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Gloggnitzer J, Akimcheva S, Srinivasan A, Kusenda B, Riehs N, Stampfl H, Bautor J, Dekrout B, Jonak C, Jiménez-Gómez JM, Parker JE, Riha K. Nonsense-mediated mRNA decay modulates immune receptor levels to regulate plant antibacterial defense. Cell Host Microbe 2015; 16:376-90. [PMID: 25211079 DOI: 10.1016/j.chom.2014.08.010] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 07/29/2014] [Accepted: 08/24/2014] [Indexed: 12/15/2022]
Abstract
Nonsense-mediated mRNA decay (NMD) is a conserved eukaryotic RNA surveillance mechanism that degrades aberrant mRNAs. NMD impairment in Arabidopsis is linked to constitutive immune response activation and enhanced antibacterial resistance, but the underlying mechanisms are unknown. Here we show that NMD contributes to innate immunity in Arabidopsis by controlling the turnover of numerous TIR domain-containing, nucleotide-binding, leucine-rich repeat (TNL) immune receptor-encoding mRNAs. Autoimmunity resulting from NMD impairment depends on TNL signaling pathway components and can be triggered through deregulation of a single TNL gene, RPS6. Bacterial infection of plants causes host-programmed inhibition of NMD, leading to stabilization of NMD-regulated TNL transcripts. Conversely, constitutive NMD activity prevents TNL stabilization and impairs plant defense, demonstrating that host-regulated NMD contributes to disease resistance. Thus, NMD shapes plant innate immunity by controlling the threshold for activation of TNL resistance pathways.
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Affiliation(s)
- Jiradet Gloggnitzer
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr.-Bohr-Gasse 3, 1030 Vienna, Austria.
| | - Svetlana Akimcheva
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr.-Bohr-Gasse 3, 1030 Vienna, Austria
| | - Arunkumar Srinivasan
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Branislav Kusenda
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr.-Bohr-Gasse 3, 1030 Vienna, Austria
| | - Nina Riehs
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr.-Bohr-Gasse 3, 1030 Vienna, Austria
| | - Hansjörg Stampfl
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr.-Bohr-Gasse 3, 1030 Vienna, Austria
| | - Jaqueline Bautor
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Bettina Dekrout
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr.-Bohr-Gasse 3, 1030 Vienna, Austria
| | - Claudia Jonak
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr.-Bohr-Gasse 3, 1030 Vienna, Austria
| | - José M Jiménez-Gómez
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany; Institut Jean-Pierre Bourgin, UMR1318, INRA-AgroParisTech, 78000 Versailles, France
| | - Jane E Parker
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Karel Riha
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr.-Bohr-Gasse 3, 1030 Vienna, Austria; CEITEC, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic.
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Kalyna M, Simpson CG, Syed NH, Lewandowska D, Marquez Y, Kusenda B, Marshall J, Fuller J, Cardle L, McNicol J, Dinh HQ, Barta A, Brown JWS. Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis. Nucleic Acids Res 2012; 40:2454-69. [PMID: 22127866 PMCID: PMC3315328 DOI: 10.1093/nar/gkr932] [Citation(s) in RCA: 338] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 09/22/2011] [Accepted: 10/10/2011] [Indexed: 11/26/2022] Open
Abstract
Alternative splicing (AS) coupled to nonsense-mediated decay (NMD) is a post-transcriptional mechanism for regulating gene expression. We have used a high-resolution AS RT-PCR panel to identify endogenous AS isoforms which increase in abundance when NMD is impaired in the Arabidopsis NMD factor mutants, upf1-5 and upf3-1. Of 270 AS genes (950 transcripts) on the panel, 102 transcripts from 97 genes (32%) were identified as NMD targets. Extrapolating from these data around 13% of intron-containing genes in the Arabidopsis genome are potentially regulated by AS/NMD. This cohort of naturally occurring NMD-sensitive AS transcripts also allowed the analysis of the signals for NMD in plants. We show the importance of AS in introns in 5' or 3'UTRs in modulating NMD-sensitivity of mRNA transcripts. In particular, we identified upstream open reading frames overlapping the main start codon as a new trigger for NMD in plants and determined that NMD is induced if 3'-UTRs were >350 nt. Unexpectedly, although many intron retention transcripts possess NMD features, they are not sensitive to NMD. Finally, we have shown that AS/NMD regulates the abundance of transcripts of many genes important for plant development and adaptation including transcription factors, RNA processing factors and stress response genes.
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Affiliation(s)
- Maria Kalyna
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria, Cell and Molecular Sciences, The James Hutton Institute, Division of Plant Sciences, University of Dundee at JHI, Biomathematics and Statistics Scotland at JHI, Invergowrie, Dundee DD2 5DA, Scotland, UK and Center for Integrative Bioinformatics, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - Craig G. Simpson
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria, Cell and Molecular Sciences, The James Hutton Institute, Division of Plant Sciences, University of Dundee at JHI, Biomathematics and Statistics Scotland at JHI, Invergowrie, Dundee DD2 5DA, Scotland, UK and Center for Integrative Bioinformatics, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - Naeem H. Syed
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria, Cell and Molecular Sciences, The James Hutton Institute, Division of Plant Sciences, University of Dundee at JHI, Biomathematics and Statistics Scotland at JHI, Invergowrie, Dundee DD2 5DA, Scotland, UK and Center for Integrative Bioinformatics, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - Dominika Lewandowska
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria, Cell and Molecular Sciences, The James Hutton Institute, Division of Plant Sciences, University of Dundee at JHI, Biomathematics and Statistics Scotland at JHI, Invergowrie, Dundee DD2 5DA, Scotland, UK and Center for Integrative Bioinformatics, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - Yamile Marquez
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria, Cell and Molecular Sciences, The James Hutton Institute, Division of Plant Sciences, University of Dundee at JHI, Biomathematics and Statistics Scotland at JHI, Invergowrie, Dundee DD2 5DA, Scotland, UK and Center for Integrative Bioinformatics, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - Branislav Kusenda
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria, Cell and Molecular Sciences, The James Hutton Institute, Division of Plant Sciences, University of Dundee at JHI, Biomathematics and Statistics Scotland at JHI, Invergowrie, Dundee DD2 5DA, Scotland, UK and Center for Integrative Bioinformatics, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - Jacqueline Marshall
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria, Cell and Molecular Sciences, The James Hutton Institute, Division of Plant Sciences, University of Dundee at JHI, Biomathematics and Statistics Scotland at JHI, Invergowrie, Dundee DD2 5DA, Scotland, UK and Center for Integrative Bioinformatics, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - John Fuller
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria, Cell and Molecular Sciences, The James Hutton Institute, Division of Plant Sciences, University of Dundee at JHI, Biomathematics and Statistics Scotland at JHI, Invergowrie, Dundee DD2 5DA, Scotland, UK and Center for Integrative Bioinformatics, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - Linda Cardle
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria, Cell and Molecular Sciences, The James Hutton Institute, Division of Plant Sciences, University of Dundee at JHI, Biomathematics and Statistics Scotland at JHI, Invergowrie, Dundee DD2 5DA, Scotland, UK and Center for Integrative Bioinformatics, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - Jim McNicol
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria, Cell and Molecular Sciences, The James Hutton Institute, Division of Plant Sciences, University of Dundee at JHI, Biomathematics and Statistics Scotland at JHI, Invergowrie, Dundee DD2 5DA, Scotland, UK and Center for Integrative Bioinformatics, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - Huy Q. Dinh
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria, Cell and Molecular Sciences, The James Hutton Institute, Division of Plant Sciences, University of Dundee at JHI, Biomathematics and Statistics Scotland at JHI, Invergowrie, Dundee DD2 5DA, Scotland, UK and Center for Integrative Bioinformatics, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - Andrea Barta
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria, Cell and Molecular Sciences, The James Hutton Institute, Division of Plant Sciences, University of Dundee at JHI, Biomathematics and Statistics Scotland at JHI, Invergowrie, Dundee DD2 5DA, Scotland, UK and Center for Integrative Bioinformatics, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
| | - John W. S. Brown
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria, Cell and Molecular Sciences, The James Hutton Institute, Division of Plant Sciences, University of Dundee at JHI, Biomathematics and Statistics Scotland at JHI, Invergowrie, Dundee DD2 5DA, Scotland, UK and Center for Integrative Bioinformatics, Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, University of Veterinary Medicine Vienna, Dr. Bohr-Gasse 9/3, A-1030 Vienna, Austria
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