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NMD mechanism and the functions of Upf proteins in plant

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Abstract

Nonsense-mediated decay (NMD) mechanism, also called mRNA surveillance, is a universal mRNA degradation pathway in eukaryotes. Hundreds of genes can be regulated by NMD whether in single-celled or higher organisms. There have been many studies on NMD and NMD factors (Upf proteins) with regard to their crucial roles in mRNA decay, especially in mammals and yeast. However, research focusing on NMD in plant is still lacking compared to the research that has been dedicated to NMD in mammals and yeast. Even so, recent study has shown that NMD factors in Arabidopsis can provide resistance against biotic and abiotic stresses. This discovery and its associated developments have given plant NMD mechanism a new outlook and since then, more and more research has focused on this area. In this review, we focused mainly on the distinctive NMD micromechanism and functions of Upf proteins in plant with references to the role of mRNA surveillance in mammals and yeast. We also highlighted recent insights into the roles of premature termination codon location, trans-elements and functions of other NMD factors to emphasize the particularity of plant NMD. Furthermore, we also discussed conventional approaches and neoteric methods used in plant NMD researches.

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References

  • Altamura N, Groudinsky O, Dujardin G, Slonimski PP (1992) NAM7 nuclear gene encodes a novel member of a family of helicases with a Zn-ligand motif and is involved in mitochondrial functions in Saccharomyces cerevisiae. J Mol Biol 224(3):575–587

    Article  PubMed  CAS  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

    Article  PubMed  CAS  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

    Article  PubMed  CAS  Google Scholar 

  • Asano K, Clayton J, Shalev A, Hinnebusch AG (2000) A multifactor complex of eukaryotic initiation factors, eIF1, eIF2, eIF3, eIF5, and initiator tRNAMet  is an important translation initiation intermediate in vivo. Genes Dev 14(19):2534–2546

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Atkin AL, Schenkman LR, Eastham M, Dahlseid JN, Lelivelt MJ, Culbertson MR (1997) Relationship between yeast polyribosomes and Upf proteins required for nonsense mRNA decay. J Biol Chem 272(35):22163–22172

    Article  PubMed  CAS  Google Scholar 

  • Bao J, Tang C, Yuan S, Porse BT, Yan W (2015) UPF2, a nonsense-mediated mRNA decay factor, is required for prepubertal Sertoli cell development and male fertility by ensuring fidelity of the transcriptome. Development 142(2):352–362

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Büttner K, Wenig K, Hopfner KP (2006) The exosome: a macromolecular cage for controlled RNA degradation. Mol Microbiol 61(6):1372–1379

    Article  PubMed  CAS  Google Scholar 

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

    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(3):316–325

    Article  PubMed  CAS  Google Scholar 

  • Craig AW, Haghighat A, Yu AT, Sonenberg N (1998) Interaction of polyadenylate-binding protein with the eIF4G homologue PAIP enhances translation. Nature 392:520–523

    Article  PubMed  CAS  Google Scholar 

  • Cruz TM, Carvalho RF, Richardson DN, Duque P (2014) Abscisic acid (ABA) regulation of Arabidopsis SR protein gene expression. Int J Mol Sci 15(10):17541–17564

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Culbertson MR, Leeds PF (2003) Looking at mRNA decay pathways through the window of molecular evolution. Curr Opin Genet 13(2):207–214

    Article  CAS  Google Scholar 

  • Czaplinski K, Weng Y, Hagan KW, Peltz SW (1995) Purification and characterization of the Upf1 protein––a factor involved in translation and mRNA degradation. RNA 1:610–623

    PubMed  PubMed Central  CAS  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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Duque P (2011) A role for SR proteins in plant stress responses. Plant Signal Behav 6(1):49–54

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Dzikiewicz-Krawczyk A, Piontek P, Szweykowska-Kulińska Z, Jarmołowski A (2008) The nuclear cap-binding protein complex is not essential for nonsense-mediated mRNA decay (NMD) in plants. Acta Biochim Pol 55(4):825–829 Epub 2008 Dec 16

    PubMed  CAS  Google Scholar 

  • Eberle AB, Lykke-Andersen S, Mühlemann O, Jensen TH (2008) SMG6 promotes endonucleolytic cleavage of nonsense mRNA in human cells. Nat Struct Mol Biol 16(1):49–55. doi:10.1038/nsmb.1530

    Article  PubMed  CAS  Google Scholar 

  • El-Bchiri J, Guilloux A, Dartigues P, Loire E, Mercier D, Buhard O, Sobhani I, de la Grange P, Auboeuf D, Praz F, Fléjou JF, Duval A (2008) Nonsense-mediated mRNA decay impacts MSI-driven carcinogenesis and anti-tumor immunity in colorectal cancers. PLoS One 3(7):e2583

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Eulalio A, Behm-Ansmant I, Izaurralde E (2007) P bodies: at the crossroads of post-transcriptional pathways. Nat Rev Mol Cell Biol 8(1):9–22

    Article  PubMed  CAS  Google Scholar 

  • Frischmeyer PA, Dietz HC (1999) Nonsense-mediated mRNA decay in health and disease. Hum Mol Genet 8(10):1893–1900

    Article  PubMed  CAS  Google Scholar 

  • Gardner LB (2010) Nonsense mediated RNA decay regulation by cellular stress; implications for tumorigenesis. Mol Cancer Res 8(3):295–308

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Garre E, Romero-Santacreu L, Barneo-Muñoz M, Miguel A, Pérez-Ortín JE, Alepuz P (2013) Nonsense-mediated mRNA decay controls the changes in yeast ribosomal protein pre-mRNAs levels upon osmotic stress. PLoS One 8(4):e61240

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gingras AC, Raught B, Sonenberg N (1999) eIF4 initiation factors: effectors of mRNA recruitment to ribosomes and regulators of translation. Annu Rev Biochem 68(1):913–963

    Article  PubMed  CAS  Google Scholar 

  • Gong P, He C (2014) Uncovering divergence of rice exon junction complex core heterodimer gene duplication reveals their essential role in growth, development, and reproduction. Plant Physiol 165(3):1047–1061

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • González CI, Bhattacharya A, Wang W, Peltz SW (2001) Nonsense-mediated mRNA decay in Saccharomyces cerevisiae. Gene 274(1–2):15–25

    Article  PubMed  Google Scholar 

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

    Article  PubMed  CAS  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

    Article  PubMed  CAS  Google Scholar 

  • Hoyle NP, Castelli LM, Campbell SG, Holmes LE, Ashe MP (2007) Stress-dependent relocalization of translationally primed mRNPs to cytoplasmic granules that are kinetically and spatially distinct from P-bodies. J Cell Biol 179(1):65–74

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Huusko P, Ponciano-Jackson D, Wolf M, Kiefer JA, Azorsa DO, Tuzmen S, Weaver D, Robbins C, Moses T, Allinen M, Hautaniemi S, Chen Y, Elkahloun A, Basik M, Bova GS, Bubendorf L, Lugli A, Sauter G, Schleutker J, Ozcelik H, Elowe S, Pawson T, Trent JM, Carpten JD, Kallioniemi OP, Mousses S (2004) Nonsense-mediated decay microarray analysis identifies mutations of EPHB2 in human prostate cancer. Nat Genet 36:979–983

    Article  PubMed  CAS  Google Scholar 

  • Hwang J, Maquat LE (2011) Nonsense-mediated mRNA decay (NMD) in animal embryogenesis: to die or not to die, that is the question. Curr Opin Genet Dev 21(4):422–430

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ionov Y, Nowak N, Perucho M, Markowitz S, Cowell JK (2004) Manipulation of nonsense mediated decay identifies gene mutations in colon cancer Cells with microsatellite instability. Oncogene 23(3):639–645

    Article  PubMed  CAS  Google Scholar 

  • Ishigaki Y, Li X, Serin G, Maquat LE (2001) Evidence for a pioneer round of translation: mRNA subject to nonsense-mediated decay in mammalian cells are bound by CBP80 and CBP20. Cell 106(5):607–617. doi:10.1016/S0092-8674(01)00475-5

    Article  PubMed  CAS  Google Scholar 

  • Isken O, Maquat LE (2008) The multiple lives of NMD factors: balancing roles in gene and genome regulation. Nat Rev Genet 9(9):699–712

    Article  PubMed  PubMed Central  CAS  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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ivanov I, Lo KC, Hawthorn L, Cowell JK, Ionov Y (2007) Identifying candidate colon cancer tumor suppressor genes using inhibition of nonsense-mediated mRNA decay in colon cancer cells. Oncogene 26(2):2873–2884. doi:10.1038/sj.onc.1210098

    Article  PubMed  CAS  Google Scholar 

  • Jeong HJ, Kim YJ, Kim SH, Kim YH, Lee IJ, Kim YK, Shin JS (2011) Nonsense-mediated mRNA decay factors, UPF1 and UPF3, contribute to plant defense. Plant Cell Physiol 52(12):2147–2156

    Article  PubMed  CAS  Google Scholar 

  • Jofuku KD, Goldberg RB (1989) Kunitz trypsin inhibitor genes are differentially expressed during the soybean life cycle and in transformed tobacco plants. Plant Cell 1(11):1079–1093

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Johnson JK, Waddell N, kConFab Investigators, Chenevix-Trench G (2012) The application of nonsense-mediated mRNA decay inhibition to the identification of breast cancer susceptibility genes. BMC Cancer 12:246. doi:10.1186/1471-2407-12-246

    Article  PubMed  PubMed Central  Google Scholar 

  • Jonas S, Weichenrieder O, Izaurralde E (2013) An unusual arrangement of two 14-3-3-like domains in the SMG5-SMG7 heterodimer is required for efficient nonsense-mediated mRNA decay. Genes Dev 27(2):211–225

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kalyna M, Barta A (2004) A plethora of plant serine/arginine-rich proteins: redundancy or evolution of novel gene functions? Biochem Soc Trans 32(4):561–564

    Article  PubMed  CAS  Google Scholar 

  • Kerényi Z, Mérai 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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kertész S, Kerényi Z, Mérai Z, Bartos I, Pálfy T, Barta E, Silhavy D (2006) Both introns and long 3′-UTRs operate as cis-acting elements to trigger nonsense-mediated decay in plants. Nucl Acid Res 34(21):6147–6157

    Article  CAS  Google Scholar 

  • Kervestin S, Jacobson A (2012) NMD: a multifaceted response to premature translational termination. Nat Rev Mol Cell Biol 13(11):700–712

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kim VN, Kataoka N, Dreyfuss G (2001) Role of the nonsense-mediated decay factor hUpf3 in the splicing-dependent exon-exon junction complex. Science 293(5536):1832–1836

    Article  PubMed  CAS  Google Scholar 

  • Koonin EV (1992) A new group of putative RNA helicases. Trends Biochem Sci 17(12):495–497

    Article  PubMed  CAS  Google Scholar 

  • Koroleva OA, Brown JW, Shaw PJ (2009) Localization of eIF4A-III in the nucleolus and splicing speckles is an indicator of plant stress. Plant Signal Behav 4(12):1148–1151

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kurihara Y, Matsui A, Hanada K, Kawashima M, Ishida J, Morosawa T, Tanaka M, Kaminuma E, Mochizuki Y, Matsushima A, Toyoda T, Shinozaki K, Seki M (2009) Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis. Proc Natl Acad Sci USA 106(7):2453–2458

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lazar G, Schaal T, Maniatis T, Goodman HM (1995) Identification of a plant serine/arginine-rich protein similar to the mammalian splicing factor SF2/ASF. Proc Natl Acad Sci USA 92(17):7672–7676

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Le Hir H, Gatfield D, Izaurralde E, Moore MJ (2001) The exon–exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay. EMBO J 20(17):4987–4997

    Article  PubMed  PubMed Central  Google Scholar 

  • Lewis BP, Green RE, Brenner SE (2003) Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc Natl Acad Sci USA 100(1):189–192

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Liu J, Rivas FV, Wohlschlegel J, Yates JR III, Parker R, Hannon GJ (2005) A role for the P-body component GW182 in microRNA function. Nat Cell Biol 7(12):1261–1266

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lopato S, Mayeda A, Krainer AR, Barta A (1996a) Pre-mRNA splicing in plants: characterization of Ser/Arg splicing factors. Proc Natl Acad Sci USA 93(7):3074–3079

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lopato S, Waigmann E, Barta A (1996b) Characterization of a novel arginine/serine-rich splicing factor in Arabidopsis. Plant Cell 8(12):2255–2264

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Mandel CR, Bai Y, Tong L (2008) Protein factors in pre-mRNA 3′-end processing. Cell Mol Life Sci 65(7–8):1099–1122

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Maquat LE, Serin G (2001) Nonsense-mediated mRNA decay: insights into mechanism from the cellular abundance of humanUpf1, Upf2, Upf3, and Upf3X proteins. Cold Spring Harb Symp Quant Biol 66:313–320

    Article  PubMed  CAS  Google Scholar 

  • Maquat LE, Hwang J, Sato H, Tang Y (2010) CBP80-promoted mRNP rearrangements during the pioneer round of translation, nonsense-mediated mRNA decay, and thereafter. Cold Spring Harbor Symp Quant Biol 75:127–134

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Mendell JT, Sharifi NA, Meyers JL, Martinez-Murillo F, Dietz HC (2004) Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat Genet 36:1073–1078

    Article  PubMed  CAS  Google Scholar 

  • Mérai Z, Benkovics AH, Nyikó T, Debreczeny M, Hiripi L, Kerényi Z, Kondorosi É, Silhavy D (2013) The late steps of plant nonsense-mediated mRNA decay. Plant J 73(1):50–62

    Article  PubMed  CAS  Google Scholar 

  • Moreno AB, Martínez de Alba AE, Bardou F, Crespi MD, Vaucheret H, Maizel A, Mallory AC (2013) Cytoplasmic and nuclear quality control and turnover of single-stranded RNA modulate post-transcriptional gene silencing in plants. Nucl Acid Res 41(8):4699–4708

    Article  CAS  Google Scholar 

  • Mufarrege EF, Gonzalez DH, Curi GC (2011) Functional interconnections of Arabidopsis exon junction complex proteins and genes at multiple steps of gene expression. J Exp Bot 62(14):5025–5036

    Article  PubMed  CAS  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

    Article  PubMed  CAS  Google Scholar 

  • Nicholson P, Mühlemann O (2010) Cutting the nonsense: the degradation of PTC-containing mRNAs. Biochem Soc Trans 38(6):1615–1620

    Article  PubMed  CAS  Google Scholar 

  • Nicholson P, Yepiskoposyan H, Metze S, Zamudio Orozco R, Kleinschmidt N, Mühlemann O (2010) Nonsense-mediated mRNA decay in human cells: mechanistic insights, functions beyond quality control and the double-lifeof NMD factors. Cell Mol Life Sci 67(5):677–700

    Article  PubMed  CAS  Google Scholar 

  • Noensie EN, Dietz HC (2001) A strategy for disease gene identification through nonsense-mediated mRNA decay inhibition. Nat Biotechnol 19(5):434–439

    Article  PubMed  CAS  Google Scholar 

  • Nyikó T, Kerényi F, Szabadkai L, Benkovics AH, Major P, Sonkoly B, Mérai Z, Barta E, Niemiec E, Kufel J, Silhavy D (2013) Plant nonsense-mediated mRNA decay is controlled by different autoregulatory circuits and can be induced by an EJC-like complex. Nucl Acid Res 41(13):6715–6728

    Article  CAS  Google Scholar 

  • Okada-Katsuhata Y, Yamashita A, Kutsuzawa K, Izumi N, Hirahara F, Ohno S (2012) N- and C-terminal Upf1 phosphorylations create binding platforms for SMG-6 and SMG-5: SMG-7 during NMD. Nucl Acid Res 40(3):1251–1266. doi:10.1093/nar/gkr791 Epub 2011 Sep 29

    Article  CAS  Google Scholar 

  • Palusa SG, Ali GS, Reddy AS (2007) Alternative splicing of pre-mRNAs of Arabidopsis serine/arginine-rich proteins: regulation by hormones and stresses. Plant J 49(6):1091–1107

    Article  PubMed  CAS  Google Scholar 

  • Park NI, Muench DG (2007) Biochemical and cellular characterization of the plant ortholog of PYM, a protein that interacts with the exon junction complex core proteins Mago and Y14. Planta 225(3):625–639

    Article  PubMed  CAS  Google Scholar 

  • Perrin-Vidoz L, Sinilnikova OM, Stoppa-Lyonnet D, Lenoir GM, Mazoyer S (2002) The nonsense-mediated mRNA decay pathway triggers degradation of most BRCA1 mRNAs bearing premature termination codons. Hum Mol Genet 11(23):2805–2814

    Article  PubMed  CAS  Google Scholar 

  • Petracek ME, Nuygen T, Thompson WF, Dickey LF (2000) Premature termination codons destabilize ferredoxin-1 mRNA when ferredoxin-1 is translated. Plant J 21(6):563–569

    Article  PubMed  CAS  Google Scholar 

  • Pontes O, Pikaard CS (2008) siRNA and miRNA processing: new functions for Cajal bodies. Curr Opin Genet Dev 18(2):197–203

    Article  PubMed  PubMed Central  CAS  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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Rayson S, Arciga-Reyes L, Wootton L, De Torres Zabala M, Truman W, Graham N, Grant M, Davies B (2012a) A Role for nonsense-mediated mRNA decay in plants: pathogen responses are induced in Arabidopsis thaliana NMD mutants. PLoS One 7(2):e31917

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Rayson S, Ashworth M, de Torres Zabala M, Grant M, Davies B (2012b) The salicylic acid dependent and independent effects of NMD in plants. Plant Signal Behav 7(11):1434–1437

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Rebbapragada I, Lykke-Andersen J (2009) Execution of nonsense-mediated mRNA decay: what defines a substrate? Curr Opin Cell Biol 21(3):394–402

    Article  PubMed  CAS  Google Scholar 

  • Reddy AS (2004) Plant serine/arginine-rich proteins and their role in pre-mRNA splicing. Trends Plant Sci 9(11):541–547

    Article  PubMed  CAS  Google Scholar 

  • Reddy AS, Shad Ali G (2011) Plant serine/arginine-rich proteins: roles in precursor messenger RNA splicing, plant development, and stress responses. Wiley Interdiscip Rev RNA 2(6):875–889

    Article  PubMed  CAS  Google Scholar 

  • Reed R, Cheng H (2005) TREX, SR proteins and export of mRNA. Curr Opin Cell Biol 17(3):269–273

    Article  PubMed  CAS  Google Scholar 

  • Rehwinkel J, Behm-Ansmant I, Gatfield D, Izaurralde E (2005) A crucial role for GW182 and the DCP1:DCP2 decapping complex in miRNA-mediated gene silencing. RNA 11(11):1640–1647

    Article  PubMed  PubMed Central  CAS  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(Pt13):2208–2216

    Article  PubMed  CAS  Google Scholar 

  • Riehs-Kearnan N, Gloggnitzer J, Dekrout B, Jonak C, Riha K (2012) Aberrant growth and lethality of Arabidopsis deficient in nonsense-mediated RNA decay factors is caused by autoimmune-like response. Nucl Acid Res 40(12):5615–5624

    Article  CAS  Google Scholar 

  • Rodriguez MS, Dargemont C, Stutz F (2004) Nuclear export of RNA. Biol Cell 96(8):639–655

    Article  PubMed  CAS  Google Scholar 

  • Rossi MR, Hawthorn L, Platt J, Burkhardt T, Cowell JK, Ionov Y (2005) Identification of inactivating mutations in the JAK1, SYNJ2, and CLPTM1 genes in prostate cancer cells using inhibition of nonsense mediated decay and microarray analysis. Cancer Genet Cytogenet 161(2):97–103

    Article  PubMed  CAS  Google Scholar 

  • Ruiz-Echevarría MJ, González CI, Peltz SW (1998) Identifying the right stop: determining how the surveillance complex recognizes and degrades an aberrant mRNA. EMBO J 17(2):575–589

    Article  PubMed  PubMed Central  Google Scholar 

  • Rymarquis LA, Souret FF, Green PJ (2011) Evidence that XRN4, an Arabidopsis homolog of exoribonuclease XRN1, preferentially impacts transcripts with certain sequences or in particular functional categories. RNA 17(3):501–511

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Schilders G, van Dijk E, Raijmakers R, Pruijn GJ (2006) Cell and molecular biology of the exosome: how to make or break an RNA. Int Rev Cytol 251:159–208

    Article  PubMed  CAS  Google Scholar 

  • Schwartz AM, Komarova TV, Skulachev MV, Zvereva AS, Dorokhov YL, Atabekov JG (2006) Stability of plant mRNAs depends on the length of the 3′-untranslated region. Biochem (Mosc) 71(12):1377–1384. doi:10.1134/S0006297906120145

    Article  CAS  Google Scholar 

  • Sheth U, Parker R (2006) Targeting of aberrant mRNAs to cytoplasmic processing bodies. Cell 125(6):1095–1109

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Shi C, Baldwin IT, Wu J (2012) Arabidopsis plants having defects in nonsense-mediated mRNA decay factors UPF1, UPF2 and UPF3 show photoperiod-dependent phenotypes in development and stress responses. J Integr Plant Biol 54(2):99–114

    Article  PubMed  CAS  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

    Article  PubMed  CAS  Google Scholar 

  • Stokes TL, Kunkel BN, Richards EJ (2002) Epigenetic variation in Arabidopsis disease resistance. Genes Dev 16(2):171–182

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Suzuki T, Izumi H, Ohno M (2010) Cajal body surveillance of U snRNA export complex assembly. J Cell Biol 190(4):603–612

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Swidzinski JA, Zaplachinski ST, Chuong SD, Wong JF, Muench DG (2001) Molecular characterization and expression analysis of a highly conserved rice mago nashi homolog. Genome 44(3):394–400

    Article  PubMed  CAS  Google Scholar 

  • Tange TØ, Shibuya T, Jurica MS, Moore MJ (2005) Biochemical analysis of the EJC reveals two new factors and a stable tetrameric protein core. RNA 11(12):1869–1883

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Unterholzner L, Izaurralde E (2004) SMG7 acts as a molecular link between mRNA surveillance and mRNA decay. Mol Cell 16(4):587–596

    Article  PubMed  CAS  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

    Article  PubMed  Google Scholar 

  • Vancanneyt G, Rosahl S, Willmitzer L (1990) Translatability of a plant-mRNA strongly influences its accumulation in transgenic plants. Nucl Acid Res 18(10):2917–2921

    Article  CAS  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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Vogel F, Hofius D, Paulus KE, Jungkunz I, Sonnewald U (2011) The second face of a known player: Arabidopsis silencing suppressor AtXRN4 acts organ-specifically. N Phytol 189:484–493

    Article  CAS  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

    Article  PubMed  CAS  Google Scholar 

  • Xu J, Chua NH (2009) Arabidopsis decapping 5 is required for mRNA decapping, P-body formation, and translational repression during postembryonic development. Plant Cell 21(10):3270–3279

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Xu J, Chua NH (2011) Processing bodies and plant development. Curr Opin Plant Biol 14(1):88–93

    Article  PubMed  CAS  Google Scholar 

  • Yi H, Richards EJ (2007) A cluster of disease resistance genes in Arabidopsis is coordinately regulated by transcriptional activation and RNA Silencing. Plant Cell 19(9):2929–2939

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Yoine M, Nishii T, Nakamura K (2006a) b) Arabidopsis UPF1 RNA helicase for nonsense-mediated mRNA decay is involved in seed size control and is essential for growth. Plant Cell Physiol 47(5):572–580

    Article  PubMed  CAS  Google Scholar 

  • Yoine M, Ohto MA, Onai K, Mita S, Nakamura K (2006b) a) 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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

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Acknowledgments

This work was supported by the Agriculture Key Research Project of in the Department of Science in Liaoning Province, China. The fund number is 2011208001(CN).

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  1. School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China

    Yiming Dai, Wenli Li & Lijia An

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  1. Yiming Dai
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Dai, Y., Li, W. & An, L. NMD mechanism and the functions of Upf proteins in plant. Plant Cell Rep 35, 5–15 (2016). https://doi.org/10.1007/s00299-015-1867-9

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  • DOI: https://doi.org/10.1007/s00299-015-1867-9

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