, Leustek T, Wallsgrove RM, Naito S (1999) Evidence for autoregulation of cystathionine gamma-synthase mRNA stability in Arabidopsis. Science 286(5443):1371–1374

    PubMed  Google Scholar 

  • Chiba Y, Sakurai R, Yoshino M, Ominato K, Ishikawa M, Onouchi H, Naito S (2003) S-adenosyl-l-methionine is an effector in the posttranscriptional autoregulation of the cystathionine gamma-synthase gene in Arabidopsis. Proc Natl Acad Sci USA 100(18):10225–10230

    PubMed  Google Scholar 

  • Chiba Y, Johnson MA, Lidder P, Vogel JT, van Erp H, Green PJ (2004) AtPARN is an essential poly(A) ribonuclease in Arabidopsis. Gene 328:95–102

    PubMed  Google Scholar 

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

    PubMed  Google Scholar 

  • Copeland PR, Wormington M (2001) The mechanism and regulation of deadenylation: identification and characterization of Xenopus PARN. Rna 7(6):875–886

    PubMed  Google Scholar 

  • Couttet P, Grange T (2004) Premature termination codons enhance mRNA decapping in human cells. Nucleic Acids Res 32(2):488–494

    PubMed  Google Scholar 

  • Daugeron MC, Mauxion F, Seraphin B (2001) The yeast POP2 gene encodes a nuclease involved in mRNA deadenylation. Nucleic Acids Res 29(12):2448–2455

    PubMed  Google Scholar 

  • Dehlin E, Wormington M, Korner CG, Wahle E (2000a) Cap-dependent deadenylation of mRNA. EMBO J 19(5):1079–1086

    Google Scholar 

  • Dehlin E, Wormington M, Korner CG, Wahle E (2000b) Cap-dependent deadenylation of mRNA. Embo J 19(5):1079–1086

    Google Scholar 

  • Denis CL, Chen J (2003) The CCR4-NOT complex plays diverse roles in mRNA metabolism. Prog Nucleic Acid Res Mol Biol 73:221–250

    PubMed  Google Scholar 

  • Dichtl B, Stevens A, Tollervey D (1997) Lithium toxicity in yeast is due to the inhibition of RNA processing enzymes. EMBO J 16(23):7184–7195

    PubMed  Google Scholar 

  • Dickey LF, Gallo-Meagher M, Thompson WF (1992) Light regulatory sequences are located within the 5′ portion of the Fed-1 message sequence. Embo J 11(6):2311–2317

    PubMed  Google Scholar 

  • Dickey LF, Nguyen TT, Allen GC, Thompson WF (1994) Light modulation of ferredoxin mRNA abundance requires an open reading frame. Plant Cell 6(8):1171–1176

    PubMed  Google Scholar 

  • Dickey LF, Petracek ME, Nguyen TT, Hansen ER, Thompson WF (1998) Light regulation of Fed-1 mRNA requires an element in the 5′ untranslated region and correlates with differential polyribosome association. Plant Cell 10(3):475–484

    PubMed  Google Scholar 

  • Doma MK, Parker R (2006) Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation. Nature 440(7083):561–564

    PubMed  Google Scholar 

  • Dunckley T, Parker R (1999) The DCP2 protein is required for mRNA decapping in Saccharomyces cerevisiae and contains a functional MutT motif. EMBO J 18(19):5411–5422

    PubMed  Google Scholar 

  • Dupressoir A, Morel AP, Barbot W, Loireau MP, Corbo L, Heidmann T (2001) Identification of four families of yCCR4- and Mg2+-dependent endonuclease-related proteins in higher eukaryotes, and characterization of orthologs of yCCR4 with a conserved leucine-rich repeat essential for hCAF1/hPOP2 binding. BMC Genomics 2(1):9

    PubMed  Google Scholar 

  • Dziembowski A, Lorentzen E, Conti E, Seraphin B (2007) A single subunit, Dis3, is essentially responsible for yeast exosome core activity. Nat Struct Mol Biol 14(1):15–22

    PubMed  Google Scholar 

  • Eberle AB, Lykke-Andersen S, Muhlemann O, Jensen TH (2009) SMG6 promotes endonucleolytic cleavage of nonsense mRNA in human cells. Nat Struct Mol Biol 16(1):49–55

    PubMed  Google Scholar 

  • Elliott RC, Dickey LF, White MJ, Thompson WF (1989) cis-Acting elements for light regulation of pea ferredoxin I gene expression are located within transcribed sequences. Plant Cell 1(7):691–698

    PubMed  Google Scholar 

  • Eulalio A, Rehwinkel J, Stricker M, Huntzinger E, Yang SF, Doerks T, Dorner S, Bork P, Boutros M, Izaurralde E (2007) Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing. Genes Dev 21(20):2558–2570

    PubMed  Google Scholar 

  • Fenger-Gr M, Fillman C, Norrild B, Lykke-Andersen J (2005) Multiple processing body factors and the are binding protein TTP activate mRNA decapping. Molecular Cell 20(6):905–915

    Google Scholar 

  • Frischmeyer PA, van Hoof A, O’Donnell K, Guerrerio AL, Parker R, Dietz HC (2002) An mRNA surveillance mechanism that eliminates transcripts lacking termination codons. Science 295(5563):2258–2261

    PubMed  Google Scholar 

  • Funakoshi Y, Doi Y, Hosoda N, Uchida N, Osawa M, Shimada I, Tsujimoto M, Suzuki T, Katada T, Hoshino S (2007) Mechanism of mRNA deadenylation: evidence for a molecular interplay between translation termination factor eRF3 and mRNA deadenylases. Genes Dev 21(23):3135–3148

    PubMed  Google Scholar 

  • Gadjieva R, Axelsson E, Olsson U, Vallon-Christersson J, Hansson M (2004) Nonsense-mediated mRNA decay in barley mutants allows the cloning of mutated genes by a microarray approach. Plant Physiol Biochem 42(7–8):681–685

    PubMed  Google Scholar 

  • Gallo-Meagher M, Sowinski DA, Elliott RC, Thompson WF (1992) Both internal and external regulatory elements control expression of the pea Fed-1 gene in transgenic tobacco seedlings. Plant Cell 4(4):389–395

    PubMed  Google Scholar 

  • Gao M, Fritz DT, Ford LP, Wilusz J (2000) Interaction between a poly(A)-specific ribonuclease and the 5′ cap influences mRNA deadenylation rates in vitro. Molecular Cell 5(3):479–488

    PubMed  Google Scholar 

  • Gatfield D, Izaurralde E (2004) Nonsense-mediated messenger RNA decay is initiated by endonucleolytic cleavage in Drosophila. Nature 429(6991):575–578

    PubMed  Google Scholar 

  • Gazzani S, Lawrenson T, Woodward C, Headon D, Sablowski R (2004) A link between mRNA turnover and RNA interference in Arabidopsis. Science 306(5698):1046–1048

    PubMed  Google Scholar 

  • German MA, Pillay M, Jeong DH, Hetawal A, Luo S, Janardhanan P, Kannan V, Rymarquis LA, Nobuta K, German R, De Paoli E, Lu C, Schroth G, Meyers BC, Green PJ (2008) Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol 26(8):941–946

    PubMed  Google Scholar 

  • Goeres DC, Van Norman JM, Zhang W, Fauver NA, Spencer ML, Sieburth LE (2007) Components of the Arabidopsis mRNA decapping complex are required for early seedling development. Plant Cell 19(5):1549–1564

    PubMed  Google Scholar 

  • Gregory BD, O’Malley RC, Lister R, Urich MA, Tonti-Filippini J, Chen H, Millar AH, Ecker JR (2008) A link between RNA metabolism and silencing affecting Arabidopsis development. Dev Cell 14(6):854–866

    PubMed  Google Scholar 

  • Gy I, Gasciolli V, Lauressergues D, Morel JB, Gombert J, Proux F, Proux C, Vaucheret H, Mallory AC (2007) Arabidopsis FIERY1, XRN2, and XRN3 are endogenous RNA silencing suppressors. Plant Cell 19(11):3451–3461

    PubMed  Google Scholar 

  • Hagan KW, Ruiz-Echevarria MJ, Quan Y, Peltz SW (1995) Characterization of cis-acting sequences and decay intermediates involved in nonsense-mediated mRNA turnover. Mol Cell Biol 15(2):809–823

    PubMed  Google Scholar 

  • Hansen ER, Petracek ME, Dickey LF, Thompson WF (2001) The 5′ end of the pea ferredoxin-1 mRNA mediates rapid and reversible light-directed changes in translation in tobacco. Plant Physiol 125(2):770–778

    PubMed  Google Scholar 

  • Hatfield L, Beelman CA, Stevens A, Parker R (1996) Mutations in trans-acting factors affecting mRNA decapping in Saccharomyces cerevisiae. Mol Cell Biol 16(10):5830–5838

    PubMed  Google Scholar 

  • Hooker TS, Lam P, Zheng H, Kunst L (2007) A core subunit of the RNA-processing/degrading exosome specifically influences cuticular wax biosynthesis in Arabidopsis. Plant Cell 19(3):904–913

    PubMed  Google Scholar 

  • Hori K, Watanabe Y (2005) UPF3 suppresses aberrant spliced mRNA in Arabidopsis. Plant J 43(4):530–540

    PubMed  Google Scholar 

  • Hori K, Watanabe Y (2007) Context analysis of termination codons in mRNA that are recognized by plant NMD. Plant Cell Physiol 48(7):1072–1078

    PubMed  Google Scholar 

  • Hosoda N, Kobayashi T, Uchida N, Funakoshi Y, Kikuchi Y, Hoshino S, Katada T (2003) Translation termination factor eRF3 mediates mRNA decay through the regulation of deadenylation. J Biol Chem 278(40):38287–38291

    PubMed  Google Scholar 

  • Houseley J, LaCava J, Tollervey D (2006) RNA-quality control by the exosome. Nat Rev Mol Cell Biol 7(7):529–539

    PubMed  Google Scholar 

  • Hsu CL, Stevens A (1993) Yeast cells lacking 5′–>3′ exoribonuclease 1 contain mRNA species that are poly(A) deficient and partially lack the 5′ cap structure. Mol Cell Biol 13(8):4826–4835

    PubMed  Google Scholar 

  • Huntzinger E, Kashima I, Fauser M, Sauliere J, Izaurralde E (2008) SMG6 is the catalytic endonuclease that cleaves mRNAs containing nonsense codons in metazoan. Rna 14(12):2609–2617

    PubMed  Google Scholar 

  • Isken O, Kim YK, Hosoda N, Mayeur GL, Hershey JW, Maquat LE (2008) Upf1 phosphorylation triggers translational repression during nonsense-mediated mRNA decay. Cell 133(2):314–327

    PubMed  Google Scholar 

  • Isshiki M, Yamamoto Y, Satoh H, Shimamoto K (2001) Nonsense-mediated decay of mutant waxy mRNA in rice. Plant Physiol 125(3):1388–1395

    PubMed  Google Scholar 

  • Ivanov PV, Gehring NH, Kunz JB, Hentze MW, Kulozik AE (2008) Interactions between UPF1, eRFs, PABP and the exon junction complex suggest an integrated model for mammalian NMD pathways. Embo J 27(5):736–747

    PubMed  Google Scholar 

  • Iwasaki S, Takeda A, Motose H, Watanabe Y (2007) Characterization of Arabidopsis decapping proteins AtDCP1 and AtDCP2, which are essential for post-embryonic development. FEBS Lett 581(13):2455–2459

    PubMed  Google Scholar 

  • Jofuku KD, Schipper RD, Goldberg RB (1989) A frameshift mutation prevents Kunitz trypsin inhibitor mRNA accumulation in soybean embryos. Plant Cell 1(5):567

    PubMed  Google Scholar 

  • Johnson AW (1997) Rat1p and Xrn1p are functionally interchangeable exoribonucleases that are restricted to and required in the nucleus and cytoplasm, respectively. Mol Cell Biol 17(10):6122–6130

    PubMed  Google Scholar 

  • Kashima I, Yamashita A, Izumi N, Kataoka N, Morishita R, Hoshino S, Ohno M, Dreyfuss G, Ohno S (2006) Binding of a novel SMG-1-Upf1-eRF1-eRF3 complex (SURF) to the exon junction complex triggers Upf1 phosphorylation and nonsense-mediated mRNA decay. Genes Dev 20(3):355–367

    PubMed  Google Scholar 

  • Kastenmayer JP, Green PJ (2000) Novel features of the XRN-family in Arabidopsis: evidence that AtXRN4, one of several orthologs of nuclear Xrn2p/Rat1p, functions in the cytoplasm. Proc Natl Acad Sci USA 97(25):13985–13990

    PubMed  Google Scholar 

  • Katiyar-Agarwal S, Gao S, Vivian-Smith A, Jin H (2007) A novel class of bacteria-induced small RNAs in Arabidopsis. Genes Dev 21(23):3123–3134

    PubMed  Google Scholar 

  • Kendrick MD, Chang C (2008) Ethylene signaling: new levels of complexity and regulation. Curr Opin Plant Biol 11(5):479–485

    PubMed  Google Scholar 

  • Kerenyi Z, Merai Z, Hiripi L, Benkovics A, Gyula P, Lacomme C, Barta E, Nagy F, Silhavy D (2008) Inter-kingdom conservation of mechanism of nonsense-mediated mRNA decay. Embo J 27(11):1585–1595

    PubMed  Google Scholar 

  • Kertesz S, Kerenyi Z, Merai Z, Bartos I, Palfy T, Barta E, Silhavy D (2006) Both introns and long 3′-UTRs operate as cis-acting elements to trigger nonsense-mediated decay in plants. Nucleic Acids Res 34(21):6147–6157

    PubMed  Google Scholar 

  • Kim B-H, von Arnim AG (2008) FIERY1 regulates light-mediated repression of cell elongation and flowering time via its 3′(2′),5′-bisphosphate nucleotidase activity. The Plant Journal (in press). doi.10.1111/j.1365-313X.2008.03770.x

  • Korner CG, Wahle E (1997) Poly(A) tail shortening by a mammalian poly(A)-specific 3′-exoribonuclease. J Biol Chem 272(16):10448–10456

    PubMed  Google Scholar 

  • Korner CG, Wormington M, Muckenthaler M, Schneider S, Dehlin E, Wahle E (1998) The deadenylating nuclease (DAN) is involved in poly(A) tail removal during the meiotic maturation of Xenopus oocytes. EMBO J 17(18):5427–5437

    PubMed  Google Scholar 

  • LaGrandeur TE, Parker R (1998) Isolation and characterization of Dcp1p, the yeast mRNA decapping enzyme. EMBO J 17(5):1487–1496

    PubMed  Google Scholar 

  • Lai WS, Kennington EA, Blackshear PJ (2003) Tristetraprolin and its family members can promote the cell-free deadenylation of AU-rich element-containing mRNAs by poly(A) ribonuclease. Mol Cell Biol 23(11):3798–3812

    PubMed  Google Scholar 

  • Lambein I, Chiba Y, Onouchi H, Naito S (2003) Decay kinetics of autogenously regulated CGS1 mRNA that codes for cystathionine gamma-synthase in Arabidopsis thaliana. Plant Cell Physiol 44(9):893–900

    PubMed  Google Scholar 

  • Le Hir H, Moore MJ, Maquat LE (2000) Pre-mRNA splicing alters mRNP composition: evidence for stable association of proteins at exon–exon junctions. Genes Dev 14(9):1098–1108

    PubMed  Google Scholar 

  • Lebreton A, Tomecki R, Dziembowski A, Seraphin B (2008) Endonucleolytic RNA cleavage by a eukaryotic exosome. Nature 456(7224):993–996

    PubMed  Google Scholar 

  • Lee HH, Kim YS, Kim KH, Heo I, Kim SK, Kim O, Kim HK, Yoon JY, Kim HS, Kim do J, Lee SJ, Yoon HJ, Kim SJ, Lee BG, Song HK, Kim VN, Park CM, Suh SW (2007) Structural and functional insights into Dom34, a key component of no-go mRNA decay. Mol Cell 27(6):938–950

    PubMed  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(3):675–687

    PubMed  Google Scholar 

  • Lin MD, Fan SJ, Hsu WS, Chou TB (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(5):601–613

    PubMed  Google Scholar 

  • Liu H, Rodgers ND, Jiao X, Kiledjian M (2002) The scavenger mRNA decapping enzyme DcpS is a member of the HIT family of pyrophosphatases. Embo J 21(17):4699–4708

    PubMed  Google Scholar 

  • Liu Q, Greimann JC, Lima CD (2006) Reconstitution, activities, and structure of the eukaryotic RNA exosome. Cell 127(6):1223–1237

    PubMed  Google Scholar 

  • Lowell JE, Rudner DZ, Sachs AB (1992) 3′-UTR-dependent deadenylation by the yeast poly(A) nuclease. Genes Dev 6(11):2088–2099

    PubMed  Google Scholar 

  • Matthews BF (1999) Lysine, thereonine, and methionine biosynthesis. In: Singh BK (ed) Plant amino acids: biochemistry and biotechnology, vol. Marcel Dekker, New York, pp 205–225

    Google Scholar 

  • Meaux S, van Hoof A, Baker KE (2008) Nonsense-mediated mRNA decay in yeast does not require PAB1 or a poly(A) tail. Mol Cell 29(1):134–140

    PubMed  Google Scholar 

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

    PubMed  Google Scholar 

  • Mitchell P, Petfalski E, Shevchenko A, Mann M, Tollervey D (1997) The exosome: a conserved eukaryotic RNA processing complex containing multiple 3′–>5′ exoribonucleases. Cell 91(4):457–466

    PubMed  Google Scholar 

  • Muhlrad D, Parker R (1994) Premature translational termination triggers mRNA decapping. Nature 370(6490):578–581

    PubMed  Google Scholar 

  • Mukherjee D, Gao M, O’Connor JP, Raijmakers R, Pruijn G, Lutz CS, Wilusz J (2002) The mammalian exosome mediates the efficient degradation of mRNAs that contain AU-rich elements. EMBO J 21(1–2):165–174

    PubMed  Google Scholar 

  • Nagy E, Maquat LE (1998) A rule for termination-codon position within intron-containing genes: when nonsense affects RNA abundance. Trends Biochem Sci 23(6):198–199

    PubMed  Google Scholar 

  • Nishimura N, Kitahata N, Seki M, Narusaka Y, Narusaka M, Kuromori T, Asami T, Shinozaki K, Hirayama T (2005) Analysis of ABA hypersensitive germination2 revealed the pivotal functions of PARN in stress response in Arabidopsis. Plant J 44(6):972–984

    PubMed  Google Scholar 

  • Olmedo G, Guo H, Gregory BD, Nourizadeh SD, Aguilar-Henonin L, Li H, An F, Guzman P, Ecker JR (2006) Ethylene-insensitive5 encodes a 5′–>3′ exoribonuclease required for regulation of the EIN3-targeting F-box proteins EBF1/2. Proc Natl Acad Sci USA 103(36):13286–13293

    PubMed  Google Scholar 

  • Ominato K, Akita H, Suzuki A, Kijima F, Yoshino T, Yoshino M, Chiba Y, Onouchi H, Naito S (2002) Identification of a short highly conserved amino acid sequence as the functional region required for posttranscriptional autoregulation of the cystathionine gamma-synthase gene in Arabidopsis. J Biol Chem 277(39):36380–36386

    PubMed  Google Scholar 

  • Onouchi H, Nagami Y, Haraguchi Y, Nakamoto M, Nishimura Y, Sakurai R, Nagao N, Kawasaki D, Kadokura Y, Naito S (2005) Nascent peptide-mediated translation elongation arrest coupled with mRNA degradation in the CGS1 gene of Arabidopsis. Genes Dev 19(15):1799–1810

    PubMed  Google Scholar 

  • Orban TI, Izaurralde E (2005) Decay of mRNAs targeted by RISC requires XRN1, the Ski complex, and the exosome. RNA 11(4):459–469

    PubMed  Google Scholar 

  • Pendle AF, Clark GP, Boon R, Lewandowska D, Lam YW, Andersen J, Mann M, Lamond AI, Brown JW, Shaw PJ (2005) Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions. Mol Biol Cell 16(1):260–269

    PubMed  Google Scholar 

  • Petracek ME, Dickey LF, Huber SC, Thompson WF (1997) Light-regulated changes in abundance and polyribosome association of ferredoxin mRNA are dependent on photosynthesis. Plant Cell 9(12):2291–2300

    PubMed  Google Scholar 

  • Petracek ME, Dickey LF, Nguyen TT, Gatz C, Sowinski DA, Allen GC, Thompson WF (1998) Ferredoxin-1 mRNA is destabilized by changes in photosynthetic electron transport. Proc Natl Acad Sci USA 95(15):9009–9013

    PubMed  Google Scholar 

  • Potuschak T, Vansiri A, Binder BM, Lechner E, Vierstra RD, Genschik P (2006) The exoribonuclease XRN4 is a component of the ethylene response pathway in Arabidopsis. Plant Cell 18(11):3047–3057

    PubMed  Google Scholar 

  • Raijmakers R, Schilders G, Pruijn GJ (2004) The exosome, a molecular machine for controlled RNA degradation in both nucleus and cytoplasm. Eur J Cell Biol 83(5):175–183

    PubMed  Google Scholar 

  • Reverdatto SV, Dutko JA, Chekanova JA, Hamilton DA, Belostotsky DA (2004) mRNA deadenylation by PARN is essential for embryogenesis in higher plants. Rna 10(8):1200–1214

    PubMed  Google Scholar 

  • Riehs N, Akimcheva S, Puizina J, Bulankova P, Idol RA, Siroky J, Schleiffer A, Schweizer D, Shippen DE, Riha K (2008) Arabidopsis SMG7 protein is required for exit from meiosis. J Cell Sci 121(Pt 13):2208–2216

    PubMed  Google Scholar 

  • Sachs AB, Deardorff JA (1992) Translation initiation requires the PAB-dependent poly(A) ribonuclease in yeast. Cell 70(6):961–973

    PubMed  Google Scholar 

  • Saito K (2004) Sulfur assimilatory metabolism. The long and smelling road. Plant Physiol 136(1):2443–2450

    PubMed  Google Scholar 

  • Sakuno T, Araki Y, Ohya Y, Kofuji S, Takahashi S, Hoshino S, Katada T (2004) Decapping reaction of mRNA requires Dcp1 in fission yeast: its characterization in different species from yeast to human. J Biochem 136(6):805–812

    PubMed  Google Scholar 

  • Sarowar S, Oh HW, Cho HS, Baek KH, Seong ES, Joung YH, Choi GJ, Lee S, Choi D (2007) Capsicum annuum CCR4-associated factor CaCAF1 is necessary for plant development and defence response. Plant J 51(5):792–802

    PubMed  Google Scholar 

  • Schaeffer D, Tsanova B, Barbas A, Reis FP, Dastidar EG, Sanchez-Rotunno M, Arraiano CM, van Hoof A (2009) The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities. Nat Struct Mol Biol 16(1):56–62

    PubMed  Google Scholar 

  • Siddiqui N, Mangus DA, Chang TC, Palermino JM, Shyu AB, Gehring K (2007) Poly(A) nuclease interacts with the C-terminal domain of polyadenylate-binding protein domain from poly(A)-binding protein. J Biol Chem 282(34):25067–25075

    PubMed  Google Scholar 

  • Souret FF, Kastenmayer JP, Green PJ (2004) AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets. Mol Cell 15(2):173–183

    PubMed  Google Scholar 

  • Takahashi S, Araki Y, Sakuno T, Katada T (2003) Interaction between Ski7p and Upf1p is required for nonsense-mediated 3′-to-5′ mRNA decay in yeast. Embo J 22(15):3951–3959

    PubMed  Google Scholar 

  • Tucker M, Valencia-Sanchez MA, Staples RR, Chen J, Denis CL, Parker R (2001) The transcription factor associated Ccr4 and Caf1 proteins are components of the major cytoplasmic mRNA deadenylase in Saccharomyces cerevisiae. Cell 104(3):377–386

    PubMed  Google Scholar 

  • Tucker M, Staples RR, Valencia-Sanchez MA, Muhlrad D, Parker R (2002) Ccr4p is the catalytic subunit of a Ccr4p/Pop2p/Notp mRNA deadenylase complex in Saccharomyces cerevisiae. Embo J 21(6):1427–1436

    PubMed  Google Scholar 

  • Uchida N, Hoshino S, Katada T (2004) Identification of a human cytoplasmic poly(A) nuclease complex stimulated by poly(A)-binding protein. J Biol Chem 279(2):1383–1391

    PubMed  Google Scholar 

  • van Hoof A, Green PJ (1996) Premature nonsense codons decrease the stability of phytohemagglutinin mRNA in a position-dependent manner. Plant J 10(3):415–424

    PubMed  Google Scholar 

  • van Hoof A, Frischmeyer PA, Dietz HC, Parker R (2002) Exosome-mediated recognition and degradation of mRNAs lacking a termination codon. Science 295(5563):2262–2264

    PubMed  Google Scholar 

  • Voelker TA, Moreno J, Chrispeels MJ (1990) Expression analysis of a pseudogene in transgenic tobacco: a frameshift mutation prevents mRNA accumulation. Plant Cell 2(3):255–261

    PubMed  Google Scholar 

  • Wang Z, Kiledjian M (2001) Functional link between the mammalian exosome and mRNA decapping. Cell 107(6):751–762

    PubMed  Google Scholar 

  • Wilson PB, Estavillo GM, Field KJ, Pornsiriwong W, Carroll AJ, Howell KA, Woo NS, Lake JA, Smith SM, Millar AH, von Caemmere S, Pogson BJ (2009) The nucleotidase/phosphatase SAL1 is a negative regulator of drought tolerance in Arabidopsis. The Plant Journal (in press). doi:10.1111/j.1365–313X.2008.03780.x

  • Wilusz J (2009) RNA stability: is it the endo’ the world as we know it? Nat Struct Mol Biol 16(1):9–10

    PubMed  Google Scholar 

  • Wu J, Kang JH, Hettenhausen C, Baldwin IT (2007) Nonsense-mediated mRNA decay (NMD) silences the accumulation of aberrant trypsin proteinase inhibitor mRNA in Nicotiana attenuata. Plant J 51(4):693–706

    PubMed  Google Scholar 

  • Xu J, Yang JY, Niu QW, Chua NH (2006) Arabidopsis DCP2, DCP1, and VARICOSE form a decapping complex required for postembryonic development. Plant Cell 18(12):3386–3398

    PubMed  Google Scholar 

  • Yamashita A, Chang TC, Yamashita Y, Zhu W, Zhong Z, Chen CY, Shyu AB (2005a) Concerted action of poly(A) nucleases and decapping enzyme in mammalian mRNA turnover. Nat Struct Mol Biol 12(12):1054–1063

    Google Scholar 

  • Yamashita A, Kashima I, Ohno S (2005b) The role of SMG-1 in nonsense-mediated mRNA decay. Biochim Biophys Acta 1754(1–2):305–315

    Google Scholar 

  • Yoine M, Ohto MA, Onai K, Mita S, Nakamura K (2006) The lba1 mutation of UPF1 RNA helicase involved in nonsense-mediated mRNA decay causes pleiotropic phenotypic changes and altered sugar signalling in Arabidopsis. Plant J 47(1):49–62

    PubMed  Google Scholar 

Download references

Acknowledgments

We would like to thank Satoshi Naito and Linda Rymarquis for critical reading and Sharon Bancroft for editorial assistance. Our work presented in this paper is supported by grants from the USDA, DOE, and NSF.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Yukako Chiba.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Chiba, Y., Green, P.J. mRNA Degradation Machinery in Plants. J. Plant Biol. 52, 114–124 (2009). https://doi.org/10.1007/s12374-009-9021-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12374-009-9021-2

Keywords

Navigation