1
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Lühmann KL, Seemann S, Martinek N, Ostendorp S, Kehr J. The glycine-rich domain of GRP7 plays a crucial role in binding long RNAs and facilitating phase separation. Sci Rep 2024; 14:16018. [PMID: 38992080 PMCID: PMC11239674 DOI: 10.1038/s41598-024-66955-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 07/05/2024] [Indexed: 07/13/2024] Open
Abstract
Microscale thermophoresis (MST) is a well-established method to quantify protein-RNA interactions. In this study, we employed MST to analyze the RNA binding properties of glycine-rich RNA binding protein 7 (GRP7), which is known to have multiple biological functions related to its ability to bind different types of RNA. However, the exact mechanism of GRP7's RNA binding is not fully understood. While the RNA-recognition motif of GRP7 is known to be involved in RNA binding, the glycine-rich region (known as arginine-glycine-glycine-domain or RGG-domain) also influences this interaction. To investigate to which extend the RGG-domain of GRP7 is involved in RNA binding, mutation studies on putative RNA interacting or modulating sites were performed. In addition to MST experiments, we examined liquid-liquid phase separation of GRP7 and its mutants, both with and without RNA. Furthermore, we systemically investigated factors that might affect RNA binding selectivity of GRP7 by testing RNAs of different sizes, structures, and modifications. Consequently, our study revealed that GRP7 exhibits a high affinity for a variety of RNAs, indicating a lack of pronounced selectivity. Moreover, we established that the RGG-domain plays a crucial role in binding longer RNAs and promoting phase separation.
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Affiliation(s)
- Kim Lara Lühmann
- Department of Biology, Molecular Plant Genetics, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Silja Seemann
- Department of Biology, Molecular Plant Genetics, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Nina Martinek
- Department of Biology, Molecular Plant Genetics, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Steffen Ostendorp
- Department of Biology, Molecular Plant Genetics, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Julia Kehr
- Department of Biology, Molecular Plant Genetics, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany.
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2
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Reichel M, Schmidt O, Rettel M, Stein F, Köster T, Butter F, Staiger D. Revealing the Arabidopsis AtGRP7 mRNA binding proteome by specific enhanced RNA interactome capture. BMC PLANT BIOLOGY 2024; 24:552. [PMID: 38877390 PMCID: PMC11177498 DOI: 10.1186/s12870-024-05249-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 06/05/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND The interaction of proteins with RNA in the cell is crucial to orchestrate all steps of RNA processing. RNA interactome capture (RIC) techniques have been implemented to catalogue RNA- binding proteins in the cell. In RIC, RNA-protein complexes are stabilized by UV crosslinking in vivo. Polyadenylated RNAs and associated proteins are pulled down from cell lysates using oligo(dT) beads and the RNA-binding proteome is identified by quantitative mass spectrometry. However, insights into the RNA-binding proteome of a single RNA that would yield mechanistic information on how RNA expression patterns are orchestrated, are scarce. RESULTS Here, we explored RIC in Arabidopsis to identify proteins interacting with a single mRNA, using the circadian clock-regulated Arabidopsis thaliana GLYCINE-RICH RNA-BINDING PROTEIN 7 (AtGRP7) transcript, one of the most abundant transcripts in Arabidopsis, as a showcase. Seedlings were treated with UV light to covalently crosslink RNA and proteins. The AtGRP7 transcript was captured from cell lysates with antisense oligonucleotides directed against the 5'untranslated region (UTR). The efficiency of RNA capture was greatly improved by using locked nucleic acid (LNA)/DNA oligonucleotides, as done in the enhanced RIC protocol. Furthermore, performing a tandem capture with two rounds of pulldown with the 5'UTR oligonucleotide increased the yield. In total, we identified 356 proteins enriched relative to a pulldown from atgrp7 mutant plants. These were benchmarked against proteins pulled down from nuclear lysates by AtGRP7 in vitro transcripts immobilized on beads. Among the proteins validated by in vitro interaction we found the family of Acetylation Lowers Binding Affinity (ALBA) proteins. Interaction of ALBA4 with the AtGRP7 RNA was independently validated via individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP). The expression of the AtGRP7 transcript in an alba loss-of-function mutant was slightly changed compared to wild-type, demonstrating the functional relevance of the interaction. CONCLUSION We adapted specific RNA interactome capture with LNA/DNA oligonucleotides for use in plants using AtGRP7 as a showcase. We anticipate that with further optimization and up scaling the protocol should be applicable for less abundant transcripts.
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Affiliation(s)
- Marlene Reichel
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany.
- Department of Biology, University of Copenhagen, København N, 2200, Denmark.
| | - Olga Schmidt
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
| | - Mandy Rettel
- Proteomics Core Facility, EMBL, 69117, Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL, 69117, Heidelberg, Germany
| | - Tino Köster
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
| | - Falk Butter
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany.
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3
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Agrofoglio YC, Iglesias MJ, Perez-Santángelo S, de Leone MJ, Koester T, Catalá R, Salinas J, Yanovsky MJ, Staiger D, Mateos JL. Arginine methylation of SM-LIKE PROTEIN 4 antagonistically affects alternative splicing during Arabidopsis stress responses. THE PLANT CELL 2024; 36:2219-2237. [PMID: 38518124 PMCID: PMC11132874 DOI: 10.1093/plcell/koae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/09/2024] [Indexed: 03/24/2024]
Abstract
Arabidopsis (Arabidopsis thaliana) PROTEIN ARGININE METHYLTRANSFERASE5 (PRMT5) post-translationally modifies RNA-binding proteins by arginine (R) methylation. However, the impact of this modification on the regulation of RNA processing is largely unknown. We used the spliceosome component, SM-LIKE PROTEIN 4 (LSM4), as a paradigm to study the role of R-methylation in RNA processing. We found that LSM4 regulates alternative splicing (AS) of a suite of its in vivo targets identified here. The lsm4 and prmt5 mutants show a considerable overlap of genes with altered AS raising the possibility that splicing of those genes could be regulated by PRMT5-dependent LSM4 methylation. Indeed, LSM4 methylation impacts AS, particularly of genes linked with stress response. Wild-type LSM4 and an unmethylable version complement the lsm4-1 mutant, suggesting that methylation is not critical for growth in normal environments. However, LSM4 methylation increases with abscisic acid and is necessary for plants to grow under abiotic stress. Conversely, bacterial infection reduces LSM4 methylation, and plants that express unmethylable-LSM4 are more resistant to Pseudomonas than those expressing wild-type LSM4. This tolerance correlates with decreased intron retention of immune-response genes upon infection. Taken together, this provides direct evidence that R-methylation adjusts LSM4 function on pre-mRNA splicing in an antagonistic manner in response to biotic and abiotic stress.
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Affiliation(s)
- Yamila Carla Agrofoglio
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET) and Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EGA Buenos Aires, Argentina
| | - María José Iglesias
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET) and Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EGA Buenos Aires, Argentina
| | - Soledad Perez-Santángelo
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405BWE Buenos Aires, Argentina
| | - María José de Leone
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405BWE Buenos Aires, Argentina
| | - Tino Koester
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Rafael Catalá
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Julio Salinas
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain
| | - Marcelo J Yanovsky
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405BWE Buenos Aires, Argentina
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Julieta L Mateos
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET) and Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EGA Buenos Aires, Argentina
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
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4
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Zhang Y, Mo Y, Li J, Liu L, Gao Y, Zhang Y, Huang Y, Ren L, Zhu H, Jiang X, Ling Y. Divergence in regulatory mechanisms of GR-RBP genes in different plants under abiotic stress. Sci Rep 2024; 14:8743. [PMID: 38627506 PMCID: PMC11021534 DOI: 10.1038/s41598-024-59341-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
The IVa subfamily of glycine-rich proteins (GRPs) comprises a group of glycine-rich RNA binding proteins referred to as GR-RBPa here. Previous studies have demonstrated functions of GR-RBPa proteins in regulating stress response in plants. However, the mechanisms responsible for the differential regulatory functions of GR-RBPa proteins in different plant species have not been fully elucidated. In this study, we identified and comprehensively studied a total of 34 GR-RBPa proteins from five plant species. Our analysis revealed that GR-RBPa proteins were further classified into two branches, with proteins in branch I being relatively more conserved than those in branch II. When subjected to identical stresses, these genes exhibited intensive and differential expression regulation in different plant species, corresponding to the enrichment of cis-acting regulatory elements involving in environmental and internal signaling in these genes. Unexpectedly, all GR-RBPa genes in branch I underwent intensive alternative splicing (AS) regulation, while almost all genes in branch II were only constitutively spliced, despite having more introns. This study highlights the complex and divergent regulations of a group of conserved RNA binding proteins in different plants when exposed to identical stress conditions. These species-specific regulations may have implications for stress responses and adaptations in different plant species.
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Affiliation(s)
- Yingjie Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yujian Mo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Junyi Li
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Li Liu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yanhu Gao
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yueqin Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yongxiang Huang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China
| | - Lei Ren
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China
| | - Hongbo Zhu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Xingyu Jiang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China.
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China.
| | - Yu Ling
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China.
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China.
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5
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Lewinski M, Steffen A, Kachariya N, Elgner M, Schmal C, Messini N, Köster T, Reichel M, Sattler M, Zarnack K, Staiger D. Arabidopsis thaliana GLYCINE RICH RNA-BINDING PROTEIN 7 interaction with its iCLIP target LHCB1.1 correlates with changes in RNA stability and circadian oscillation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:203-224. [PMID: 38124335 DOI: 10.1111/tpj.16601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/09/2023] [Indexed: 12/23/2023]
Abstract
The importance of RNA-binding proteins (RBPs) for plant responses to environmental stimuli and development is well documented. Insights into the portfolio of RNAs they recognize, however, clearly lack behind the understanding gathered in non-plant model organisms. Here, we characterize binding of the circadian clock-regulated Arabidopsis thaliana GLYCINE-RICH RNA-BINDING PROTEIN 7 (AtGRP7) to its target transcripts. We identified novel RNA targets from individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) data using an improved bioinformatics pipeline that will be broadly applicable to plant RBP iCLIP data. 2705 transcripts with binding sites were identified in plants expressing AtGRP7-GFP that were not recovered in plants expressing an RNA-binding dead variant or GFP alone. A conserved RNA motif enriched in uridine residues was identified at the AtGRP7 binding sites. NMR titrations confirmed the preference of AtGRP7 for RNAs with a central U-rich motif. Among the bound RNAs, circadian clock-regulated transcripts were overrepresented. Peak abundance of the LHCB1.1 transcript encoding a chlorophyll-binding protein was reduced in plants overexpressing AtGRP7 whereas it was elevated in atgrp7 mutants, indicating that LHCB1.1 was regulated by AtGRP7 in a dose-dependent manner. In plants overexpressing AtGRP7, the LHCB1.1 half-life was shorter compared to wild-type plants whereas in atgrp7 mutant plants, the half-life was significantly longer. Thus, AtGRP7 modulates circadian oscillations of its in vivo binding target LHCB1.1 by affecting RNA stability.
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Affiliation(s)
- Martin Lewinski
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Alexander Steffen
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Nitin Kachariya
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg, 85764, Germany
- Department of Bioscience, Bavarian NMR Center, Technical University of Munich, TUM School of Natural Sciences, Garching, 85747, Germany
| | - Mareike Elgner
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Christoph Schmal
- Institute for Theoretical Biology, Humboldt-Universität zu Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Niki Messini
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg, 85764, Germany
- Department of Bioscience, Bavarian NMR Center, Technical University of Munich, TUM School of Natural Sciences, Garching, 85747, Germany
| | - Tino Köster
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Marlene Reichel
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Michael Sattler
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg, 85764, Germany
- Department of Bioscience, Bavarian NMR Center, Technical University of Munich, TUM School of Natural Sciences, Garching, 85747, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
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6
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Wang J, Ma X, Hu Y, Feng G, Guo C, Zhang X, Ma H. Regulation of micro- and small-exon retention and other splicing processes by GRP20 for flower development. NATURE PLANTS 2024; 10:66-85. [PMID: 38195906 PMCID: PMC10808074 DOI: 10.1038/s41477-023-01605-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 11/29/2023] [Indexed: 01/11/2024]
Abstract
Pre-mRNA splicing is crucial for gene expression and depends on the spliceosome and splicing factors. Plant exons have an average size of ~180 nucleotides and typically contain motifs for interactions with spliceosome and splicing factors. Micro exons (<51 nucleotides) are found widely in eukaryotes and in genes for plant development and environmental responses. However, little is known about transcript-specific regulation of splicing in plants and about the regulators for micro exon splicing. Here we report that glycine-rich protein 20 (GRP20) is an RNA-binding protein and required for splicing of ~2,100 genes including those functioning in flower development and/or environmental responses. Specifically, GRP20 is required for micro-exon retention in transcripts of floral homeotic genes; these micro exons are conserved across angiosperms. GRP20 is also important for small-exon (51-100 nucleotides) splicing. In addition, GRP20 is required for flower development. Furthermore, GRP20 binds to poly-purine motifs in micro and small exons and a spliceosome component; both RNA binding and spliceosome interaction are important for flower development and micro-exon retention. Our results provide new insights into the mechanisms of micro-exon retention in flower development.
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Affiliation(s)
- Jun Wang
- Department of Biology, Eberly College of Science, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Xinwei Ma
- Department of Biology, Eberly College of Science, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Yi Hu
- Department of Biology, Eberly College of Science, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Guanhua Feng
- Department of Biology, Eberly College of Science, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Chunce Guo
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang, China
| | - Xin Zhang
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Eberly College of Science, Pennsylvania State University, University Park, PA, USA
| | - Hong Ma
- Department of Biology, Eberly College of Science, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
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7
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Abdeeva IA, Maloshenok LG, Pogorelko GV, Bruskin SA. Using an RNA Aptamer to Inhibit the Action of Effector Proteins of Plant Pathogens. Int J Mol Sci 2023; 24:16604. [PMID: 38068927 PMCID: PMC10705891 DOI: 10.3390/ijms242316604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/10/2023] [Accepted: 11/18/2023] [Indexed: 12/18/2023] Open
Abstract
In previous work, we experimentally demonstrated the possibility of using RNA aptamers to inhibit endogenous protein expression and their function within plant cells In the current work, we show that our proposed method is suitable for inhibiting the functions of exogenous, foreign proteins delivered into the plant via various mechanisms, including pathogen proteins. Stringent experimentation produced robust RNA aptamers that are able to bind to the recombinant HopU1 effector protein of P. syringae bacteria. This research uses genetic engineering methods to constitutively express/transcribe HopU1 RNA aptamers in transgenic A. thaliana. Our findings support the hypothesis that HopU1 aptamers can actively interfere with the function of the HopU1 protein and thereby increase resistance to phytopathogens of the genus P. syringae pv. tomato DC 3000.
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Affiliation(s)
- Inna A. Abdeeva
- N.I. Vavilov Institute of General Genetics Russian Academy of Sciences, Gubkina Str. 3, 119333 Moscow, Russia (S.A.B.)
| | - Liliya G. Maloshenok
- N.I. Vavilov Institute of General Genetics Russian Academy of Sciences, Gubkina Str. 3, 119333 Moscow, Russia (S.A.B.)
| | - Gennady V. Pogorelko
- N.I. Vavilov Institute of General Genetics Russian Academy of Sciences, Gubkina Str. 3, 119333 Moscow, Russia (S.A.B.)
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Sergey A. Bruskin
- N.I. Vavilov Institute of General Genetics Russian Academy of Sciences, Gubkina Str. 3, 119333 Moscow, Russia (S.A.B.)
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8
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Pradhan UK, Meher PK, Naha S, Pal S, Gupta S, Gupta A, Parsad R. RBPLight: a computational tool for discovery of plant-specific RNA-binding proteins using light gradient boosting machine and ensemble of evolutionary features. Brief Funct Genomics 2023; 22:401-410. [PMID: 37158175 DOI: 10.1093/bfgp/elad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/12/2023] [Accepted: 04/21/2023] [Indexed: 05/10/2023] Open
Abstract
RNA-binding proteins (RBPs) are essential for post-transcriptional gene regulation in eukaryotes, including splicing control, mRNA transport and decay. Thus, accurate identification of RBPs is important to understand gene expression and regulation of cell state. In order to detect RBPs, a number of computational models have been developed. These methods made use of datasets from several eukaryotic species, specifically from mice and humans. Although some models have been tested on Arabidopsis, these techniques fall short of correctly identifying RBPs for other plant species. Therefore, the development of a powerful computational model for identifying plant-specific RBPs is needed. In this study, we presented a novel computational model for locating RBPs in plants. Five deep learning models and ten shallow learning algorithms were utilized for prediction with 20 sequence-derived and 20 evolutionary feature sets. The highest repeated five-fold cross-validation accuracy, 91.24% AU-ROC and 91.91% AU-PRC, was achieved by light gradient boosting machine. While evaluated using an independent dataset, the developed approach achieved 94.00% AU-ROC and 94.50% AU-PRC. The proposed model achieved significantly higher accuracy for predicting plant-specific RBPs as compared to the currently available state-of-art RBP prediction models. Despite the fact that certain models have already been trained and assessed on the model organism Arabidopsis, this is the first comprehensive computer model for the discovery of plant-specific RBPs. The web server RBPLight was also developed, which is publicly accessible at https://iasri-sg.icar.gov.in/rbplight/, for the convenience of researchers to identify RBPs in plants.
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Affiliation(s)
- Upendra K Pradhan
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
| | - Prabina K Meher
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
| | - Sanchita Naha
- Division of Computer Applications, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
| | - Soumen Pal
- Division of Computer Applications, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
| | - Sagar Gupta
- CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur (HP) 176061, India
| | - Ajit Gupta
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
| | - Rajender Parsad
- ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
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9
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Mateos JL, Staiger D. Toward a systems view on RNA-binding proteins and associated RNAs in plants: Guilt by association. THE PLANT CELL 2023; 35:1708-1726. [PMID: 36461946 PMCID: PMC10226577 DOI: 10.1093/plcell/koac345] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/08/2022] [Accepted: 11/17/2022] [Indexed: 05/30/2023]
Abstract
RNA-binding proteins (RBPs) have a broad impact on most biochemical, physiological, and developmental processes in a plant's life. RBPs engage in an on-off relationship with their RNA partners, accompanying virtually every stage in RNA processing and function. While the function of a plethora of RBPs in plant development and stress responses has been described, we are lacking a systems-level understanding of components in RNA-based regulation. Novel techniques have substantially enlarged the compendium of proteins with experimental evidence for binding to RNAs in the cell, the RNA-binding proteome. Furthermore, ribonomics methods have been adapted for use in plants to profile the in vivo binding repertoire of RBPs genome-wide. Here, we discuss how recent technological achievements have provided novel insights into the mode of action of plant RBPs at a genome-wide scale. Furthermore, we touch upon two emerging topics, the connection of RBPs to phase separation in the cell and to extracellular RNAs. Finally, we define open questions to be addressed to move toward an integrated understanding of RBP function.
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Affiliation(s)
- Julieta L Mateos
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET-UBA), Buenos Aires, Argentina
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
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10
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Wang L, Xu F, Yu F. Two environmental signal-driven RNA metabolic processes: Alternative splicing and translation. PLANT, CELL & ENVIRONMENT 2023; 46:718-732. [PMID: 36609800 DOI: 10.1111/pce.14537] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/29/2022] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
Plants live in fixed locations and have evolved adaptation mechanisms that integrate multiple responses to various environmental signals. Among the different components of these response pathways, receptors/sensors represent nodes that recognise environmental signals. Additionally, RNA metabolism plays an essential role in the regulation of gene expression and protein synthesis. With the development of RNA biotechnology, recent advances have been made in determining the roles of RNA metabolism in response to different environmental signals-especially the roles of alternative splicing and translation. In this review, we discuss recent progress in research on how the environmental adaptation mechanisms in plants are affected at the posttranscriptional level. These findings improve our understanding of the mechanism through which plants adapt to environmental changes by regulating the posttranscriptional level and are conducive for breeding stress-tolerant plants to cope with dynamic and rapidly changing environments.
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Affiliation(s)
- Long Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
| | - Fan Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
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11
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Lu X, Yang Z, Song W, Miao J, Zhao H, Ji P, Li T, Si J, Yin Z, Jing M, Shen D, Dou D. The Phytophthora sojae effector PsFYVE1 modulates immunity-related gene expression by targeting host RZ-1A protein. PLANT PHYSIOLOGY 2023; 191:925-945. [PMID: 36461945 PMCID: PMC9922423 DOI: 10.1093/plphys/kiac552] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Oomycete pathogens secrete numerous effectors to manipulate plant immunity and promote infection. However, relatively few effector types have been well characterized. In this study, members of an FYVE domain-containing protein family that are highly expanded in oomycetes were systematically identified, and one secreted protein, PsFYVE1, was selected for further study. PsFYVE1 enhanced Phytophthora capsici infection in Nicotiana benthamiana and was necessary for Phytophthora sojae virulence. The FYVE domain of PsFYVE1 had PI3P-binding activity that depended on four conserved amino acid residues. Furthermore, PsFYVE1 targeted RNA-binding proteins RZ-1A/1B/1C in N. benthamiana and soybean (Glycine max), and silencing of NbRZ-1A/1B/1C genes attenuated plant immunity. NbRZ-1A was associated with the spliceosome complex that included three important components, glycine-rich RNA-binding protein 7 (NbGRP7), glycine-rich RNA-binding protein 8 (NbGRP8), and a specific component of the U1 small nuclear ribonucleoprotein complex (NbU1-70K). Notably, PsFYVE1 disrupted NbRZ-1A-NbGRP7 interaction. RNA-seq and subsequent experimental analysis demonstrated that PsFYVE1 and NbRZ-1A not only modulated pre-mRNA alternative splicing (AS) of the necrotic spotted lesions 1 (NbNSL1) gene, but also co-regulated transcription of hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase (NbHCT), ethylene insensitive 2 (NbEIN2), and sucrose synthase 4 (NbSUS4) genes, which participate in plant immunity. Collectively, these findings indicate that the FYVE domain-containing protein family includes potential uncharacterized effector types and also highlight that plant pathogen effectors can regulate plant immunity-related genes at both AS and transcription levels to promote disease.
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Affiliation(s)
- Xinyu Lu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Zitong Yang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wen Song
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinlu Miao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Hanqing Zhao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Peiyun Ji
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianli Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jierui Si
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhiyuan Yin
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Maofeng Jing
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
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12
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Fan T, Aslam MM, Zhou JL, Chen MX, Zhang J, Du S, Zhang KL, Chen YS. A crosstalk of circadian clock and alternative splicing under abiotic stresses in the plants. FRONTIERS IN PLANT SCIENCE 2022; 13:976807. [PMID: 36275558 PMCID: PMC9583901 DOI: 10.3389/fpls.2022.976807] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/05/2022] [Indexed: 06/16/2023]
Abstract
The circadian clock is an internal time-keeping mechanism that synchronizes the physiological adaptation of an organism to its surroundings based on day and night transition in a period of 24 h, suggesting the circadian clock provides fitness by adjusting environmental constrains. The circadian clock is driven by positive and negative elements that regulate transcriptionally and post-transcriptionally. Alternative splicing (AS) is a crucial transcriptional regulator capable of generating large numbers of mRNA transcripts from limited numbers of genes, leading to proteome diversity, which is involved in circadian to deal with abiotic stresses. Over the past decade, AS and circadian control have been suggested to coordinately regulate plant performance under fluctuating environmental conditions. However, only a few reports have reported the regulatory mechanism of this complex crosstalk. Based on the emerging evidence, this review elaborates on the existing links between circadian and AS in response to abiotic stresses, suggesting an uncovered regulatory network among circadian, AS, and abiotic stresses. Therefore, the rhythmically expressed splicing factors and core clock oscillators fill the role of temporal regulators participating in improving plant growth, development, and increasing plant tolerance against abiotic stresses.
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Affiliation(s)
- Tao Fan
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, China
- Co-Innovation Center for Sustainable Forestry in Southern China & Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Mehtab Muhammad Aslam
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Jian-Li Zhou
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, China
| | - Mo-Xian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China & Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Shenxiu Du
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Kai-Lu Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China & Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Yun-Sheng Chen
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, China
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13
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Li X, Yang Y, Zeng N, Qu G, Fu D, Zhu B, Luo Y, Ostersetzer-Biran O, Zhu H. Glycine-rich RNA-binding cofactor RZ1AL is associated with tomato ripening and development. HORTICULTURE RESEARCH 2022; 9:uhac134. [PMID: 35937858 PMCID: PMC9350831 DOI: 10.1093/hr/uhac134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 06/04/2022] [Indexed: 06/15/2023]
Abstract
Tomato ripening is a complex and dynamic process coordinated by many regulatory elements, including plant hormones, transcription factors, and numerous ripening-related RNAs and proteins. Although recent studies have shown that some RNA-binding proteins are involved in the regulation of the ripening process, understanding of how RNA-binding proteins affect fruit ripening is still limited. Here, we report the analysis of a glycine-rich RNA-binding protein, RZ1A-Like (RZ1AL), which plays an important role in tomato ripening, especially fruit coloring. To analyze the functions of RZ1AL in fruit development and ripening, we generated knockout cr-rz1al mutant lines via the CRISPR/Cas9 gene-editing system. Knockout of RZ1AL reduced fruit lycopene content and weight in the cr-rz1al mutant plants. RZ1AL encodes a nucleus-localized protein that is associated with Cajal-related bodies. RNA-seq data demonstrated that the expression levels of genes that encode several key enzymes associated with carotenoid biosynthesis and metabolism were notably downregulated in cr-rz1al fruits. Proteomic analysis revealed that the levels of various ribosomal subunit proteins were reduced. This could affect the translation of ripening-related proteins such as ZDS. Collectively, our findings demonstrate that RZ1AL may participate in the regulation of carotenoid biosynthesis and metabolism and affect tomato development and fruit ripening.
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Affiliation(s)
- Xindi Li
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77840, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77840, USA
| | - Yongfang Yang
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ni Zeng
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Guiqin Qu
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Daqi Fu
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Benzhong Zhu
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yunbo Luo
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem 9190401, Israel
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14
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Alexandre Moraes T, Mengin V, Peixoto B, Encke B, Krohn N, Höhne M, Krause U, Stitt M. The circadian clock mutant lhy cca1 elf3 paces starch mobilization to dawn despite severely disrupted circadian clock function. PLANT PHYSIOLOGY 2022; 189:2332-2356. [PMID: 35567528 PMCID: PMC9348821 DOI: 10.1093/plphys/kiac226] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
Many plants, including Arabidopsis (Arabidopsis thaliana), accumulate starch in the daytime and remobilize it to support maintenance and growth at night. Starch accumulation is increased when carbon is in short supply, for example, in short photoperiods. Mobilization is paced to exhaust starch around dawn, as anticipated by the circadian clock. This diel pattern of turnover is largely robust against loss of day, dawn, dusk, or evening clock components. Here, we investigated diel starch turnover in the triple circadian clock mutant lhy cca1 elf3, which lacks the LATE ELONGATED HYPOCOTYL and the CIRCADIAN CLOCK-ASSOCIATED1 (CCA1) dawn components and the EARLY FLOWERING3 (ELF3) evening components of the circadian clock. The diel oscillations of transcripts for the remaining clock components and related genes like REVEILLE and PHYTOCHROME-INTERACING FACTOR family members exhibited attenuated amplitudes and altered peak time, weakened dawn dominance, and decreased robustness against changes in the external light-dark cycle. The triple mutant was unable to increase starch accumulation in short photoperiods. However, it was still able to pace starch mobilization to around dawn in different photoperiods and growth irradiances and to around 24 h after the previous dawn in T17 and T28 cycles. The triple mutant was able to slow down starch mobilization after a sudden low-light day or a sudden early dusk, although in the latter case it did not fully compensate for the lengthened night. Overall, there was a slight trend to less linear mobilization of starch. Thus, starch mobilization can be paced rather robustly to dawn despite a major disruption of the transcriptional clock. It is proposed that temporal information can be delivered from clock components or a semi-autonomous oscillator.
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Affiliation(s)
| | - Virginie Mengin
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - Bruno Peixoto
- Instituto Gulbenkian de Ciência, Oeiras 2780-156,Portugal
- GREEN-IT Bioresources for Sustainability, ITQB NOVA, Oeiras 2780-157,Portugal
| | - Beatrice Encke
- Systematic Botany and Biodiversity, Humboldt University of Berlin, Berlin D-10115, Germany
| | - Nicole Krohn
- Abteilung für Parodontologie und Synoptische Zahnmedizin, Charité Universitätsmedizin, Berlin 14197, Germany
| | - Melanie Höhne
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Ursula Krause
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
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15
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Xu W, Dou Y, Geng H, Fu J, Dan Z, Liang T, Cheng M, Zhao W, Zeng Y, Hu Z, Huang W. OsGRP3 Enhances Drought Resistance by Altering Phenylpropanoid Biosynthesis Pathway in Rice ( Oryza sativa L.). Int J Mol Sci 2022; 23:ijms23137045. [PMID: 35806050 PMCID: PMC9266740 DOI: 10.3390/ijms23137045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/17/2022] [Accepted: 06/22/2022] [Indexed: 02/07/2023] Open
Abstract
As a sessile organism, rice often faces various kinds of abiotic stresses, such as drought stress. Drought stress seriously harms plant growth and damages crop yield every year. Therefore, it is urgent to elucidate the mechanisms of drought resistance in rice. In this study, we identified a glycine-rich RNA-binding protein, OsGRP3, in rice. Evolutionary analysis showed that it was closely related to OsGR-RBP4, which was involved in various abiotic stresses. The expression of OsGRP3 was shown to be induced by several abiotic stress treatments and phytohormone treatments. Then, the drought tolerance tests of transgenic plants confirmed that OsGRP3 enhanced drought resistance in rice. Meanwhile, the yeast two-hybrid assay, bimolecular luminescence complementation assay and bimolecular fluorescence complementation assay demonstrated that OsGRP3 bound with itself may affect the RNA chaperone function. Subsequently, the RNA-seq analysis, physiological experiments and histochemical staining showed that OsGRP3 influenced the phenylpropanoid biosynthesis pathway and further modulated lignin accumulation. Herein, our findings suggested that OsGRP3 enhanced drought resistance in rice by altering the phenylpropanoid biosynthesis pathway and further increasing lignin accumulation.
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Affiliation(s)
- Wuwu Xu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yangfan Dou
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Han Geng
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jinmei Fu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhiwu Dan
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ting Liang
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Mingxing Cheng
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Weibo Zhao
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yafei Zeng
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhongli Hu
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wenchao Huang
- State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan 430072, China; (W.X.); (Y.D.); (H.G.); (J.F.); (Z.D.); (T.L.); (M.C.); (W.Z.); (Y.Z.); (Z.H.)
- College of Life Sciences, Wuhan University, Wuhan 430072, China
- Correspondence:
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16
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Li J, Feng H, Liu S, Liu P, Chen X, Yang J, He L, Yang J, Chen J. Phosphorylated viral protein evades plant immunity through interfering the function of RNA-binding protein. PLoS Pathog 2022; 18:e1010412. [PMID: 35294497 PMCID: PMC8959173 DOI: 10.1371/journal.ppat.1010412] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/28/2022] [Accepted: 03/01/2022] [Indexed: 12/31/2022] Open
Abstract
Successful pathogen infection in plant depends on a proper interaction between the invading pathogen and its host. Post-translational modification (PTM) plays critical role(s) in plant-pathogen interaction. However, how PTM of viral protein regulates plant immunity remains poorly understood. Here, we found that S162 and S165 of Chinese wheat mosaic virus (CWMV) cysteine-rich protein (CRP) are phosphorylated by SAPK7 and play key roles in CWMV infection. Furthermore, the phosphorylation-mimic mutant of CRP (CRPS162/165D) but not the non-phosphorylatable mutant of CRP (CRPS162/165A) interacts with RNA-binding protein UBP1-associated protein 2C (TaUBA2C). Silencing of TaUBA2C expression in wheat plants enhanced CWMV infection. In contrast, overexpression of TaUBA2C in wheat plants inhibited CWMV infection. TaUBA2C inhibits CWMV infection through recruiting the pre-mRNA of TaNPR1, TaPR1 and TaRBOHD to induce cell death and H2O2 production. This effect can be supressed by CRPS162/165D through changing TaUBA2C chromatin-bound status and attenuating it’s the RNA- or DNA-binding activities. Taken together, our findings provide new knowledge on how CRP phosphorylation affects CWMV infection as well as the arms race between virus and wheat plants. Chinese wheat mosaic virus (CWMV) causes a damaging disease in cereal plants. However, CWMV interacts with host factors to facilitate virus infection is not clear yet. Here, we found that S162 and S165 of CWMV cysteine-rich protein (CRP) are phosphorylated by SAPK7 in vivo and in vitro. Mutational analyses have indicated that these two phosphorylation sites of CRP (CRPS162/165D) promoting CWMV infection in plants, due to the supressed cell death and H2O2 production. Further investigations found the CRPS162/165D can interact with TaUBA2C, while the non-phosphorylatable mutant of CRP (CRPS162/165A) does not. Futhermore, we have determined that CRPS162/165D and TaUBA2C interaction inhibited the formation of TaUBA2C speckles in nucleus to attenuate its RNA- and DNA-binding activity. We also showed that TaUBA2C recruit the pre-mRNA of TaNPR1, TaPR1 and TaRBOHD to up-regulated these genes expressions and then induce cell death and H2O2 production in plant. This effect can be supressed by the expression of CRPS162/165D, in a dose-dependent manner. Taken together, our discovery may provide a new sight for the arms race between virus and its host plants.
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Affiliation(s)
- Juan Li
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Huimin Feng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Shuang Liu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Peng Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Xuan Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jin Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Long He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jian Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- * E-mail: (JY); (JC)
| | - Jianping Chen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- * E-mail: (JY); (JC)
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17
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Du C, Bai HY, Chen JJ, Wang JH, Wang ZF, Zhang ZH. Alternative Splicing Regulation of Glycine-Rich Proteins via Target of Rapamycin-Reactive Oxygen Species Pathway in Arabidopsis Seedlings Upon Glucose Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:830140. [PMID: 35498646 PMCID: PMC9051487 DOI: 10.3389/fpls.2022.830140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/16/2022] [Indexed: 05/05/2023]
Abstract
Glucose can serve as both the source of energy and regulatory signaling molecule in plant. Due to the environmental and metabolic change, sugar levels could affect various developmental processes. High glucose environment is hardly conductive to the plant growth but cause development arrest. Increasing evidence indicate that alternative splicing (AS) plays a pivotal role in sugar signaling. However, the regulatory mechanism upon glucose stress remains unclear. The full-length transcriptomes were obtained from the samples of Arabidopsis seedlings with 3% glucose and mock treatment, using Oxford Nanopore sequencing technologies. Further analysis indicated that many genes involved in photosynthesis were significantly repressed and many genes involved in glycolysis, mitochondrial function, and the response to oxidative stress were activated. In total, 1,220 significantly differential alternative splicing (DAS) events related to 619 genes were identified, among which 75.74% belong to intron retention (IR). Notably, more than 20% of DAS events come from a large set of glycine-rich protein (GRP) family genes, such as GRP7, whose AS types mostly belong to IR. Besides the known productive GRP transcript isoforms, we identified a lot of splicing variants with diverse introns spliced in messenger RNA (mRNA) region coding the glycine-rich (GR) domain. The AS pattern of GRPs changed and particularly, the productive GRPs increased upon glucose stress. These ASs of GRP pre-mRNAs triggered by glucose stress could be abolished by AZD-8055, which is an ATP competitive inhibitor for the target of rapamycin (TOR) kinase but could be mimicked by H2O2. Additionally, AS pattern change of arginine/serine-rich splicing factor 31(RS31) via TOR pathway, which was previously described in response to light and sucrose signaling, was also induced in a similar manner by both glucose stress and reactive oxygen species (ROS). Here we conclude that (i) glucose stress suppresses photosynthesis and activates the glycolysis-mitochondria energy relay and ROS scavenging system; (ii) glucose stress triggers transcriptome-wide AS pattern changes including a large set of splicing factors, such as GRPs and RS31; (iii) high sugars regulate AS pattern change of both GRPs and RS31 via TOR-ROS pathway. The results from this study will deepen our understanding of the AS regulation mechanism in sugar signaling.
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18
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Tang Y, Huang C, Li Y, Wang Y, Zhang C. Genome-wide identification, phylogenetic analysis, and expression profiling of glycine-rich RNA-binding protein (GRPs) genes in seeded and seedless grapes ( Vitis vinifera). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2231-2243. [PMID: 34744363 PMCID: PMC8526680 DOI: 10.1007/s12298-021-01082-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Glycine-rich RNA-binding proteins (GRPs) are essential for many physiological and biochemical processes in plants, especially the response to environmental stresses. GRPs exist widely in angiosperms and gymnosperms plant species; however, their roles in Vitis vinifera are still poorly understood. To characterize VviGRP gene family, we performed a genomic survey, bioinformatics and expression analysis of VviGRPs in grape. We identified nineteen VviGRPs gene family members. The result of bioinformatics analysis showed their motif distribution, gene structure characteristics and chromosomal locations. Then we carried out synteny and phylogenetic analysis to study the origin and evolutionary relationship of GRPs. Tissue-specific expression analysis showed that VviGRPs have different expression patterns. Meanwhile, we studied expression profiles of seventeen ovule-expressed genes during seed development of stenospermocarpic seedless and seeded grapes, and the result showed that most of them have much higher relative expression levels in stenospermocarpic seedless grapes than that of seeded one before 25 days after full bloom (DAFB). It is suggested that VviGRPs may involve in the seed development process. Taken together, our research indicated that VviGRPs are related to seed development and will be beneficial for further investigations into the seed abortion mechanism under stenospermocarpic grapes. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01082-3.
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Affiliation(s)
- Yujin Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, People’s Republic of China, Yangling, 712100 Shaanxi China
| | - Congbo Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, People’s Republic of China, Yangling, 712100 Shaanxi China
| | - Yan Li
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi China
| | - Yuejin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, People’s Republic of China, Yangling, 712100 Shaanxi China
| | - Chaohong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, People’s Republic of China, Yangling, 712100 Shaanxi China
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19
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Liu L, Tang Z, Liu F, Mao F, Yujuan G, Wang Z, Zhao X. Normal, novel or none: versatile regulation from alternative splicing. PLANT SIGNALING & BEHAVIOR 2021; 16:1917170. [PMID: 33882794 PMCID: PMC8205018 DOI: 10.1080/15592324.2021.1917170] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
Pre-mRNA splicing is a vital step in the posttranscriptional regulation of gene expression. Splicing is catalyzed by the spliceosome, a multidalton RNA-protein complex, through two successive transesterifications to yield mature mRNAs. In Arabidopsis, more than 61% of all transcripts from intron-containing genes are alternatively spliced, thereby resulting in transcriptome and subsequent proteome diversities for cellular processes. Moreover, it is estimated that more alternative splicing (AS) events induced by adverse stimuli occur to confer stress tolerance. Recently, increasing AS variants encoding normal or novel proteins, or degraded by nonsense-mediated decay (NMD) and their corresponding splicing factors or regulators acting at the posttranscriptional level have been functionally characterized. This review comprehensively summarizes and highlights the advances in our understanding of the biological functions and underlying mechanisms of AS events and their regulators in Arabidopsis and provides prospects for further research on AS in crops.
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Affiliation(s)
- Lei Liu
- Jiangsu Key Laboratory for Eco-agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’anChina
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’anChina
| | - Ziwei Tang
- Jiangsu Key Laboratory for Eco-agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’anChina
| | - Fuxia Liu
- Jiangsu Key Laboratory for Eco-agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’anChina
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’anChina
| | - Feng Mao
- Jiangsu Key Laboratory for Eco-agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’anChina
| | - Gu Yujuan
- Jiangsu Key Laboratory for Eco-agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’anChina
| | - Zhijuan Wang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, WuhanChina
| | - Xiangxiang Zhao
- Jiangsu Key Laboratory for Eco-agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’anChina
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’anChina
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20
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Ma L, Cheng K, Li J, Deng Z, Zhang C, Zhu H. Roles of Plant Glycine-Rich RNA-Binding Proteins in Development and Stress Responses. Int J Mol Sci 2021; 22:ijms22115849. [PMID: 34072567 PMCID: PMC8198583 DOI: 10.3390/ijms22115849] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 01/02/2023] Open
Abstract
In recent years, much progress has been made in elucidating the functional roles of plant glycine-rich RNA-binding proteins (GR-RBPs) during development and stress responses. Canonical GR-RBPs contain an RNA recognition motif (RRM) or a cold-shock domain (CSD) at the N-terminus and a glycine-rich domain at the C-terminus, which have been associated with several different RNA processes, such as alternative splicing, mRNA export and RNA editing. However, many aspects of GR-RBP function, the targeting of their RNAs, interacting proteins and the consequences of the RNA target process are not well understood. Here, we discuss recent findings in the field, newly defined roles for GR-RBPs and the actions of GR-RBPs on target RNA metabolism.
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Affiliation(s)
- Liqun Ma
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (L.M.); (K.C.); (J.L.); (Z.D.)
| | - Ke Cheng
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (L.M.); (K.C.); (J.L.); (Z.D.)
| | - Jinyan Li
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (L.M.); (K.C.); (J.L.); (Z.D.)
| | - Zhiqi Deng
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (L.M.); (K.C.); (J.L.); (Z.D.)
| | - Chunjiao Zhang
- Supervision, Inspection & Testing Center of Agricultural Products Quality, Ministry of Agriculture and Rural Affairs, Beijing 100083, China;
| | - Hongliang Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (L.M.); (K.C.); (J.L.); (Z.D.)
- Correspondence:
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21
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Burjoski V, Reddy ASN. The Landscape of RNA-Protein Interactions in Plants: Approaches and Current Status. Int J Mol Sci 2021; 22:2845. [PMID: 33799602 PMCID: PMC7999938 DOI: 10.3390/ijms22062845] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/25/2021] [Accepted: 03/10/2021] [Indexed: 12/28/2022] Open
Abstract
RNAs transmit information from DNA to encode proteins that perform all cellular processes and regulate gene expression in multiple ways. From the time of synthesis to degradation, RNA molecules are associated with proteins called RNA-binding proteins (RBPs). The RBPs play diverse roles in many aspects of gene expression including pre-mRNA processing and post-transcriptional and translational regulation. In the last decade, the application of modern techniques to identify RNA-protein interactions with individual proteins, RNAs, and the whole transcriptome has led to the discovery of a hidden landscape of these interactions in plants. Global approaches such as RNA interactome capture (RIC) to identify proteins that bind protein-coding transcripts have led to the identification of close to 2000 putative RBPs in plants. Interestingly, many of these were found to be metabolic enzymes with no known canonical RNA-binding domains. Here, we review the methods used to analyze RNA-protein interactions in plants thus far and highlight the understanding of plant RNA-protein interactions these techniques have provided us. We also review some recent protein-centric, RNA-centric, and global approaches developed with non-plant systems and discuss their potential application to plants. We also provide an overview of results from classical studies of RNA-protein interaction in plants and discuss the significance of the increasingly evident ubiquity of RNA-protein interactions for the study of gene regulation and RNA biology in plants.
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Affiliation(s)
| | - Anireddy S. N. Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA;
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22
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Yepes-Molina L, Bárzana G, Carvajal M. Controversial Regulation of Gene Expression and Protein Transduction of Aquaporins under Drought and Salinity Stress. PLANTS 2020; 9:plants9121662. [PMID: 33261103 PMCID: PMC7761296 DOI: 10.3390/plants9121662] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/31/2022]
Abstract
Enhancement of the passage of water through membranes is one of the main mechanisms via which cells can maintain their homeostasis under stress conditions, and aquaporins are the main participants in this process. However, in the last few years, a number of studies have reported discrepancies between aquaporin messenger RNA (mRNA) expression and the number of aquaporin proteins synthesised in response to abiotic stress. These observations suggest the existence of post-transcriptional mechanisms which regulate plasma membrane intrinsic protein (PIP) trafficking to the plasma membrane. This indicates that the mRNA synthesis of some aquaporins could be modulated by the accumulation of the corresponding encoded protein, in relation to the turnover of the membranes. This aspect is discussed in terms of the results obtained: on the one hand, with isolated vesicles, in which the level of proteins present provides the membranes with important characteristics such as resistance and stability and, on the other, with isolated proteins reconstituted in artificial liposomes as an in vitro method to address the in vivo physiology of the entire plant.
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23
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Lin A, Ma J, Xu F, Xu W, Jiang H, Zhang H, Qu C, Wei L, Li J. Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed. PLANTS (BASEL, SWITZERLAND) 2020; 9:E977. [PMID: 32752101 PMCID: PMC7465011 DOI: 10.3390/plants9080977] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/21/2020] [Accepted: 07/28/2020] [Indexed: 12/16/2022]
Abstract
Yellow seed coat color is a desirable characteristic in rapeseed (Brassica napus), as it is associated with higher oil content and higher quality of meal. Alternative splicing (AS) is a vital post-transcriptional regulatory process contributing to plant cell differentiation and organ development. To identify novel transcripts and differences at the isoform level that are associated with seed color in B. napus, we compared 31 RNA-seq libraries of yellow- and black-seeded B. napus at five different developmental stages. AS events in the different samples were highly similar, and intron retention accounted for a large proportion of the observed AS pattern. AS mainly occurred in the early and middle stage of seed development. Weighted gene co-expression network analysis (WGCNA) identified 23 co-expression modules composed of differentially spliced genes, and we picked out two of the modules whose functions were highly associated with seed color. In the two modules, we found candidate DAS (differentially alternative splicing) genes related to the flavonoid pathway, such as TT8 (BnaC09g24870D), TT5 (BnaA09g34840D and BnaC08g26020D), TT12 (BnaC06g17050D and BnaA07g18120D), AHA10 (BnaA08g23220D and BnaC08g17280D), CHI (BnaC09g50050D), BAN (BnaA03g60670D) and DFR (BnaC09g17150D). Gene BnaC03g23650D, encoding RNA-binding family protein, was also identified. The splicing of the candidate genes identified in this study might be used to develop stable, yellow-seeded B. napus. This study provides insight into the formation of seed coat color in B. napus.
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Affiliation(s)
- Ai Lin
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (A.L.); (J.M.); (F.X.); (W.X.); (H.J); (H.Z.); (C.Q.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Jinqi Ma
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (A.L.); (J.M.); (F.X.); (W.X.); (H.J); (H.Z.); (C.Q.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Fei Xu
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (A.L.); (J.M.); (F.X.); (W.X.); (H.J); (H.Z.); (C.Q.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Wen Xu
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (A.L.); (J.M.); (F.X.); (W.X.); (H.J); (H.Z.); (C.Q.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Huanhuan Jiang
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (A.L.); (J.M.); (F.X.); (W.X.); (H.J); (H.Z.); (C.Q.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Haoran Zhang
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (A.L.); (J.M.); (F.X.); (W.X.); (H.J); (H.Z.); (C.Q.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Cunmin Qu
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (A.L.); (J.M.); (F.X.); (W.X.); (H.J); (H.Z.); (C.Q.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Lijuan Wei
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (A.L.); (J.M.); (F.X.); (W.X.); (H.J); (H.Z.); (C.Q.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Jiana Li
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (A.L.); (J.M.); (F.X.); (W.X.); (H.J); (H.Z.); (C.Q.)
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
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24
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Wang L, Yang T, Wang B, Lin Q, Zhu S, Li C, Ma Y, Tang J, Xing J, Li X, Liao H, Staiger D, Hu Z, Yu F. RALF1-FERONIA complex affects splicing dynamics to modulate stress responses and growth in plants. SCIENCE ADVANCES 2020; 6:eaaz1622. [PMID: 32671204 PMCID: PMC7314565 DOI: 10.1126/sciadv.aaz1622] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 03/06/2020] [Indexed: 05/21/2023]
Abstract
The environmentally responsive signaling pathways that link global transcriptomic changes through alternative splicing (AS) to plant fitness remain unclear. Here, we found that the interaction of the extracellular rapid alkalinization FACTOR 1 (RALF1) peptide with its receptor FERONIA (FER) triggered a rapid and massive RNA AS response by interacting with and phosphorylating glycine-rich RNA binding protein7 (GRP7) to elevate GRP7 nuclear accumulation in Arabidopsis thaliana. FER-dependent GRP7 phosphorylation enhanced its mRNA binding ability and its association with the spliceosome component U1-70K to enable splice site selection, modulating dynamic AS. Genetic reversal of a RALF1-FER-dependent splicing target partly rescued mutants deficient in GRP7. AS of GRP7 itself induced nonsense-mediated decay feedback to the RALF1-FER-GRP7 module, fine-tuning stress responses, and cell growth. The RALF1-FER-GRP7 module provides a paradigm for regulatory mechanisms of RNA splicing in response to external stimuli.
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Affiliation(s)
- Long Wang
- National Engineering Laboratory for Rice and By-product Deep Processing, Central South University of Forestry and Technology, Changsha 410004, P.R. China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
| | - Tao Yang
- National Engineering Laboratory for Rice and By-product Deep Processing, Central South University of Forestry and Technology, Changsha 410004, P.R. China
| | - Bingqian Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
| | - Qinlu Lin
- National Engineering Laboratory for Rice and By-product Deep Processing, Central South University of Forestry and Technology, Changsha 410004, P.R. China
| | - Sirui Zhu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
| | - Chiyu Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
| | - Youchu Ma
- National Engineering Laboratory for Rice and By-product Deep Processing, Central South University of Forestry and Technology, Changsha 410004, P.R. China
| | - Jing Tang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
| | - Junjie Xing
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, P.R. China
| | - Xiushan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
| | - Hongdong Liao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, D-33615 Bielefeld, Germany
| | - Zhiqiang Hu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, and Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082, P.R. China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, P.R. China
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25
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Yan Y, Ham BK, Chong YH, Yeh SD, Lucas WJ. A Plant SMALL RNA-BINDING PROTEIN 1 Family Mediates Cell-to-Cell Trafficking of RNAi Signals. MOLECULAR PLANT 2020; 13:321-335. [PMID: 31812689 DOI: 10.1016/j.molp.2019.12.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/30/2019] [Accepted: 12/02/2019] [Indexed: 05/20/2023]
Abstract
In plants, RNA interference (RNAi) plays a pivotal role in growth and development, and responses to environmental inputs, including pathogen attack. The intercellular and systemic trafficking of small interfering RNA (siRNA)/microRNA (miRNA) is a central component in this regulatory pathway. Currently, little is known with regards to the molecular agents involved in the movement of these si/miRNAs. To address this situation, we employed a biochemical approach to identify and characterize a conserved SMALL RNA-BINDING PROTEIN 1 (SRBP1) family that mediates non-cell-autonomous small RNA (sRNA) trafficking. In Arabidopsis, AtSRBP1 is a glycine-rich (GR) RNA-binding protein, also known as AtGRP7, which we show binds single-stranded siRNA. A viral vector, Zucchini yellow mosaic virus (ZYMV), was employed to functionally characterized the AtSRBP1-4 (AtGRP7/2/4/8) RNA recognition motif and GR domains. Cellular-based studies revealed the GR domain as being necessary and sufficient for SRBP1 cell-to-cell movement. Taken together, our findings provide a foundation for future research into the mechanism and function of mobile sRNA signaling agents in plants.
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Affiliation(s)
- Yan Yan
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Byung-Kook Ham
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Yee Hang Chong
- Department of Plant Pathology, National Chung-Hsing University, Taichung
| | - Shyi-Dong Yeh
- Department of Plant Pathology, National Chung-Hsing University, Taichung
| | - William J Lucas
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA.
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26
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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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27
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Steffen A, Elgner M, Staiger D. Regulation of Flowering Time by the RNA-Binding Proteins AtGRP7 and AtGRP8. PLANT & CELL PHYSIOLOGY 2019; 60:2040-2050. [PMID: 31241165 DOI: 10.1093/pcp/pcz124] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/18/2019] [Indexed: 05/20/2023]
Abstract
The timing of floral initiation is a tightly controlled process in plants. The circadian clock regulated glycine-rich RNA-binding protein (RBP) AtGRP7, a known regulator of splicing, was previously shown to regulate flowering time mainly by affecting the MADS-box repressor FLOWERING LOCUS C (FLC). Loss of AtGRP7 leads to elevated FLC expression and late flowering in the atgrp7-1 mutant. Here, we analyze genetic interactions of AtGRP7 with key regulators of the autonomous and the thermosensory pathway of floral induction. RNA interference- mediated reduction of the level of the paralogous AtGRP8 in atgrp7-1 further delays floral transition compared of with atgrp7-1. AtGRP7 acts in parallel to FCA, FPA and FLK in the branch of the autonomous pathway (AP) comprised of RBPs. It acts in the same branch as FLOWERING LOCUS D, and AtGRP7 loss-of-function mutants show elevated levels of dimethylated lysine 4 of histone H3, a mark for active transcription. In addition to its role in the AP, AtGRP7 acts in the thermosensory pathway of flowering time control by regulating alternative splicing of the floral repressor FLOWERING LOCUS M (FLM). Overexpression of AtGRP7 selectively favors the formation of the repressive isoform FLM-β. Our results suggest that the RBPs AtGRP7 and AtGRP8 influence MADS-Box transcription factors in at least two different pathways of flowering time control. This highlights the importance of RBPs to fine-tune the integration of varying cues into flowering time control and further strengthens the view that the different pathways, although genetically separable, constitute a tightly interwoven network to ensure plant reproductive success under changing environmental conditions.
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Affiliation(s)
- Alexander Steffen
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Universit�tsstrasse 25, D-33615 Bielefeld, Germany
| | - Mareike Elgner
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Universit�tsstrasse 25, D-33615 Bielefeld, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Universit�tsstrasse 25, D-33615 Bielefeld, Germany
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28
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Wang R, Liu H, Liu Z, Zou J, Meng J, Wang J. Genome-wide analysis of alternative splicing divergences between Brassica hexaploid and its parents. PLANTA 2019; 250:603-628. [PMID: 31139927 DOI: 10.1007/s00425-019-03198-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 05/24/2019] [Indexed: 05/23/2023]
Abstract
Compared with its parents, Brassica hexaploid underwent significant AS changes, which may provide diversified gene expression regulation patterns and could enhance its adaptability during evolution Polyploidization is considered a significant evolution force that promotes species formation. Alternative splicing (AS) plays a crucial role in multiple biological processes during plant growth and development. To explore the effects of allopolyploidization on the AS patterns of genes, a genome-wide AS analysis was performed by RNA-seq in Brassica hexaploid and its parents. In total, we found 7913 (27540 AS events), 14447 (70179 AS events), and 13205 (60804 AS events) AS genes in Brassica rapa, Brassica carinata, and Brassica hexaploid, respectively. A total of 920 new AS genes were discovered in Brassica hexaploid. There were 56 differently spliced genes between Brassica hexaploid and its parents. In addition, most of the alternative 5' splice sites were located 4 bp upstream of the dominant 5' splice sites, and most of the alternative 3' splice sites were located 3 bp downstream of the dominant 3' splice sites in Brassica hexapliod, which was similar to B. carinata. Furthermore, we cloned and sequenced all amplicons from the RT-PCR products of GRP7/8, namely, Bol045859, Bol016025 and Bol02880. The three genes were found to produce AS transcripts in a new way. The AS patterns of genes were diverse between Brassica hexaploid and its parents, including the loss and gain of AS events. Allopolyploidization changed alternative splicing sites of pre-mRNAs in Brassica hexaploid, which brought about alterations in the sequences of transcripts. Our study provided novel insights into the AS patterns of genes in allopolyploid plants, which may provide a reference for the study of polyploidy adaptability.
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Affiliation(s)
- Ruihua Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Helian Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhengyi Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.
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29
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Huang X, Yu R, Li W, Geng L, Jing X, Zhu C, Liu H. Identification and characterisation of a glycine-rich RNA-binding protein as an endogenous suppressor of RNA silencing from Nicotiana glutinosa. PLANTA 2019; 249:1811-1822. [PMID: 30840177 DOI: 10.1007/s00425-019-03122-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/27/2019] [Indexed: 05/08/2023]
Abstract
MAIN CONCLUSION This study shows that NgRBP suppresses both local and systemic RNA silencing induced by sense- or double-stranded RNA, and the RNA binding activity is essential for its function. To counteract host defence, many plant viruses encode viral suppressors of RNA silencing targeting various stages of RNA silencing. There is increasing evidence that the plants also encode endogenous suppressors of RNA silencing (ESR) to regulate this pathway. In this study, using Agrobacterium infiltration assays, we characterized NgRBP, a glycine-rich RNA-binding protein from Nicotiana glutinosa, as an ESR. Our results indicated that NgRBP suppressed both local and systemic RNA silencing induced by sense- or double-stranded RNA. We also demonstrated that NgRBP could promote Potato Virus X (PVX) infection in N. benthamiana. NgRBP knockdown by virus-induced gene silencing enhanced PVX and Cucumber mosaic virus resistance in N. glutinosa. RNA immunoprecipitation and electrophoretic mobility shift assays showed that NgRBP bound to GFP mRNA, dsRNA rather than siRNA. These findings provide the evidence that NgRBP acts as an ESR and the RNA affinity of NgRBP plays the key role in its ESR activity. NgRBP responds to multiple signals such as ABA, MeJA, SA, and Tobacco mosaic virus infection. Therefore, it could participate in the regulation of gene expression under specific conditions.
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Affiliation(s)
- Xu Huang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Ru Yu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Wenjing Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Liwei Geng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Xiuli Jing
- Institute of Immunology, Taishan Medical University, Tai'an, Shandong, China
| | - Changxiang Zhu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Hongmei Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China.
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Franzini VI, Azcón R, Ruiz-Lozano JM, Aroca R. Rhizobial symbiosis modifies root hydraulic properties in bean plants under non-stressed and salinity-stressed conditions. PLANTA 2019; 249:1207-1215. [PMID: 30603790 DOI: 10.1007/s00425-018-03076-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 12/19/2018] [Indexed: 05/10/2023]
Abstract
Rhizobial symbiosis improved the water status of bean plants under salinity-stress conditions, in part by increasing their osmotic root water flow. One of the main problems for agriculture worldwide is the increasing salinization of farming lands. The use of soil beneficial microorganisms stands up as a way to tackle this problem. One approach is the use of rhizobial N2-fixing, nodule-forming bacteria. Salinity-stress causes leaf dehydration due to an imbalance between water lost through stomata and water absorbed by roots. The aim of the present study was to elucidate how rhizobial symbiosis modulates the water status of bean (Phaseolus vulgaris) plants under salinity-stress conditions, by assessing the effects on root hydraulic properties. Bean plants were inoculated or not with a Rhizobium leguminosarum strain and subjected to moderate salinity-stress. The rhizobial symbiosis was found to improve leaf water status and root osmotic water flow under such conditions. Higher content of nitrogen and lower values of sodium concentration in root tissues were detected when compared to not inoculated plants. In addition, a drop in the osmotic potential of xylem sap and increased amount of PIP aquaporins could favour higher root osmotic water flow in the inoculated plants. Therefore, it was found that rhizobial symbiosis may also improve root osmotic water flow of the host plants under salinity stress.
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Affiliation(s)
- Vinicius Ide Franzini
- Department of Soil Microbiology and Symbiotic System, Estación Experimental del Zaidín (CSIC), Profesor Albareda 1, 18008, Granada, Spain
| | - Rosario Azcón
- Department of Soil Microbiology and Symbiotic System, Estación Experimental del Zaidín (CSIC), Profesor Albareda 1, 18008, Granada, Spain
| | - Juan Manuel Ruiz-Lozano
- Department of Soil Microbiology and Symbiotic System, Estación Experimental del Zaidín (CSIC), Profesor Albareda 1, 18008, Granada, Spain
| | - Ricardo Aroca
- Department of Soil Microbiology and Symbiotic System, Estación Experimental del Zaidín (CSIC), Profesor Albareda 1, 18008, Granada, Spain.
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McClung CR. The Plant Circadian Oscillator. BIOLOGY 2019; 8:E14. [PMID: 30870980 PMCID: PMC6466001 DOI: 10.3390/biology8010014] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/17/2019] [Accepted: 03/09/2019] [Indexed: 12/20/2022]
Abstract
It has been nearly 300 years since the first scientific demonstration of a self-sustaining circadian clock in plants. It has become clear that plants are richly rhythmic, and many aspects of plant biology, including photosynthetic light harvesting and carbon assimilation, resistance to abiotic stresses, pathogens, and pests, photoperiodic flower induction, petal movement, and floral fragrance emission, exhibit circadian rhythmicity in one or more plant species. Much experimental effort, primarily, but not exclusively in Arabidopsis thaliana, has been expended to characterize and understand the plant circadian oscillator, which has been revealed to be a highly complex network of interlocked transcriptional feedback loops. In addition, the plant circadian oscillator has employed a panoply of post-transcriptional regulatory mechanisms, including alternative splicing, adjustable rates of translation, and regulated protein activity and stability. This review focuses on our present understanding of the regulatory network that comprises the plant circadian oscillator. The complexity of this oscillatory network facilitates the maintenance of robust rhythmicity in response to environmental extremes and permits nuanced control of multiple clock outputs. Consistent with this view, the clock is emerging as a target of domestication and presents multiple targets for targeted breeding to improve crop performance.
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Affiliation(s)
- C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA.
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NPR1 and Redox Rhythmx: Connections, between Circadian Clock and Plant Immunity. Int J Mol Sci 2019; 20:ijms20051211. [PMID: 30857376 PMCID: PMC6429127 DOI: 10.3390/ijms20051211] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/06/2019] [Accepted: 03/06/2019] [Indexed: 01/08/2023] Open
Abstract
The circadian clock in plants synchronizes biological processes that display cyclic 24-h oscillation based on metabolic and physiological reactions. This clock is a precise timekeeping system, that helps anticipate diurnal changes; e.g., expression levels of clock-related genes move in synchrony with changes in pathogen infection and help prepare appropriate defense responses in advance. Salicylic acid (SA) is a plant hormone and immune signal involved in systemic acquired resistance (SAR)-mediated defense responses. SA signaling induces cellular redox changes, and degradation and rhythmic nuclear translocation of the non-expresser of PR genes 1 (NPR1) protein. Recent studies demonstrate the ability of the circadian clock to predict various potential attackers, and of redox signaling to determine appropriate defense against pathogen infection. Interaction of the circadian clock with redox rhythm promotes the balance between immunity and growth. We review here a variety of recent evidence for the intricate relationship between circadian clock and plant immune response, with a focus on the roles of redox rhythm and NPR1 in the circadian clock and plant immunity.
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Beyond Transcription: Fine-Tuning of Circadian Timekeeping by Post-Transcriptional Regulation. Genes (Basel) 2018; 9:genes9120616. [PMID: 30544736 PMCID: PMC6315869 DOI: 10.3390/genes9120616] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 11/29/2018] [Accepted: 12/03/2018] [Indexed: 12/28/2022] Open
Abstract
The circadian clock is an important endogenous timekeeper, helping plants to prepare for the periodic changes of light and darkness in their environment. The clockwork of this molecular timer is made up of clock proteins that regulate transcription of their own genes with a 24 h rhythm. Furthermore, the rhythmically expressed clock proteins regulate time-of-day dependent transcription of downstream genes, causing messenger RNA (mRNA) oscillations of a large part of the transcriptome. On top of the transcriptional regulation by the clock, circadian rhythms in mRNAs rely in large parts on post-transcriptional regulation, including alternative pre-mRNA splicing, mRNA degradation, and translational control. Here, we present recent insights into the contribution of post-transcriptional regulation to core clock function and to regulation of circadian gene expression in Arabidopsis thaliana.
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Genome-wide identification and expression analysis of glycine-rich RNA-binding protein family in sweet potato wild relative Ipomoea trifida. Gene 2018; 686:177-186. [PMID: 30453066 DOI: 10.1016/j.gene.2018.11.044] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 10/08/2018] [Accepted: 11/15/2018] [Indexed: 01/31/2023]
Abstract
Glycine-rich RNA-binding proteins (GRPs) contain RNA recognition motif (RRM) and glycine-rich domains at the N- or C-terminus, respectively, and they participate in varied physiological and biochemical processes, as well as environmental stresses. Sweet potato from the genus Ipomoea is one of the most important crops. However, the role of the GRP gene family in Ipomoea plant species has not been reported yet. At the same time, the genome of sweet potato remains to be elucidated, but the genome of I. trifida which is most probably the progenitor of the sweet potato was released recently. In this regard, we carried out genome-wide analysis of GRP family members in I. trifida. Here, we identified nine GRP genes in I. trifida and investigated their motif distribution, promoters and gene structure. Subsequently, we performed phylogenetic analysis with the GRP genes from I. trifida, Arabidopsis thaliana, Zea mays L. and Oryza sativa to investigate their phylogenetic relationship. Moreover, we studied the expression patterns of ItGRPs in the roots, stems, young and mature leaves and flowers and found that ItGRP genes were tissue-specific. Meanwhile, the expression profiles under four abiotic stress conditions, including heat, cold, salt and drought stress treatments, revealed that some genes were markedly up-regulated or down-regulated. Taken together, our findings will provide reference to studies on the function of GRP genes in the development and stress response of I. trifida.
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Filatova EN, Utkin OV. The Role of Noncoding mRNA Isoforms in the Regulation of Gene Expression. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418080057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Borrelli GM, Mazzucotelli E, Marone D, Crosatti C, Michelotti V, Valè G, Mastrangelo AM. Regulation and Evolution of NLR Genes: A Close Interconnection for Plant Immunity. Int J Mol Sci 2018; 19:E1662. [PMID: 29867062 PMCID: PMC6032283 DOI: 10.3390/ijms19061662] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/01/2018] [Accepted: 06/02/2018] [Indexed: 12/12/2022] Open
Abstract
NLR (NOD-like receptor) genes belong to one of the largest gene families in plants. Their role in plants' resistance to pathogens has been clearly described for many members of this gene family, and dysregulation or overexpression of some of these genes has been shown to induce an autoimmunity state that strongly affects plant growth and yield. For this reason, these genes have to be tightly regulated in their expression and activity, and several regulatory mechanisms are described here that tune their gene expression and protein levels. This gene family is subjected to rapid evolution, and to maintain diversity at NLRs, a plethora of genetic mechanisms have been identified as sources of variation. Interestingly, regulation of gene expression and evolution of this gene family are two strictly interconnected aspects. Indeed, some examples have been reported in which mechanisms of gene expression regulation have roles in promotion of the evolution of this gene family. Moreover, co-evolution of the NLR gene family and other gene families devoted to their control has been recently demonstrated, as in the case of miRNAs.
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Affiliation(s)
- Grazia M Borrelli
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 673, km 25.2, 71122 Foggia, Italy.
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Daniela Marone
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 673, km 25.2, 71122 Foggia, Italy.
| | - Cristina Crosatti
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Vania Michelotti
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Giampiero Valè
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, Italy.
| | - Anna M Mastrangelo
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, via Stezzano 24, 24126 Bergamo, Italy.
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Wang B, Wang G, Shen F, Zhu S. A Glycine-Rich RNA-Binding Protein, CsGR-RBP3, Is Involved in Defense Responses Against Cold Stress in Harvested Cucumber ( Cucumis sativus L.) Fruit. FRONTIERS IN PLANT SCIENCE 2018; 9:540. [PMID: 29740470 PMCID: PMC5925850 DOI: 10.3389/fpls.2018.00540] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 04/06/2018] [Indexed: 05/09/2023]
Abstract
Plant glycine-rich RNA-binding proteins (GR-RBPs) have been shown to play important roles in response to abiotic stresses in actively proliferating organs such as young plants, root tips, and flowers, but their roles in chilling responses of harvested fruit remains largely unknown. Here, we investigated the role of CsGR-RBP3 in the chilling response of cucumber fruit. Pre-storage cold acclimation at 10°C (PsCA) for 3 days significantly enhanced chilling tolerance of cucumber fruit compared with the control fruit that were stored at 5°C. In the control fruit, only one of the six cucumber CsGR-RBP genes, CsGR-RBP2, was enhanced whereas the other five, i.e., CsGR-RBP3, CsGR-RBP4, CsGR-RBP5, CsGR-RBP-blt801, and CsGR-RBP-RZ1A were not. However, in the fruit exposed to PsCA before storage at 5°C, CsGR-RBP2 transcript levels were not obviously different from those in the controls, whereas the other five were highly upregulated, with CsGR-RBP3 the most significantly induced. Treatment with endogenous ABA and NO biosynthesis inhibitors, tungstate and L-nitro-arginine methyl ester, respectively, prior to PsCA treatment, clearly downregulated CsGR-RBP3 expression and significantly aggravated chilling injury. These results suggest a strong connection between CsGR-RBP3 expression and chilling tolerance in cucumber fruit. Transient expression in tobacco suggests CsGR-RBP3 was located in the mitochondria, implying a role for CsGR-RBP3 in maintaining mitochondria-related functions under low temperature. Arabidopsis lines overexpressing CsGR-RBP3 displayed faster growth at 23°C, lower electrolyte leakage and higher Fv/Fm ratio at 0°C, and higher survival rate at -20°C, than wild-type plants. Under cold stress conditions, Arabidopsis plants overexpressing CsGR-RBP3 displayed lower reactive oxygen species levels, and higher catalase and superoxide dismutase expression and activities, compared with the wild-type plants. In addition, overexpression of CsGR-RBP3 significantly upregulated nine Arabidopsis genes involved in defense responses to various stresses, including chilling. These results strongly suggest CsGR-RBP3 plays a positive role in defense against chilling stress.
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Affiliation(s)
| | | | | | - Shijiang Zhu
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, China
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Köster T, Meyer K. Plant Ribonomics: Proteins in Search of RNA Partners. TRENDS IN PLANT SCIENCE 2018; 23:352-365. [PMID: 29429586 DOI: 10.1016/j.tplants.2018.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 01/08/2018] [Accepted: 01/15/2018] [Indexed: 06/08/2023]
Abstract
Research into the regulation of gene expression underwent a shift from focusing on DNA-binding proteins as key transcriptional regulators to RNA-binding proteins (RBPs) that come into play once transcription has been initiated. RBPs orchestrate all RNA-processing steps in the cell. To obtain a global view of in vivo targets, the RNA complement associated with particular RBPs is determined via immunoprecipitation of the RBP and subsequent identification of bound RNAs via RNA-seq. Here, we describe technical advances in identifying RBP in vivo targets and their binding motifs. We provide an up-to-date view of targets of nucleocytoplasmic RBPs collected in arabidopsis. We also discuss current experimental limitations and provide an outlook on how the approaches may advance our understanding of post-transcriptional networks.
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Affiliation(s)
- Tino Köster
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany.
| | - Katja Meyer
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
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Czolpinska M, Rurek M. Plant Glycine-Rich Proteins in Stress Response: An Emerging, Still Prospective Story. FRONTIERS IN PLANT SCIENCE 2018; 9:302. [PMID: 29568308 PMCID: PMC5852109 DOI: 10.3389/fpls.2018.00302] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 02/21/2018] [Indexed: 05/21/2023]
Abstract
Seed plants are sessile organisms that have developed a plethora of strategies for sensing, avoiding, and responding to stress. Several proteins, including the glycine-rich protein (GRP) superfamily, are involved in cellular stress responses and signaling. GRPs are characterized by high glycine content and the presence of conserved segments including glycine-containing structural motifs composed of repetitive amino acid residues. The general structure of this superfamily facilitates division of GRPs into five main subclasses. Although the participation of GRPs in plant stress response has been indicated in numerous model and non-model plant species, relatively little is known about the key physiological processes and molecular mechanisms in which those proteins are engaged. Class I, II, and IV members are known to be involved in hormone signaling, stress acclimation, and floral development, and are crucial for regulation of plant cells growth. GRPs of class IV [RNA-binding proteins (RBPs)] are involved in alternative splicing or regulation of transcription and stomatal movement, seed, pollen, and stamen development; their accumulation is regulated by the circadian clock. Owing to the fact that the overexpression of GRPs can confer tolerance to stress (e.g., some are involved in cold acclimation and may improve growth at low temperatures), these proteins could play a promising role in agriculture through plant genetic engineering. Consequently, isolation, cloning, characterization, and functional validation of novel GRPs expressed in response to the diverse stress conditions are expected to be growing areas of research in the coming years. According to our knowledge, this is the first comprehensive review on participation of plant GRPs in the response to diverse stress stimuli.
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Systems Approaches to Map In Vivo RNA–Protein Interactions in Arabidopsis thaliana. RNA TECHNOLOGIES 2018. [PMCID: PMC7122672 DOI: 10.1007/978-3-319-92967-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Proteins that specifically interact with mRNAs orchestrate mRNA processing steps all the way from transcription to decay. Thus, these RNA-binding proteins represent an important control mechanism to double check which proportion of nascent pre-mRNAs is ultimately available for translation into distinct proteins. Here, we discuss recent progress to obtain a systems-level understanding of in vivo RNA–protein interactions in the reference plant Arabidopsis thaliana using protein-centric and RNA-centric methods as well as combined protein binding site and structure probing.
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Meyer K, Köster T, Nolte C, Weinholdt C, Lewinski M, Grosse I, Staiger D. Adaptation of iCLIP to plants determines the binding landscape of the clock-regulated RNA-binding protein AtGRP7. Genome Biol 2017; 18:204. [PMID: 29084609 PMCID: PMC5663106 DOI: 10.1186/s13059-017-1332-x] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/29/2017] [Indexed: 12/11/2022] Open
Abstract
Background Functions for RNA-binding proteins in orchestrating plant development and environmental responses are well established. However, the lack of a genome-wide view of their in vivo binding targets and binding landscapes represents a gap in understanding the mode of action of plant RNA-binding proteins. Here, we adapt individual nucleotide resolution crosslinking and immunoprecipitation (iCLIP) genome-wide to determine the binding repertoire of the circadian clock-regulated Arabidopsis thaliana glycine-rich RNA-binding protein AtGRP7. Results iCLIP identifies 858 transcripts with significantly enriched crosslink sites in plants expressing AtGRP7-GFP that are absent in plants expressing an RNA-binding-dead AtGRP7 variant or GFP alone. To independently validate the targets, we performed RNA immunoprecipitation (RIP)-sequencing of AtGRP7-GFP plants subjected to formaldehyde fixation. Of the iCLIP targets, 452 were also identified by RIP-seq and represent a set of high-confidence binders. AtGRP7 can bind to all transcript regions, with a preference for 3′ untranslated regions. In the vicinity of crosslink sites, U/C-rich motifs are overrepresented. Cross-referencing the targets against transcriptome changes in AtGRP7 loss-of-function mutants or AtGRP7-overexpressing plants reveals a predominantly negative effect of AtGRP7 on its targets. In particular, elevated AtGRP7 levels lead to damping of circadian oscillations of transcripts, including DORMANCY/AUXIN ASSOCIATED FAMILY PROTEIN2 and CCR-LIKE. Furthermore, several targets show changes in alternative splicing or polyadenylation in response to altered AtGRP7 levels. Conclusions We have established iCLIP for plants to identify target transcripts of the RNA-binding protein AtGRP7. This paves the way to investigate the dynamics of posttranscriptional networks in response to exogenous and endogenous cues. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1332-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katja Meyer
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Tino Köster
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Christine Nolte
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Claus Weinholdt
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Martin Lewinski
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Ivo Grosse
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
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Covarrubias AA, Cuevas-Velazquez CL, Romero-Pérez PS, Rendón-Luna DF, Chater CCC. Structural disorder in plant proteins: where plasticity meets sessility. Cell Mol Life Sci 2017; 74:3119-3147. [PMID: 28643166 PMCID: PMC11107788 DOI: 10.1007/s00018-017-2557-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/01/2017] [Indexed: 01/08/2023]
Abstract
Plants are sessile organisms. This intriguing nature provokes the question of how they survive despite the continual perturbations caused by their constantly changing environment. The large amount of knowledge accumulated to date demonstrates the fascinating dynamic and plastic mechanisms, which underpin the diverse strategies selected in plants in response to the fluctuating environment. This phenotypic plasticity requires an efficient integration of external cues to their growth and developmental programs that can only be achieved through the dynamic and interactive coordination of various signaling networks. Given the versatility of intrinsic structural disorder within proteins, this feature appears as one of the leading characters of such complex functional circuits, critical for plant adaptation and survival in their wild habitats. In this review, we present information of those intrinsically disordered proteins (IDPs) from plants for which their high level of predicted structural disorder has been correlated with a particular function, or where there is experimental evidence linking this structural feature with its protein function. Using examples of plant IDPs involved in the control of cell cycle, metabolism, hormonal signaling and regulation of gene expression, development and responses to stress, we demonstrate the critical importance of IDPs throughout the life of the plant.
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Affiliation(s)
- Alejandra A Covarrubias
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250, Cuernavaca, Mexico.
| | - Cesar L Cuevas-Velazquez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250, Cuernavaca, Mexico
| | - Paulette S Romero-Pérez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250, Cuernavaca, Mexico
| | - David F Rendón-Luna
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250, Cuernavaca, Mexico
| | - Caspar C C Chater
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250, Cuernavaca, Mexico
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Lu H, McClung CR, Zhang C. Tick Tock: Circadian Regulation of Plant Innate Immunity. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:287-311. [PMID: 28590878 DOI: 10.1146/annurev-phyto-080516-035451] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Many living organisms on Earth have evolved the ability to integrate environmental and internal signals to determine time and thereafter adjust appropriately their metabolism, physiology, and behavior. The circadian clock is the endogenous timekeeper critical for multiple biological processes in many organisms. A growing body of evidence supports the importance of the circadian clock for plant health. Plants activate timed defense with various strategies to anticipate daily attacks of pathogens and pests and to modulate responses to specific invaders in a time-of-day-dependent manner (gating). Pathogen infection is also known to reciprocally modulate clock activity. Such a cross talk likely reflects the adaptive nature of plants to coordinate limited resources for growth, development, and defense. This review summarizes recent progress in circadian regulation of plant innate immunity with a focus on the molecular events linking the circadian clock and defense. More and better knowledge of clock-defense cross talk could help to improve disease resistance and productivity in economically important crops.
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Affiliation(s)
- Hua Lu
- Department of Biological Sciences, University of Maryland-Baltimore County, Baltimore, Maryland 21052;
| | - C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755
| | - Chong Zhang
- Department of Biological Sciences, University of Maryland-Baltimore County, Baltimore, Maryland 21052;
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Up-Frameshift Protein UPF1 Regulates Neurospora crassa Circadian and Diurnal Growth Rhythms. Genetics 2017; 206:1881-1893. [PMID: 28600326 DOI: 10.1534/genetics.117.202788] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 05/31/2017] [Indexed: 01/24/2023] Open
Abstract
Nonsense-mediated RNA decay (NMD) is a crucial post-transcriptional regulatory mechanism that recognizes and eliminates aberrantly processed transcripts, and mediates the expression of normal gene transcripts. In this study, we report that in the filamentous fungus Neurospora crassa, the NMD factors play a conserved role in regulating the surveillance of NMD targets including premature termination codon (PTC)-containing transcripts and normal transcripts. The circadian rhythms in all of the knockout strains of upf1-3 genes, which encode the Up-frameshift proteins, were aberrant. The upf1 knockout strain displays a shortened circadian period, which can be restored by constantly expressing exogenous Up-frameshift protein 1 (UPF1). UPF1 regulates the circadian clock by modulating the splicing of the core clock gene frequency (frq) through spliceosome and spliceosome-related arginine/serine-rich splicing factors, which partly account for the short periods in the upf1 knockout strain. We also demonstrated that the clock genes including White Collar (WC)-1, WC-2, and FRQ are involved in controlling the diurnal growth rhythm, and UPF1 may affect the growth rhythms by mediating the FRQ protein levels in the daytime. These findings suggest that the NMD factors play important roles in regulating the circadian clock and diurnal growth rhythms in Neurospora.
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Naoumkina M, Thyssen GN, Fang DD, Hinchliffe DJ, Florane CB, Jenkins JN. Small RNA sequencing and degradome analysis of developing fibers of short fiber mutants Ligon-lintles-1 (Li 1 ) and -2 (Li 2 ) revealed a role for miRNAs and their targets in cotton fiber elongation. BMC Genomics 2016; 17:360. [PMID: 27184029 PMCID: PMC4869191 DOI: 10.1186/s12864-016-2715-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/06/2016] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The length of cotton fiber is an important agronomic trait that directly affects the quality of yarn and fabric. Understanding the molecular basis of fiber elongation would provide a means for improvement of fiber length. Ligon-lintless-1 (Li 1 ) and -2 (Li 2 ) are monogenic and dominant mutations that result in an extreme reduction in the length of lint fiber on mature seeds. In a near-isogenic state with wild type cotton these two short fiber mutants provide an effective model system to study the mechanisms of fiber elongation. Plant miRNAs regulate many aspects of growth and development. However, the mechanism underlying the miRNA-mediated regulation of fiber development is largely unknown. RESULTS Small RNA libraries constructed from developing fiber cells of the short fiber mutants Li 1 and Li 2 and their near-isogenic wild type lines were sequenced. We identified 24 conservative and 147 novel miRNA families with targets that were detected through degradome sequencing. The distribution of the target genes into functional categories revealed the largest set of genes were transcription factors. Expression profiles of 20 miRNAs were examined across a fiber developmental time course in wild type and short fiber mutations. We conducted correlation analysis between miRNA transcript abundance and the length of fiber for 11 diverse Upland cotton lines. The expression patterns of 4 miRNAs revealed significant negative correlation with fiber lengths of 11 cotton lines. CONCLUSIONS Our results suggested that the mutations have changed the regulation of miRNAs expression during fiber development. Further investigations of differentially expressed miRNAs in the Li 1 and Li 2 mutants will contribute to better understanding of the regulatory mechanisms of cotton fiber development. Four miRNAs negatively correlated with fiber length are good candidates for further investigations of miRNA regulation of important genotype dependent fiber traits. Thus, our results will contribute to further studies on the role of miRNAs in cotton fiber development and will provide a tool for fiber improvement through molecular breeding.
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Affiliation(s)
- Marina Naoumkina
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, 1100 Robert E. Lee Blvd, New Orleans, LA, 70124, USA.
| | - Gregory N Thyssen
- Cotton Chemistry and Utilization Research Unit, USDA-ARS, Southern Regional Research Center, 1100 Robert E. Lee Blvd, New Orleans, LA, 70124, USA
| | - David D Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, 1100 Robert E. Lee Blvd, New Orleans, LA, 70124, USA
| | - Doug J Hinchliffe
- Cotton Chemistry and Utilization Research Unit, USDA-ARS, Southern Regional Research Center, 1100 Robert E. Lee Blvd, New Orleans, LA, 70124, USA
| | - Christopher B Florane
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, 1100 Robert E. Lee Blvd, New Orleans, LA, 70124, USA
| | - Johnie N Jenkins
- Genetics and Sustainable Agriculture Research Unit, USDA-ARS, 810 Highway 12 East, Mississippi State, MS, 39762, USA
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Liang C, Cheng S, Zhang Y, Sun Y, Fernie AR, Kang K, Panagiotou G, Lo C, Lim BL. Transcriptomic, proteomic and metabolic changes in Arabidopsis thaliana leaves after the onset of illumination. BMC PLANT BIOLOGY 2016; 16:43. [PMID: 26865323 PMCID: PMC4750186 DOI: 10.1186/s12870-016-0726-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 01/28/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Light plays an important role in plant growth and development. In this study, the impact of light on physiology of 20-d-old Arabidopsis leaves was examined through transcriptomic, proteomic and metabolomic analysis. Since the energy-generating electron transport chains in chloroplasts and mitochondria are encoded by both nuclear and organellar genomes, sequencing total RNA after removal of ribosomal RNAs provides essential information on transcription of organellar genomes. The changes in the levels of ADP, ATP, NADP(+), NADPH and 41 metabolites upon illumination were also quantified. RESULTS Upon illumination, while the transcription of the genes encoded by the plastid genome did not change significantly, the transcription of nuclear genes encoding different functional complexes in the photosystem are differentially regulated whereas members of the same complex are co-regulated with each other. The abundance of mRNAs and proteins encoded by all three genomes are, however, not always positively correlated. One such example is the negative correlation between mRNA and protein abundances of the photosystem components, which reflects the importance of post-transcriptional regulation in plant physiology. CONCLUSION This study provides systems-wide datasets which allow plant researchers to examine the changes in leaf transcriptomes, proteomes and key metabolites upon illumination and to determine whether there are any correlations between changes in transcript and protein abundances of a particular gene or pathway upon illumination. The integration of data of the organelles and the photosystems, Calvin-Benson cycle, carbohydrate metabolism, glycolysis, the tricarboxylic acid cycle and respiratory chain, thereby provides a more complete picture to the changes in plant physiology upon illumination than has been attained to date.
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Affiliation(s)
- Chao Liang
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Shifeng Cheng
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Youjun Zhang
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
| | - Yuzhe Sun
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
| | - Kang Kang
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Gianni Panagiotou
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Clive Lo
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Boon Leong Lim
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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Kim JY, Ryu JY, Baek K, Park CM. High temperature attenuates the gravitropism of inflorescence stems by inducing SHOOT GRAVITROPISM 5 alternative splicing in Arabidopsis. THE NEW PHYTOLOGIST 2016; 209:265-279. [PMID: 26256266 DOI: 10.1111/nph.13602] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 07/09/2015] [Indexed: 06/04/2023]
Abstract
In higher plants, gravitropism proceeds through three sequential steps in the responding organs: perception of gravity signals, signal transduction and asymmetric cell elongation. Light and temperature also influence the gravitropic orientation of plant organs. A series of Arabidopsis shoot gravitropism (sgr) mutants has been shown to exhibit disturbed shoot gravitropism. SGR5 is functionally distinct from other SGR members in that it mediates the early events of gravitropic responses in inflorescence stems. Here, we demonstrated that SGR5 alternative splicing produces two protein variants (SGR5α and SGR5β) in modulating the gravitropic response of inflorescence stems at high temperatures. SGR5β inhibits SGR5α function by forming non-DNA-binding heterodimers. Transgenic plants overexpressing SGR5β (35S:SGR5β) exhibit reduced gravitropic growth of inflorescence stems, as observed in the SGR5-deficient sgr5-5 mutant. Interestingly, SGR5 alternative splicing is accelerated at high temperatures, resulting in the high-level accumulation of SGR5β transcripts. When plants were exposed to high temperatures, whereas gravitropic curvature was reduced in Col-0 inflorescence stems, it was uninfluenced in the inflorescence stems of 35S:SGR5β transgenic plants and sgr5-5 mutant. We propose that the thermoresponsive alternative splicing of SGR5 provides an adaptation strategy by which plants protect the shoots from hot air under high temperature stress in natural habitats.
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Affiliation(s)
- Joo-Young Kim
- Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
| | - Jae Yong Ryu
- Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
| | - Kon Baek
- Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-742, Korea
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Lewinski M, Hallmann A, Staiger D. Genome-wide identification and phylogenetic analysis of plant RNA binding proteins comprising both RNA recognition motifs and contiguous glycine residues. Mol Genet Genomics 2015; 291:763-73. [DOI: 10.1007/s00438-015-1144-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 11/06/2015] [Indexed: 11/28/2022]
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Gutierrez-Carbonell E, Lattanzio G, Albacete A, Rios JJ, Kehr J, Abadía A, Grusak MA, Abadía J, López-Millán AF. Effects of Fe deficiency on the protein profile of Brassica napus phloem sap. Proteomics 2015; 15:3835-53. [PMID: 26316195 DOI: 10.1002/pmic.201400464] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 07/14/2015] [Accepted: 08/24/2015] [Indexed: 01/18/2023]
Abstract
The aim of this work was to study the effect of Fe deficiency on the protein profile of phloem sap exudates from Brassica napus using 2DE (IEF-SDS-PAGE). The experiment was repeated thrice and two technical replicates per treatment were done. Phloem sap purity was assessed by measuring sugar concentrations. Two hundred sixty-three spots were consistently detected and 15.6% (41) of them showed significant changes in relative abundance (22 decreasing and 19 increasing) as a result of Fe deficiency. Among them, 85% (35 spots), were unambiguously identified. Functional categories containing the largest number of protein species showing changes as a consequence of Fe deficiency were signaling and regulation (32%), and stress and redox homeostasis (17%). The Phloem sap showed a higher oxidative stress and significant changes in the hormonal profile as a result of Fe deficiency. Results indicate that Fe deficiency elicits major changes in signaling pathways involving Ca and hormones, which are generally associated with flowering and developmental processes, causes an alteration in ROS homeostasis processes, and induces decreases in the abundances of proteins involved in sieve element repair, suggesting that Fe-deficient plants may have an impaired capacity to heal sieve elements upon injury.
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Affiliation(s)
| | - Giuseppe Lattanzio
- Plant Nutrition Department, CSIC, Aula Dei Experimental Station, Zaragoza, Spain
| | - Alfonso Albacete
- Department of Plant Nutrition, CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, Spain
| | - Juan José Rios
- Plant Nutrition Department, CSIC, Aula Dei Experimental Station, Zaragoza, Spain
| | - Julia Kehr
- Department of Molecular Plant Genetics, Biocenter Klein Flottbek, University Hamburg, Hamburg, Germany
| | - Anunciación Abadía
- Plant Nutrition Department, CSIC, Aula Dei Experimental Station, Zaragoza, Spain
| | - Michael A Grusak
- USDA-ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Javier Abadía
- Plant Nutrition Department, CSIC, Aula Dei Experimental Station, Zaragoza, Spain
| | - Ana Flor López-Millán
- Plant Nutrition Department, CSIC, Aula Dei Experimental Station, Zaragoza, Spain.,USDA-ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
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Abstract
Alternative pre-messenger RNA splicing in higher plants emerges as an important layer of regulation upon exposure to exogenous and endogenous cues. Accordingly, mutants defective in RNA-binding proteins predicted to function in the splicing process show severe phenotypic alterations. Among those are developmental defects, impaired responses to pathogen threat or abiotic stress factors, and misregulation of the circadian timing system. A suite of splicing factors has been identified in the model plant Arabidopsis thaliana. Here we summarize recent insights on how defects in these splicing factors impair plant performance.
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