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Plant upstream ORFs can trigger nonsense-mediated mRNA decay in a size-dependent manner

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Abstract

Nonsense-mediated decay (NMD) is a quality control mechanism that identifies and degrades aberrant mRNAs containing premature termination codons (PTC). NMD also regulates the expression of many wild-type genes. In plants, NMD identifies a stop codon as a PTC and initiates the rapid degradation of the transcript if the 3′untranslated region (UTR) is unusually long or if it harbors an intron. Approximately 20% of plant transcripts have an upstream ORF (uORF) in the 5′UTR. In theory, if a uORF is translated, the 3′UTR downstream of the uORF will be long and harbor introns, thus these transcripts might be degraded by NMD. Therefore, if uORFs can trigger NMD, uORF containing transcripts would be a major group of NMD regulated wild-type plant mRNAs. The aim of this study was to clarify whether plant uORFs could activate NMD. Here we demonstrate that plant uORFs induce NMD in a size-dependent manner, a 50 amino acid (aa) long uORF triggered NMD efficiently, whereas similar but shorter (31 and 15 aa long) uORFs failed to activate NMD response. We have found that only ~2% of annotated Arabidopsis genes contain a first uORF that is longer than 35 aa, thus we propose that NMD regulates only a small fraction of uORF containing transcripts. However, as mRNAs having uORF that is longer than the critical size are strongly overrepresented within the up-regulated transcripts of NMD deficient plants, it is likely that this subset of natural NMD targets induces NMD because of containing a relatively long translatable uORF.

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Abbreviations

NMD:

Nonsense-mediated mRNA decay

uORF:

Upstream ORF

VIGS:

Virus-induced gene silencing

UTR:

Untranslated region

EJC:

Exon-junction complex

eRF:

Eukaryotic releasing factor

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Acknowledgments

We are grateful to C. Lacomme (University of Edinburgh), D. Baulcombe (University of Cambridge) and S. P. Dinesh-Kumar (Yale University) for TRV vectors. This research was supported by grants from the OTKA (K60102 and C77086) and from the National Office for Research and Technology (4/064/2004, “Búzakalász”). We thank E. Barta (University of Debrecen) for his help with bioinformatical studies. D. Silhavy was supported by the Bolyai János Scholarship. T. Nyikó and Zs. Mérai are graduate students of ELTE “Classical and Molecular Genetics” PhD program. A. Hangyáné Benkovics is a graduate student of Corvinus University of Budapest (“Program of Viticulture” at the Doctoral School of Horticulture).

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Authors and Affiliations

  1. Agricultural Biotechnology Center, Szent-Györgyi 4, 2100, Gödöllő, Hungary

    Tünde Nyikó, Boglárka Sonkoly, Zsuzsanna Mérai, Anna Hangyáné Benkovics & Dániel Silhavy

  2. Faculty of Horticultural Science, Corvinus University of Budapest, Villányi 29-43, 1118, Budapest, Hungary

    Anna Hangyáné Benkovics

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  1. Tünde Nyikó
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  2. Boglárka Sonkoly
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  3. Zsuzsanna Mérai
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  4. Anna Hangyáné Benkovics
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  5. Dániel Silhavy
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Correspondence to Dániel Silhavy.

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Tünde Nyikó and Boglárka Sonkoly contributed equally to this work.

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Nyikó, T., Sonkoly, B., Mérai, Z. et al. Plant upstream ORFs can trigger nonsense-mediated mRNA decay in a size-dependent manner. Plant Mol Biol 71, 367 (2009). https://doi.org/10.1007/s11103-009-9528-4

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