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Zhang H, Yin L, Song F, Jiang M. SKIP Silencing Decreased Disease Resistance Against Botrytis cinerea and Pseudomonas syringae pv. tomato DC3000 in Tomato. FRONTIERS IN PLANT SCIENCE 2020; 11:593267. [PMID: 33381133 PMCID: PMC7767821 DOI: 10.3389/fpls.2020.593267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/19/2020] [Indexed: 05/29/2023]
Abstract
SKIP, a component of the spliceosome, is involved in numerous signaling pathways. However, there is no direct genetic evidence supporting the function of SKIP in defense responses. In this paper, two SKIPs, namely, SlSKIP1a and SlSKIP1b, were analyzed in tomato. qRT-PCR analysis showed that the SlSKIP1b expression was triggered via Pseudomonas syringae pv. tomato (Pst) DC3000 and Botrytis cinerea (B. cinerea), together with the defense-associated signals. In addition, the functions of SlSKIP1a and SlSKIP1b in disease resistance were analyzed in tomato through the virus-induced gene silencing (VIGS) technique. VIGS-mediated SlSKIP1b silencing led to increased accumulation of reactive oxygen species (ROS), along with the decreased expression of defense-related genes (DRGs) after pathogen infection, suggesting that it reduced B. cinerea and Pst DC3000 resistance. There was no significant difference in B. cinerea and Pst DC3000 resistance in TRV-SlSKIP1a-infiltrated plants compared with the TRV-GUS-silencing counterparts. As suggested by the above findings, SlSKIP1b plays a vital role in disease resistance against pathogens possibly by regulating the accumulation of ROS as well as the expression of DRGs.
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Affiliation(s)
- Huijuan Zhang
- Life Science Collegue, Taizhou University, Taizhou, China
| | - Longfei Yin
- Life Science Collegue, Taizhou University, Taizhou, China
| | - Fengming Song
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Ming Jiang
- Life Science Collegue, Taizhou University, Taizhou, China
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Feng G, Yoo M, Davenport R, Boatwright JL, Koh J, Chen S, Barbazuk WB. Jasmonate induced alternative splicing responses in Arabidopsis. PLANT DIRECT 2020; 4:e00245. [PMID: 32875268 PMCID: PMC7450174 DOI: 10.1002/pld3.245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 06/04/2020] [Accepted: 06/24/2020] [Indexed: 05/14/2023]
Abstract
Jasmonate is an essential phytohormone regulating plant growth, development, and defense. Alternative splicing (AS) in jasmonate ZIM-domain (JAZ) repressors is well-characterized and plays an important role in jasmonate signaling regulation. However, it is unknown whether other genes in the jasmonate signaling pathway are regulated by AS. We explore the potential for AS regulation in three Arabidopsis genotypes (WT, jaz2, jaz7) in response to methyl jasmonate (MeJA) treatment with respect to: (a) differential AS, (b) differential miRNA targeted AS, and (c) AS isoforms with novel functions. AS events identified from transcriptomic data were validated with proteomic data. Protein interaction networks identified two genes, SKIP and ALY4 whose products have both DNA- and RNA-binding affinities, as potential key regulators mediating jasmonate signaling and AS regulation. We observed cases where AS alone, or AS and transcriptional regulation together, can influence gene expression in response to MeJA. Twenty-one genes contain predicted miRNA target sites subjected to AS, which implies that AS is coupled to miRNA regulation. We identified 30 cases where alternatively spliced isoforms may have novel functions. For example, AS of bHLH160 generates an isoform without a basic domain, which may convert it from an activator to a repressor. Our study identified potential key regulators in AS regulation of jasmonate signaling pathway. These findings highlight the importance of AS regulation in the jasmonate signaling pathway, both alone and in collaboration with other regulators. SIGNIFICANCE STATEMENT By exploring alternative splicing, we demonstrate its regulation in the jasmonate signaling pathway alone or in collaboration with other posttranscriptional regulations such as nonsense and microRNA-mediated decay. A signal transduction network model for alternative splicing in jasmonate signaling pathway was generated, contributing to our understanding for this important, prevalent, but relatively unexplored regulatory mechanism in plants.
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Affiliation(s)
- Guanqiao Feng
- Plant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFLUSA
| | - Mi‐Jeong Yoo
- Department of BiologyUniversity of FloridaGainesvilleFLUSA
| | - Ruth Davenport
- Department of BiologyUniversity of FloridaGainesvilleFLUSA
| | | | - Jin Koh
- The Interdisciplinary Center for Biotechnology Research (ICBR)University of FloridaGainesvilleFLUSA
| | - Sixue Chen
- Plant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFLUSA
- Department of BiologyUniversity of FloridaGainesvilleFLUSA
- The Interdisciplinary Center for Biotechnology Research (ICBR)University of FloridaGainesvilleFLUSA
- The Genetics InstituteUniversity of FloridaGainesvilleFLUSA
| | - W. Brad Barbazuk
- Plant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFLUSA
- Department of BiologyUniversity of FloridaGainesvilleFLUSA
- The Interdisciplinary Center for Biotechnology Research (ICBR)University of FloridaGainesvilleFLUSA
- The Genetics InstituteUniversity of FloridaGainesvilleFLUSA
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Cui Z, Tong A, Huo Y, Yan Z, Yang W, Yang X, Wang XX. SKIP controls flowering time via the alternative splicing of SEF pre-mRNA in Arabidopsis. BMC Biol 2017; 15:80. [PMID: 28893254 PMCID: PMC5594616 DOI: 10.1186/s12915-017-0422-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 08/25/2017] [Indexed: 12/04/2022] Open
Abstract
Background Similar to other eukaryotes, splicing is emerging as an important process affecting development and stress tolerance in plants. Ski-interacting protein (SKIP), a splicing factor, is essential for circadian clock function and abiotic stress tolerance; however, the mechanisms whereby it regulates flowering time are unknown. Results In this study, we found that SKIP is required for the splicing of serratedleaves and early flowering (SEF) pre-messenger RNA (mRNA), which encodes a component of the ATP-dependent SWR1 chromatin remodeling complex (SWR1-C). Defects in the splicing of SEF pre-mRNA reduced H2A.Z enrichment at FLC, MAF4, and MAF5, suppressed the expression of these genes, and produced an early flowering phenotype in skip-1 plants. Conclusions Our findings indicate that SKIP regulates SWR1-C function via alternative splicing to control the floral transition in Arabidopsis thaliana. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0422-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhibo Cui
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Aizi Tong
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yiqiong Huo
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhiqiang Yan
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Weiqi Yang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xianli Yang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xiao-Xue Wang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China.
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Zhang Z, He Z, Xu S, Li X, Guo W, Yang Y, Zhong C, Zhou R, Shi S. Transcriptome analyses provide insights into the phylogeny and adaptive evolution of the mangrove fern genus Acrostichum. Sci Rep 2016; 6:35634. [PMID: 27782130 PMCID: PMC5080628 DOI: 10.1038/srep35634] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 10/03/2016] [Indexed: 12/26/2022] Open
Abstract
The mangrove fern genus Acrostichum grows in the extremely unstable marine intertidal zone under harsh conditions, such as high salt concentrations, tidal rhythms and long-term climate changes. To explore the phylogenetic relationships and molecular mechanisms underlying adaptations in this genus, we sequenced the transcriptomes of two species of Acrostichum, A. aureum and A. speciosum, as well as a species in the sister genus, Ceratopteris thalictroides. We obtained 47,517, 36,420 and 60,823 unigenes for the three ferns, of which 24.39-45.63% were annotated using public databases. The estimated divergence time revealed that Acrostichum adapted to the coastal region during the late Cretaceous, whereas the two mangrove ferns from the Indo West-Pacific (IWP) area diverged more recently. Two methods (the modified branch-site model and the Kh method) were used to identify several positively selected genes, which may contribute to differential adaptation of the two Acrostichum species to different light and salt conditions. Our study provides abundant transcriptome data and new insights into the evolution and adaptations of mangrove ferns in the inhospitable intertidal zone.
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Affiliation(s)
- Zhang Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Ziwen He
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Xinnian Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Wuxia Guo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yuchen Yang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Cairong Zhong
- Hainan Dongzhai Harbor National Nature Reserve, Haikou, 571129, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, 510275, China
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Li Y, Xia C, Feng J, Yang D, Wu F, Cao Y, Li L, Ma L. The SNW Domain of SKIP Is Required for Its Integration into the Spliceosome and Its Interaction with the Paf1 Complex in Arabidopsis. MOLECULAR PLANT 2016; 9:1040-50. [PMID: 27130079 DOI: 10.1016/j.molp.2016.04.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 04/03/2016] [Accepted: 04/18/2016] [Indexed: 05/07/2023]
Abstract
SKIP is a conserved protein from yeasts to plants and humans. In plant cells, SKIP is a bifunctional regulator that works in the nucleus as a splicing factor by integrating into the spliceosome and as a transcriptional activator by interacting with the Paf1 complex. In this study, we identified two nuclear localization signals in SKIP and confirmed that each is sufficient to target SKIP to the nucleus. The SNW domain of SKIP is required for both its function as a splicing factor by promoting integration into the spliceosome in response to stress, and its function as a transcriptional activator by controlling its interaction with the Paf1 complex to participate in flowering. Truncated proteins that included the SNW domain and the N- or C-terminus of SKIP were still able to carry out the functions of the full-length protein in gene splicing and transcriptional activation in Arabidopsis. In addition, we found that SKIP undergoes 26S proteasome-mediated degradation, and that the C-terminus of SKIP is required to maintain the stability of the protein in plant cells. Together, our findings demonstrate the structural domain organization of SKIP and reveal the core domains and motifs underlying SKIP function in plants.
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Affiliation(s)
- Yan Li
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050021, China; Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, Beijing 100048, China; College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Congcong Xia
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, Beijing 100048, China; College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Jinlin Feng
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, Beijing 100048, China; College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Dong Yang
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, Beijing 100048, China; College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Fangming Wu
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, Beijing 100048, China; College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Ying Cao
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, Beijing 100048, China; College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Legong Li
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, Beijing 100048, China; College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Ligeng Ma
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, Beijing 100048, China; College of Life Sciences, Capital Normal University, Beijing 100048, China.
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