The salicylic acid dependent and independent effects of NMD in plants

References

• Maquat LE. Nonsense-mediated mRNA decay in mammals. J Cell Sci 2005; 118:1773 - 6; http://www.ncbi.nlm.nih.gov/pubmed/15860725 10.1242/jcs.01701; PMID: 15860725
   PubMed Web of Science ®Google Scholar
• He F, Li XR, Spatrick P, Casillo R, Dong SY, Jacobson A. Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5′ to 3′ mRNA decay pathways in yeast. Molecular Cell 20003; 12:1439-52; PMID:14690598; http://www.ncbi.nlm.nih.gov/pubmed/14690598
   Google Scholar
• Mendell JT, Sharifi NA, Meyers JL, Martinez-Murillo F, Dietz HC. Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat Genet 2004; 36:1073 - 8; http://www.ncbi.nlm.nih.gov/pubmed/15448691 10.1038/ng1429; PMID: 15448691
   PubMed Web of Science ®Google Scholar
• Rehwinkel A, Letunic I, Raes J, Bork P, Izaurralde E. Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets. RNA-a Publication of the RNA Society 2005; 11:1530-44; PMID:16199763; http://www.ncbi.nlm.nih.gov/pubmed/16199763
   Google Scholar
• Guan QN, Zheng W, Tang SJ, Liu XS, Zinkel RA, Tsui KW, et al. Impact of nonsense-mediated mRNA decay on the global expression profile of budding yeast. PLoS Genet 2006; 2:e203; http://www.ncbi.nlm.nih.gov/pubmed/17166056 10.1371/journal.pgen.0020203; PMID: 17166056
   PubMed Web of Science ®Google Scholar
• Kurihara Y, Matsui A, Hanada K, Kawashima M, Ishida J, Morosawa T, et al. Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis. Proc Natl Acad Sci U S A 2009; 106:2453 - 8; http://www.ncbi.nlm.nih.gov/pubmed/19181858 10.1073/pnas.0808902106; PMID: 19181858
   PubMed Web of Science ®Google Scholar
• Hori K, Watanabe Y. UPF3 supresses aberrant spliced mRNA in Arabidopsis. Plant J 2006; 43:530 - 40; http://www.ncbi.nlm.nih.gov/pubmed/16098107 10.1111/j.1365-313X.2005.02473.x
   Web of Science ®Google Scholar
• Yoine M, Nishii T, Nakamura K. Arabidopsis UPF1 RNA helicase for nonsense-mediated mRNA decay is involved in seed size control and is essential for growth. Plant Cell Physiol 2006; 47:572 - 80; http://www.ncbi.nlm.nih.gov/pubmed/16540482 10.1093/pcp/pcj035; PMID: 16540482
   PubMed Web of Science ®Google Scholar
• Arciga-Reyes L, Wootton L, Kieffer M, Davies B. UPF1 is required for nonsense-mediated mRNA decay (NMD) and RNAi in Arabidopsis. Plant J 2006; 47:480 - 9; http://www.ncbi.nlm.nih.gov/pubmed/16813578 10.1111/j.1365-313X.2006.02802.x; PMID: 16813578
   PubMed Web of Science ®Google Scholar
• Kerényi Z, Mérai Z, Hiripi L, Benkovics A, Gyula P, Lacomme C, et al. Inter-kingdom conservation of mechanism of nonsense-mediated mRNA decay. EMBO J 2008; 27:1585 - 95; http://www.ncbi.nlm.nih.gov/pubmed/18451801 10.1038/emboj.2008.88; PMID: 18451801
   PubMed Web of Science ®Google Scholar
• Kertész S, Kerényi Z, Mérai Z, Bartos I, Pálfy T, Barta E, et al. Both introns and long 3′-UTRs operate as cis-acting elements to trigger nonsense-mediated decay in plants. Nucleic Acids Res 2006; 34:6147 - 57; http://www.ncbi.nlm.nih.gov/pubmed/17088291 10.1093/nar/gkl737; PMID: 17088291
   PubMed Web of Science ®Google Scholar
• Nyikó T, Sonkoly B, Mérai Z, Benkovics AH, Silhavy D. Plant upstream ORFs can trigger nonsense-mediated mRNA decay in a size-dependent manner. Plant Mol Biol 2009; 71:367 - 78; http://www.ncbi.nlm.nih.gov/pubmed/19653106 10.1007/s11103-009-9528-4; PMID: 19653106
   PubMed Web of Science ®Google Scholar
• Rayson S, Arciga-Reyes L, Wootton L, De Torres Zabala M, Truman W, Graham N, et al. A role for nonsense-mediated mRNA decay in plants: pathogen responses are induced in Arabidopsis thaliana NMD mutants. PLoS One 2012; 7:e31917; http://www.ncbi.nlm.nih.gov/pubmed/22384098 10.1371/journal.pone.0031917; PMID: 22384098
   PubMed Web of Science ®Google Scholar
• Riehs-Kearnan N, Gloggnitzer J, Dekrout B, Jonak C, Riha K. Aberrant growth and lethality of Arabidopsis deficient in nonsense-mediated RNA decay factors is caused by autoimmune-like response. Nucleic Acids Research 2012; doi: 10.1093/nar/gks195; PMID:22379136; http://www.ncbi.nlm.nih.gov/pubmed/22379136
   Google Scholar
• Shi C, Baldwin IT, Wu J. 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 2012; 54:99 - 114; http://www.ncbi.nlm.nih.gov/pubmed/22353561 10.1111/j.1744-7909.2012.01093.x; PMID: 22353561
   PubMed Web of Science ®Google Scholar
• Jeong H-J, Kim YJ, Kim SH, Kim Y-H, Lee I-J, Kim YK. Nonsense-mediated mRNA decay factors, UPF1 and UPF3, contribute to plant defense. Plant & Cell Physiology 2011; 52: 2147-56; PMID: 22025558; http://www.ncbi.nlm.nih.gov/pubmed/ 22025558.
   Google Scholar
• Wildermuth MC, Dewdney J, Wu G, Ausubel FM. Isochorismate synthase is required to synthesize salicylic acid for plant defence. Nature 2001; 414:562 - 5; http://www.ncbi.nlm.nih.gov/pubmed/11734859 10.1038/35107108; PMID: 11734859
   PubMed Web of Science ®Google Scholar
• Hayden CA, Jorgensen RA. Identification of novel conserved peptide uORF homology groups in Arabidopsis and rice reveals ancient eukaryotic origin of select groups and preferential association with transcription factor-encoding genes. BMC Biol 2007; 5:32; http://www.ncbi.nlm.nih.gov/pubmed/17663791 10.1186/1741-7007-5-32; PMID: 17663791
   PubMed Web of Science ®Google Scholar
• Tran MK, Schultz CJ, Baumann U. Conserved upstream open reading frames in higher plants. BMC Genomics 2008; 9:361; http://www.ncbi.nlm.nih.gov/pubmed/18667093 10.1186/1471-2164-9-361; PMID: 18667093
   PubMed Web of Science ®Google Scholar
• Takahashi H, Takahashi A, Naito S, Onouchi H. BAIUCAS: a novel BLAST-based algorithm for the identification of upstream open reading frames with conserved amino acid sequences, and its application to the Arabidopsis thaliana genome. Bioinformatics 2012; PMID:22618534; http://www.ncbi.nlm.nih.gov/pubmed/22618534
   Google Scholar
• Kawaguchi R, Bailey-Serres J. mRNA sequence features that contribute to translational regulation in Arabidopsis.. Nucleic Acids Res 2005; 33:955 - 65; http://www.ncbi.nlm.nih.gov/pubmed/15716313 10.1093/nar/gki240; PMID: 15716313
   PubMed Web of Science ®Google Scholar
• Cao J, Geballe AP. Inhibition of nascent-peptide release at translation termination. Mol Cell Biol 1996; 16:7109 - 14; http://www.ncbi.nlm.nih.gov/pubmed/8943366 PMID: 8943366
   PubMed Web of Science ®Google Scholar
• Luo Z, Sachs MS. Role of an upstream open reading frame in mediating arginine-specific translational control in Neurospora crassa.. J Bacteriol 1996; 178:2172 - 7; http://www.ncbi.nlm.nih.gov/pubmed/8636015 PMID: 8636015
   PubMed Web of Science ®Google Scholar
• Ruan H, Shantz LM, Pegg AE, Morris DR. The upstream open reading frame of the mRNA encoding S-adenosylmethionine decarboxylase is a polyamine-responsive translational control element. J Biol Chem 1996; 271:29576 - 82; http://www.ncbi.nlm.nih.gov/pubmed/8939886 10.1074/jbc.271.47.29576; PMID: 8939886
   PubMed Web of Science ®Google Scholar
• Gaba A, Jacobson A, Sachs MS. Ribosome occupancy of the yeast CPA1 upstream open reading frame termination codon modulates nonsense-mediated mRNA decay. Mol Cell 2005; 20:449 - 60; http://www.ncbi.nlm.nih.gov/pubmed/16285926 10.1016/j.molcel.2005.09.019; PMID: 16285926
   PubMed Web of Science ®Google Scholar
• Jirage D, Tootle TL, Reuber TL, Frost LN, Feys BJ, Parker JE, et al. Arabidopsis thaliana PAD4 encodes a lipase-like gene that is important for salicylic acid signaling. Proc Natl Acad Sci U S A 1999; 96:13583 - 8; http://www.ncbi.nlm.nih.gov/pubmed/10557364 10.1073/pnas.96.23.13583; PMID: 10557364
   PubMed Web of Science ®Google Scholar
• Feys BJ, Moisan LJ, Newman M-A, Parker JE. Direct interaction between the Arabidopsis disease resistance signaling proteins, EDS1 and PAD4. EMBO J 2001; 20:5400 - 11; http://www.ncbi.nlm.nih.gov/pubmed/11574472 10.1093/emboj/20.19.5400; PMID: 11574472
   PubMed Web of Science ®Google Scholar
• Craigon DJ, James N, Okyere J, Higgins J, Jotham J, May S. NASCArrays: a repository for microarray data generated by NASC’s transcriptomics service. Nucleic Acids Res 2004; 32:Database issue D575 - 7; http://www.ncbi.nlm.nih.gov/pubmed/14681484 10.1093/nar/gkh133; PMID: 14681484
   PubMed Web of Science ®Google Scholar