1
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Nagarajan VK, Stuart CJ, DiBattista AT, Accerbi M, Caplan JL, Green PJ. RNA degradome analysis reveals DNE1 endoribonuclease is required for the turnover of diverse mRNA substrates in Arabidopsis. THE PLANT CELL 2023; 35:1936-1955. [PMID: 37070465 PMCID: PMC10226599 DOI: 10.1093/plcell/koad085] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 03/01/2023] [Accepted: 03/04/2023] [Indexed: 05/30/2023]
Abstract
In plants, cytoplasmic mRNA decay is critical for posttranscriptionally controlling gene expression and for maintaining cellular RNA homeostasis. Arabidopsis DCP1-ASSOCIATED NYN ENDORIBONUCLEASE 1 (DNE1) is a cytoplasmic mRNA decay factor that interacts with proteins involved in mRNA decapping and nonsense-mediated mRNA decay (NMD). There is limited information on the functional role of DNE1 in RNA turnover, and the identities of its endogenous targets are unknown. In this study, we utilized RNA degradome approaches to globally investigate DNE1 substrates. Monophosphorylated 5' ends, produced by DNE1, should accumulate in mutants lacking the cytoplasmic exoribonuclease XRN4, but be absent from DNE1 and XRN4 double mutants. In seedlings, we identified over 200 such transcripts, most of which reflect cleavage within coding regions. While most DNE1 targets were NMD-insensitive, some were upstream ORF (uORF)-containing and NMD-sensitive transcripts, indicating that this endoribonuclease is required for turnover of a diverse set of mRNAs. Transgenic plants expressing DNE1 cDNA with an active-site mutation in the endoribonuclease domain abolished the in planta cleavage of transcripts, demonstrating that DNE1 endoribonuclease activity is required for cleavage. Our work provides key insights into the identity of DNE1 substrates and enhances our understanding of DNE1-mediated mRNA decay.
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Affiliation(s)
- Vinay K Nagarajan
- Delaware Biotechnology Institute, University of Delaware,
Newark, DE 19713-1316, USA
| | - Catherine J Stuart
- Delaware Biotechnology Institute, University of Delaware,
Newark, DE 19713-1316, USA
| | - Anna T DiBattista
- Delaware Biotechnology Institute, University of Delaware,
Newark, DE 19713-1316, USA
| | - Monica Accerbi
- Delaware Biotechnology Institute, University of Delaware,
Newark, DE 19713-1316, USA
| | - Jeffrey L Caplan
- Bio-Imaging Center, Delaware Biotechnology Institute, University of
Delaware, Newark, DE 19713-1316, USA
| | - Pamela J Green
- Delaware Biotechnology Institute, University of Delaware,
Newark, DE 19713-1316, USA
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2
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The biological functions of nonsense-mediated mRNA decay in plants: RNA quality control and beyond. Biochem Soc Trans 2023; 51:31-39. [PMID: 36695509 DOI: 10.1042/bst20211231] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/26/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is an evolutionarily conserved quality control pathway that inhibits the expression of transcripts containing premature termination codon. Transcriptome and phenotypic studies across a range of organisms indicate roles of NMD beyond RNA quality control and imply its involvement in regulating gene expression in a wide range of physiological processes. Studies in moss Physcomitrella patens and Arabidopsis thaliana have shown that NMD is also important in plants where it contributes to the regulation of pathogen defence, hormonal signalling, circadian clock, reproduction and gene evolution. Here, we provide up to date overview of the biological functions of NMD in plants. In addition, we discuss several biological processes where NMD factors implement their function through NMD-independent mechanisms.
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3
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Wang Y, Deng XW, Zhu D. From molecular basics to agronomic benefits: Insights into noncoding RNA-mediated gene regulation in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2290-2308. [PMID: 36453685 DOI: 10.1111/jipb.13420] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
The development of plants is largely dependent on their growth environment. To better adapt to a particular habitat, plants have evolved various subtle regulatory mechanisms for altering gene expression. Non coding RNAs (ncRNAs) constitute a major portion of the transcriptomes of eukaryotes. Various ncRNAs have been recognized as important regulators of the expression of genes involved in essential biological processes throughout the whole life cycles of plants. In this review, we summarize the current understanding of the biogenesis and contributions of small nucle olar RNA (snoRNA)- and regulatory long non coding RNA (lncRNA)-mediated gene regulation in plant development and environmental responses. Many regulatory ncRNAs appear to be associated with increased yield, quality and disease resistance of various species and cultivars. These ncRNAs may potentially be used as genetic resources for improving agronomic traits and for molecular breeding. The challenges in understanding plant ncRNA biology and the possibilities to make better use of these valuable gene resources in the future are discussed in this review.
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Affiliation(s)
- Yuqiu Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325, China
| | - Danmeng Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
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4
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Smith CCR, Rieseberg LH, Hulke BS, Kane NC. Aberrant RNA splicing due to genetic incompatibilities in sunflower hybrids. Evolution 2021; 75:2747-2758. [PMID: 34533836 DOI: 10.1111/evo.14360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 06/27/2021] [Accepted: 09/01/2021] [Indexed: 01/18/2023]
Abstract
Genome-scale studies have revealed divergent mRNA splicing patterns between closely related species or populations. However, it is unclear whether splicing differentiation is a simple byproduct of population divergence, or whether it also acts as a mechanism for reproductive isolation. We examined mRNA splicing in wild × domesticated sunflower hybrids and observed 45 novel splice forms that were not found in the wild or domesticated parents, in addition to 16 high-expression parental splice forms that were absent in one or more hybrids. We identify loci associated with variation in the levels of these splice forms, finding that many aberrant transcripts were regulated by multiple alleles with nonadditive interactions. We identified particular spliceosome components that were associated with 21 aberrant isoforms, more than half of which were located in or near regulatory QTL. These incompatibilities often resulted in alteration in the protein-coding regions of the novel transcripts in the form of frameshifts and truncations. By associating the splice variation in these genes with size and growth rate measurements, we found that the cumulative expression of all aberrant transcripts was correlated with a significant reduction in growth rate. Our results lead us to propose a model where divergent splicing regulatory loci could act as incompatibility loci that contribute to the evolution of reproductive isolation.
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Affiliation(s)
- Chris C R Smith
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, 80309
| | - Loren H Rieseberg
- Department of Botany, University of British Columbia, Vancouver, BC, VCR 2A5, Canada
| | - Brent S Hulke
- Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, North Dakota, 58102
| | - Nolan C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, 80309
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5
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Raxwal VK, Simpson CG, Gloggnitzer J, Entinze JC, Guo W, Zhang R, Brown JWS, Riha K. Nonsense-Mediated RNA Decay Factor UPF1 Is Critical for Posttranscriptional and Translational Gene Regulation in Arabidopsis. THE PLANT CELL 2020; 32:2725-2741. [PMID: 32665305 PMCID: PMC7474300 DOI: 10.1105/tpc.20.00244] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/23/2020] [Accepted: 07/08/2020] [Indexed: 05/19/2023]
Abstract
Nonsense-mediated RNA decay (NMD) is an RNA control mechanism that has also been implicated in the broader regulation of gene expression. Nevertheless, a role for NMD in genome regulation has not yet been fully assessed, partially because NMD inactivation is lethal in many organisms. Here, we performed an in-depth comparative analysis of Arabidopsis (Arabidopsis thaliana) mutants lacking the NMD-related proteins UPF3, UPF1, and SMG7. We found different impacts of these proteins on NMD and the Arabidopsis transcriptome, with UPF1 having the biggest effect. Transcriptome assembly in UPF1-null plants revealed genome-wide changes in alternative splicing, suggesting that UPF1 functions in splicing. The inactivation of UPF1 led to translational repression, as manifested by a global shift in mRNAs from polysomes to monosomes and the downregulation of genes involved in translation and ribosome biogenesis. Despite these global changes, NMD targets and mRNAs expressed at low levels with short half-lives were enriched in the polysomes of upf1 mutants, indicating that UPF1/NMD suppresses the translation of aberrant RNAs. Particularly striking was an increase in the translation of TIR domain-containing, nucleotide binding, leucine-rich repeat (TNL) immune receptors. The regulation of TNLs via UPF1/NMD-mediated mRNA stability and translational derepression offers a dynamic mechanism for the rapid activation of TNLs in response to pathogen attack.
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Affiliation(s)
- Vivek K Raxwal
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Craig G Simpson
- Cell and Molecular Sciences, James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | | | - Juan Carlos Entinze
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - Wenbin Guo
- Information and Computational Sciences, James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - Runxuan Zhang
- Information and Computational Sciences, James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - John W S Brown
- Cell and Molecular Sciences, James Hutton Institute, Dundee DD2 5DA, United Kingdom
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - Karel Riha
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
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6
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Niyikiza D, Piya S, Routray P, Miao L, Kim WS, Burch-Smith T, Gill T, Sams C, Arelli PR, Pantalone V, Krishnan HB, Hewezi T. Interactions of gene expression, alternative splicing, and DNA methylation in determining nodule identity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1744-1766. [PMID: 32491251 DOI: 10.1111/tpj.14861] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/19/2020] [Accepted: 05/20/2020] [Indexed: 06/11/2023]
Abstract
Soybean nodulation is a highly controlled process that involves complex gene regulation at both transcriptional and post-transcriptional levels. In the present study, we profiled gene expression changes, alternative splicing events, and DNA methylation patterns during nodule formation, development, and senescence. The transcriptome data uncovered key transcription patterns of nodule development that included 9669 core genes and 7302 stage-specific genes. Alternative splicing analysis uncovered a total of 2323 genes that undergo alternative splicing events in at least one nodule developmental stage, with activation of exon skipping and repression of intron retention being the most common splicing events in nodules compared to roots. Approximately 40% of the differentially spliced genes were also differentially expressed at the same nodule developmental stage, implying a substantial association between gene expression and alternative splicing. Genome-wide-DNA methylation analysis revealed dynamic changes in nodule methylomes that were specific to each nodule stage, occurred in a sequence-specific manner, and impacted the expression of 1864 genes. An attractive hypothesis raised by our data is that increased DNA methylation may contribute to the efficiency of alternative splicing. Together, our results provide intriguing insights into the associations between gene expression, alternative splicing, and DNA methylation that may shape transcriptome complexity and proteome specificity in developing soybean nodules.
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Affiliation(s)
- Daniel Niyikiza
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Pratyush Routray
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Long Miao
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Won-Seok Kim
- Plant Science Division, University of Missouri, Columbia, MI, 65211, USA
| | - Tessa Burch-Smith
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996-0840, USA
| | - Tom Gill
- Smith Center for International Sustainable Agriculture, University of Tennessee, Knoxville, TN, 37996, USA
| | - Carl Sams
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | | | - Vince Pantalone
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Hari B Krishnan
- Plant Science Division, University of Missouri, Columbia, MI, 65211, USA
- Plant Genetics Research, USDA-Agricultural Research Service, Columbia, MI, 65211, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
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7
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Jung HW, Panigrahi GK, Jung GY, Lee YJ, Shin KH, Sahoo A, Choi ES, Lee E, Man Kim K, Yang SH, Jeon JS, Lee SC, Kim SH. Pathogen-Associated Molecular Pattern-Triggered Immunity Involves Proteolytic Degradation of Core Nonsense-Mediated mRNA Decay Factors During the Early Defense Response. THE PLANT CELL 2020; 32:1081-1101. [PMID: 32086363 PMCID: PMC7145493 DOI: 10.1105/tpc.19.00631] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 02/04/2020] [Accepted: 02/18/2020] [Indexed: 05/06/2023]
Abstract
Nonsense-mediated mRNA decay (NMD), an mRNA quality control process, is thought to function in plant immunity. A subset of fully spliced (FS) transcripts of Arabidopsis (Arabidopsis thaliana) resistance (R) genes are upregulated during bacterial infection. Here, we report that 81.2% and 65.1% of FS natural TIR-NBS-LRR (TNL) and CC-NBS-LRR transcripts, respectively, retain characteristics of NMD regulation, as their transcript levels could be controlled posttranscriptionally. Both bacterial infection and the perception of bacteria by pattern recognition receptors initiated the destruction of core NMD factors UP-FRAMESHIFT1 (UPF1), UPF2, and UPF3 in Arabidopsis within 30 min of inoculation via the independent ubiquitination of UPF1 and UPF3 and their degradation via the 26S proteasome pathway. The induction of UPF1 and UPF3 ubiquitination was delayed in mitogen-activated protein kinase3 (mpk3) and mpk6, but not in salicylic acid-signaling mutants, during the early immune response. Finally, previously uncharacterized TNL-type R transcripts accumulated in upf mutants and conferred disease resistance to infection with a virulent Pseudomonas strain in plants. Our findings demonstrate that NMD is one of the main regulatory processes through which PRRs fine-tune R transcript levels to reduce fitness costs and achieve effective immunity.
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Affiliation(s)
- Ho Won Jung
- Department of Applied Bioscience, Dong-A University, Busan 49315, Korea
| | - Gagan Kumar Panigrahi
- Department of Biosciences and Bioinformatics, Myongji University, Yongin 17058, Korea
- RNA Genomics Center, Myongji University, Yongin 17058, Korea
- School of Applied Sciences, Centurion University of Technology and Management, Odisha 752050, India
| | - Ga Young Jung
- Department of Applied Bioscience, Dong-A University, Busan 49315, Korea
| | - Yu Jeong Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Korea
| | - Ki Hun Shin
- Department of Biosciences and Bioinformatics, Myongji University, Yongin 17058, Korea
- RNA Genomics Center, Myongji University, Yongin 17058, Korea
| | - Annapurna Sahoo
- Department of Biosciences and Bioinformatics, Myongji University, Yongin 17058, Korea
- RNA Genomics Center, Myongji University, Yongin 17058, Korea
| | - Eun Su Choi
- Department of Applied Bioscience, Dong-A University, Busan 49315, Korea
| | - Eunji Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Korea
| | - Kyung Man Kim
- Department of Biosciences and Bioinformatics, Myongji University, Yongin 17058, Korea
- RNA Genomics Center, Myongji University, Yongin 17058, Korea
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu 59626, Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
| | - Sung Chul Lee
- School of Biological Sciences, Chung-Ang University, Seoul 06974, Korea
| | - Sang Hyon Kim
- Department of Biosciences and Bioinformatics, Myongji University, Yongin 17058, Korea
- RNA Genomics Center, Myongji University, Yongin 17058, Korea
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8
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Nagarajan VK, Kukulich PM, von Hagel B, Green PJ. RNA degradomes reveal substrates and importance for dark and nitrogen stress responses of Arabidopsis XRN4. Nucleic Acids Res 2019; 47:9216-9230. [PMID: 31428786 PMCID: PMC6755094 DOI: 10.1093/nar/gkz712] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 07/26/2019] [Accepted: 08/13/2019] [Indexed: 12/12/2022] Open
Abstract
XRN4, the plant cytoplasmic homolog of yeast and metazoan XRN1, catalyzes exoribonucleolytic degradation of uncapped mRNAs from the 5' end. Most studies of cytoplasmic XRN substrates have focused on polyadenylated transcripts, although many substrates are likely first deadenylated. Here, we report the global investigation of XRN4 substrates in both polyadenylated and nonpolyadenylated RNA to better understand the impact of the enzyme in Arabidopsis. RNA degradome analysis demonstrated that xrn4 mutants overaccumulate many more decapped deadenylated intermediates than those that are polyadenylated. Among these XRN4 substrates that have 5' ends precisely at cap sites, those associated with photosynthesis, nitrogen responses and auxin responses were enriched. Moreover, xrn4 was found to be defective in the dark stress response and lateral root growth during N resupply, demonstrating that XRN4 is required during both processes. XRN4 also contributes to nonsense-mediated decay (NMD) and xrn4 accumulates 3' fragments of select NMD targets, despite the lack of the metazoan endoribonuclease SMG6 in plants. Beyond demonstrating that XRN4 is a major player in multiple decay pathways, this study identified intriguing molecular impacts of the enzyme, including those that led to new insights about mRNA decay and discovery of functional contributions at the whole-plant level.
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Affiliation(s)
- Vinay K Nagarajan
- Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
| | - Patrick M Kukulich
- Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
| | - Bryan von Hagel
- Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
| | - Pamela J Green
- Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
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9
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Ohtani M, Wachter A. NMD-Based Gene Regulation-A Strategy for Fitness Enhancement in Plants? PLANT & CELL PHYSIOLOGY 2019; 60:1953-1960. [PMID: 31111919 DOI: 10.1093/pcp/pcz090] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/22/2019] [Indexed: 05/20/2023]
Abstract
Post-transcriptional RNA quality control is a vital issue for all eukaryotes to secure accurate gene expression, both on a qualitative and quantitative level. Among the different mechanisms, nonsense-mediated mRNA decay (NMD) is an essential surveillance system that triggers degradation of both aberrant and physiological transcripts. By targeting a substantial fraction of all transcripts for degradation, including many alternative splicing variants, NMD has a major impact on shaping transcriptomes. Recent progress on the transcriptome-wide profiling and physiological analyses of NMD-deficient plant mutants revealed crucial roles for NMD in gene regulation and environmental responses. In this review, we will briefly summarize our current knowledge of the recognition and degradation of NMD targets, followed by an account of NMD's regulation and physiological functions. We will specifically discuss plant-specific aspects of RNA quality control and its functional contribution to the fitness and environmental responses of plants.
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Affiliation(s)
- Misato Ohtani
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Andreas Wachter
- Institute for Molecular Physiology (imP), University of Mainz, Johannes von M�ller-Weg 6, Mainz, Germany
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10
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Chiam NC, Fujimura T, Sano R, Akiyoshi N, Hiroyama R, Watanabe Y, Motose H, Demura T, Ohtani M. Nonsense-Mediated mRNA Decay Deficiency Affects the Auxin Response and Shoot Regeneration in Arabidopsis. PLANT & CELL PHYSIOLOGY 2019; 60:2000-2014. [PMID: 31386149 DOI: 10.1093/pcp/pcz154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 07/21/2019] [Indexed: 06/10/2023]
Abstract
Plants generally possess a strong ability to regenerate organs; for example, in tissue culture, shoots can regenerate from callus, a clump of actively proliferating, undifferentiated cells. Processing of pre-mRNA and ribosomal RNAs is important for callus formation and shoot regeneration. However, our knowledge of the roles of RNA quality control via the nonsense-mediated mRNA decay (NMD) pathway in shoot regeneration is limited. Here, we examined the shoot regeneration phenotypes of the low-beta-amylase1 (lba1)/upstream frame shift1-1 (upf1-1) and upf3-1 mutants, in which the core NMD components UPF1 and UPF3 are defective. These mutants formed callus from hypocotyl explants normally, but this callus behaved abnormally during shoot regeneration: the mutant callus generated numerous adventitious root structures instead of adventitious shoots in an auxin-dependent manner. Quantitative RT-PCR and microarray analyses showed that the upf mutations had widespread effects during culture on shoot-induction medium. In particular, the expression patterns of early auxin response genes, including those encoding AUXIN/INDOLE ACETIC ACID (AUX/IAA) family members, were significantly affected in the upf mutants. Also, the upregulation of shoot apical meristem-related transcription factor genes, such as CUP-SHAPED COTYLEDON1 (CUC1) and CUC2, was inhibited in the mutants. Taken together, these results indicate that NMD-mediated transcriptomic regulation modulates the auxin response in plants and thus plays crucial roles in the early stages of shoot regeneration.
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Affiliation(s)
- Nyet-Cheng Chiam
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Tomoyo Fujimura
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Ryosuke Sano
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Nobuhiro Akiyoshi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Ryoko Hiroyama
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Yuichiro Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroyasu Motose
- Department of Biological Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Taku Demura
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Misato Ohtani
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
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11
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Kesarwani AK, Lee HC, Ricca PG, Sullivan G, Faiss N, Wagner G, Wunderling A, Wachter A. Multifactorial and Species-Specific Feedback Regulation of the RNA Surveillance Pathway Nonsense-Mediated Decay in Plants. PLANT & CELL PHYSIOLOGY 2019; 60:1986-1999. [PMID: 31368494 DOI: 10.1093/pcp/pcz141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 07/06/2019] [Indexed: 05/16/2023]
Abstract
Nonsense-mediated decay (NMD) is an RNA surveillance mechanism that detects aberrant transcript features and triggers degradation of erroneous as well as physiological RNAs. Originally considered to be constitutive, NMD is now recognized to be tightly controlled in response to inherent signals and diverse stresses. To gain a better understanding of NMD regulation and its functional implications, we systematically examined feedback control of the central NMD components in two dicot and one monocot species. On the basis of the analysis of transcript features, turnover rates and steady-state levels, up-frameshift (UPF) 1, UPF3 and suppressor of morphological defects on genitalia (SMG) 7, but not UPF2, are under feedback control in both dicots. In the monocot investigated in this study, only SMG7 was slightly induced upon NMD inhibition. The detection of the endogenous NMD factor proteins in Arabidopsis thaliana substantiated a negative correlation between NMD activity and SMG7 amounts. Furthermore, evidence was provided that SMG7 is required for the dephosphorylation of UPF1. Our comprehensive and comparative study of NMD feedback control in plants reveals complex and species-specific attenuation of this RNA surveillance pathway, with critical implications for the numerous functions of NMD in physiology and stress responses.
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Affiliation(s)
- Anil K Kesarwani
- Center for Plant Molecular Biology (ZMBP), University of T�bingen, Auf der Morgenstelle, 32 T�bingen, Germany
| | - Hsin-Chieh Lee
- Center for Plant Molecular Biology (ZMBP), University of T�bingen, Auf der Morgenstelle, 32 T�bingen, Germany
| | - Patrizia G Ricca
- Center for Plant Molecular Biology (ZMBP), University of T�bingen, Auf der Morgenstelle, 32 T�bingen, Germany
| | - Gabriele Sullivan
- Center for Plant Molecular Biology (ZMBP), University of T�bingen, Auf der Morgenstelle, 32 T�bingen, Germany
| | - Natalie Faiss
- Center for Plant Molecular Biology (ZMBP), University of T�bingen, Auf der Morgenstelle, 32 T�bingen, Germany
| | - Gabriele Wagner
- Center for Plant Molecular Biology (ZMBP), University of T�bingen, Auf der Morgenstelle, 32 T�bingen, Germany
| | - Anna Wunderling
- Center for Plant Molecular Biology (ZMBP), University of T�bingen, Auf der Morgenstelle, 32 T�bingen, Germany
| | - Andreas Wachter
- Center for Plant Molecular Biology (ZMBP), University of T�bingen, Auf der Morgenstelle, 32 T�bingen, Germany
- Institute for Molecular Physiology (imP), University of Mainz, Johannes von M�ller-Weg 6, Mainz, Germany
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12
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Kishor A, Fritz SE, Hogg JR. Nonsense-mediated mRNA decay: The challenge of telling right from wrong in a complex transcriptome. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1548. [PMID: 31131562 DOI: 10.1002/wrna.1548] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/01/2019] [Accepted: 05/07/2019] [Indexed: 12/18/2022]
Abstract
The nonsense-mediated mRNA decay pathway selects and degrades its targets using a dense network of RNA-protein and protein-protein interactions. Together, these interactions allow the pathway to collect copious information about the translating mRNA, including translation termination status, splice junction positions, mRNP composition, and 3'UTR length and structure. The core NMD machinery, centered on the RNA helicase UPF1, integrates this information to determine the efficiency of decay. A picture of NMD is emerging in which many factors contribute to the dynamics of decay complex assembly and disassembly, thereby influencing the probability of decay. The ability of the NMD pathway to recognize mRNP features of diverse potential substrates allows it to simultaneously perform quality control and regulatory functions. In vertebrates, increased transcriptome complexity requires balance between these two functions since high NMD efficiency is desirable for maintenance of quality control fidelity but may impair expression of normal mRNAs. NMD has adapted to this challenge by employing mechanisms to enhance identification of certain potential substrates, while using sequence-specific RNA-binding proteins to shield others from detection. These elaborations on the conserved NMD mechanism permit more sensitive post-transcriptional gene regulation but can have severe deleterious consequences, including the failure to degrade pathogenic aberrant mRNAs in many B cell lymphomas. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms.
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Affiliation(s)
- Aparna Kishor
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Sarah E Fritz
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - J Robert Hogg
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
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Lukhovitskaya N, Ryabova LA. Cauliflower mosaic virus transactivator protein (TAV) can suppress nonsense-mediated decay by targeting VARICOSE, a scaffold protein of the decapping complex. Sci Rep 2019; 9:7042. [PMID: 31065034 PMCID: PMC6504953 DOI: 10.1038/s41598-019-43414-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/12/2019] [Indexed: 01/09/2023] Open
Abstract
During pathogenesis, viruses hijack the host cellular machinery to access molecules and sub-cellular structures needed for infection. We have evidence that the multifunctional viral translation transactivator/viroplasmin (TAV) protein from Cauliflower mosaic virus (CaMV) can function as a suppressor of nonsense-mediated mRNA decay (NMD). TAV interacts specifically with a scaffold protein of the decapping complex VARICOSE (VCS) in the yeast two-hybrid system, and co-localizes with components of the decapping complex in planta. Notably, plants transgenic for TAV accumulate endogenous NMD-elicited mRNAs, while decay of AU-rich instability element (ARE)-signal containing mRNAs are not affected. Using an agroinfiltration-based transient assay we confirmed that TAV specifically stabilizes mRNA containing a premature termination codon (PTC) in a VCS-dependent manner. We have identified a TAV motif consisting of 12 of the 520 amino acids in the full-length sequence that is critical for both VCS binding and the NMD suppression effect. Our data suggest that TAV can intercept NMD by targeting the decapping machinery through the scaffold protein VARICOSE, indicating that 5'-3' mRNA decapping is a late step in NMD-related mRNA degradation in plants.
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Affiliation(s)
- Nina Lukhovitskaya
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Lyubov A Ryabova
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France.
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14
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Poidevin L, Unal D, Belda-Palazón B, Ferrando A. Polyamines as Quality Control Metabolites Operating at the Post-Transcriptional Level. PLANTS 2019; 8:plants8040109. [PMID: 31022874 PMCID: PMC6524035 DOI: 10.3390/plants8040109] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/17/2019] [Accepted: 04/19/2019] [Indexed: 01/04/2023]
Abstract
Plant polyamines (PAs) have been assigned a large number of physiological functions with unknown molecular mechanisms in many cases. Among the most abundant and studied polyamines, two of them, namely spermidine (Spd) and thermospermine (Tspm), share some molecular functions related to quality control pathways for tightly regulated mRNAs at the level of translation. In this review, we focus on the roles of Tspm and Spd to facilitate the translation of mRNAs containing upstream ORFs (uORFs), premature stop codons, and ribosome stalling sequences that may block translation, thus preventing their degradation by quality control mechanisms such as the nonsense-mediated decay pathway and possible interactions with other mRNA quality surveillance pathways.
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Affiliation(s)
- Laetitia Poidevin
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, 46022 Valencia, Spain.
| | - Dilek Unal
- Biotechnology Application and Research Center, and Department of Molecular Biology, Faculty of Science and Letter, Bilecik Seyh Edebali University, 11230 Bilecik, Turkey.
| | - Borja Belda-Palazón
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, 46022 Valencia, Spain.
| | - Alejandro Ferrando
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, 46022 Valencia, Spain.
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15
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Capitao C, Shukla N, Wandrolova A, Mittelsten Scheid O, Riha K. Functional Characterization of SMG7 Paralogs in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2018; 9:1602. [PMID: 30459790 PMCID: PMC6232500 DOI: 10.3389/fpls.2018.01602] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 10/17/2018] [Indexed: 05/07/2023]
Abstract
SMG7 proteins are evolutionary conserved across eukaryotes and primarily known for their function in nonsense mediated RNA decay (NMD). In contrast to other NMD factors, SMG7 proteins underwent independent expansions during evolution indicating their propensity to adopt novel functions. Here we characterized SMG7 and SMG7-like (SMG7L) paralogs in Arabidopsis thaliana. SMG7 retained its role in NMD and additionally appears to have acquired another function in meiosis. We inactivated SMG7 by CRISPR/Cas9 mutagenesis and showed that, in contrast to our previous report, SMG7 is not an essential gene in Arabidopsis. Furthermore, our data indicate that the N-terminal phosphoserine-binding domain is required for both NMD and meiosis. Phenotypic analysis of SMG7 and SMG7L double mutants did not indicate any functional redundancy between the two genes, suggesting neofunctionalization of SMG7L. Finally, protein sequence comparison together with a phenotyping of T-DNA insertion mutants identified several conserved regions specific for SMG7 that may underlie its role in NMD and meiosis. This information provides a framework for deciphering the non-canonical functions of SMG7-family proteins.
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Affiliation(s)
- Claudio Capitao
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Neha Shukla
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Aneta Wandrolova
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Karel Riha
- Central European Institute of Technology, Masaryk University, Brno, Czechia
- *Correspondence: Karel Riha,
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16
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Cui P, Chen T, Qin T, Ding F, Wang Z, Chen H, Xiong L. The RNA Polymerase II C-Terminal Domain Phosphatase-Like Protein FIERY2/CPL1 Interacts with eIF4AIII and Is Essential for Nonsense-Mediated mRNA Decay in Arabidopsis. THE PLANT CELL 2016; 28:770-85. [PMID: 26887918 PMCID: PMC4826008 DOI: 10.1105/tpc.15.00771] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 02/04/2016] [Accepted: 02/15/2016] [Indexed: 05/18/2023]
Abstract
Nonsense-mediated decay (NMD) is a posttranscriptional surveillance mechanism in eukaryotes that recognizes and degrades transcripts with premature translation-termination codons. The RNA polymerase II C-terminal domain phosphatase-like protein FIERY2 (FRY2; also known as C-TERMINAL DOMAIN PHOSPHATASE-LIKE1 [CPL1]) plays multiple roles in RNA processing in Arabidopsis thaliana Here, we found that FRY2/CPL1 interacts with two NMD factors, eIF4AIII and UPF3, and is involved in the dephosphorylation of eIF4AIII. This dephosphorylation retains eIF4AIII in the nucleus and limits its accumulation in the cytoplasm. By analyzing RNA-seq data combined with quantitative RT-PCR validation, we found that a subset of alternatively spliced transcripts and 5'-extended mRNAs with NMD-eliciting features accumulated in the fry2-1 mutant, cycloheximide-treated wild type, and upf3 mutant plants, indicating that FRY2 is essential for the degradation of these NMD transcripts.
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Affiliation(s)
- Peng Cui
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Tao Chen
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Tao Qin
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Feng Ding
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Zhenyu Wang
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Hao Chen
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Liming Xiong
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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17
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Hug N, Longman D, Cáceres JF. Mechanism and regulation of the nonsense-mediated decay pathway. Nucleic Acids Res 2016; 44:1483-95. [PMID: 26773057 PMCID: PMC4770240 DOI: 10.1093/nar/gkw010] [Citation(s) in RCA: 322] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/31/2015] [Indexed: 12/11/2022] Open
Abstract
The Nonsense-mediated mRNA decay (NMD) pathway selectively degrades mRNAs harboring premature termination codons (PTCs) but also regulates the abundance of a large number of cellular RNAs. The central role of NMD in the control of gene expression requires the existence of buffering mechanisms that tightly regulate the magnitude of this pathway. Here, we will focus on the mechanism of NMD with an emphasis on the role of RNA helicases in the transition from NMD complexes that recognize a PTC to those that promote mRNA decay. We will also review recent strategies aimed at uncovering novel trans-acting factors and their functional role in the NMD pathway. Finally, we will describe recent progress in the study of the physiological role of the NMD response.
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Affiliation(s)
- Nele Hug
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Dasa Longman
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Javier F Cáceres
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
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18
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Vexler K, Cymerman MA, Berezin I, Fridman A, Golani L, Lasnoy M, Saul H, Shaul O. The Arabidopsis NMD Factor UPF3 Is Feedback-Regulated at Multiple Levels and Plays a Role in Plant Response to Salt Stress. FRONTIERS IN PLANT SCIENCE 2016; 7:1376. [PMID: 27746786 PMCID: PMC5040709 DOI: 10.3389/fpls.2016.01376] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 08/29/2016] [Indexed: 05/22/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is a eukaryotic RNA surveillance mechanism that degrades aberrant transcripts and controls the levels of many normal mRNAs. It was shown that balanced expression of the NMD factor UPF3 is essential for the maintenance of proper NMD homeostasis in Arabidopsis. UPF3 expression is controlled by a negative feedback loop that exposes UPF3 transcript to NMD. It was shown that the long 3' untranslated region (3' UTR) of UPF3 exposes its transcript to NMD. Long 3' UTRs that subject their transcripts to NMD were identified in several eukaryotic NMD factors. Interestingly, we show here that a construct that contains all the regulatory regions of the UPF3 gene except this long 3' UTR is also feedback-regulated by NMD. This indicates that UPF3 expression is feedback-regulated at multiple levels. UPF3 is constitutively expressed in different plant tissues, and its expression is equal in leaves of plants of different ages. This finding is in agreement with the possibility that UPF3 is ubiquitously operative in the Arabidopsis NMD pathway. Expression mediated by the regulatory regions of UPF3 is significantly induced by salt stress. We found that both a deficiency and a strong excess of UPF3 expression are detrimental to plant resistance to salt stress. This indicates that UPF3 plays a role in plant response to salt stress, and that balanced expression of the UPF3 gene is essential for coping with this stress.
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19
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Shaul O. Unique Aspects of Plant Nonsense-Mediated mRNA Decay. TRENDS IN PLANT SCIENCE 2015; 20:767-779. [PMID: 26442679 DOI: 10.1016/j.tplants.2015.08.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 08/17/2015] [Accepted: 08/20/2015] [Indexed: 05/20/2023]
Abstract
Nonsense-mediated mRNA Decay (NMD) is a eukaryotic quality-control mechanism that governs the stability of both aberrant and normal transcripts. Although plant and mammalian NMD share great similarity, they differ in certain mechanistic and regulatory aspects. Whereas SMG6 (from Caenorhabditis elegans 'suppressor with morphogenetic effect on genitalia')-catalyzed endonucleolytic cleavage is a prominent step in mammalian NMD, plant NMD targets are degraded by an SMG7-induced exonucleolytic pathway. Both mammalian and plant NMD are downregulated by stress, thereby enhancing the expression of defense response genes. However, the target genes and processes affected differ. Several plant and mammalian NMD factors are regulated by negative feedback-loops. However, while the loop regulating UPF3 (up-frameshift 3) expression in not vital for mammalian NMD, the sensitivity of UPF3 to NMD is crucial for the overall regulation of plant NMD.
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Affiliation(s)
- Orit Shaul
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel.
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