Jasmonate induced alternative splicing responses in Arabidopsis
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...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2020-08-01
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| Series: | Plant Direct |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/pld3.245 |
| _version_ | 1819320038821199872 |
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| author | Guanqiao Feng Mi‐Jeong Yoo Ruth Davenport J. Lucas Boatwright Jin Koh Sixue Chen W. Brad Barbazuk |
| author_facet | Guanqiao Feng Mi‐Jeong Yoo Ruth Davenport J. Lucas Boatwright Jin Koh Sixue Chen W. Brad Barbazuk |
| author_sort | Guanqiao Feng |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-24T11:13:14Z |
| format | Article |
| id | doaj.art-512dd99b04ef494d9737873055c07a50 |
| institution | Directory Open Access Journal |
| issn | 2475-4455 |
| language | English |
| last_indexed | 2024-12-24T11:13:14Z |
| publishDate | 2020-08-01 |
| publisher | Wiley |
| record_format | Article |
| series | Plant Direct |
| spelling | doaj.art-512dd99b04ef494d9737873055c07a502022-12-21T16:58:27ZengWileyPlant Direct2475-44552020-08-0148n/an/a10.1002/pld3.245Jasmonate induced alternative splicing responses in ArabidopsisGuanqiao Feng0Mi‐Jeong Yoo1Ruth Davenport2J. Lucas Boatwright3Jin Koh4Sixue Chen5W. Brad Barbazuk6Plant Molecular and Cellular Biology Program University of Florida Gainesville FL USADepartment of Biology University of Florida Gainesville FL USADepartment of Biology University of Florida Gainesville FL USADepartment of Biology University of Florida Gainesville FL USAThe Interdisciplinary Center for Biotechnology Research (ICBR) University of Florida Gainesville FL USAPlant Molecular and Cellular Biology Program University of Florida Gainesville FL USAPlant Molecular and Cellular Biology Program University of Florida Gainesville FL USAAbstract 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.https://doi.org/10.1002/pld3.245alternative splicinggene networkjasmonate signalingmiRNAsplicing factortranscription factor |
| spellingShingle | Guanqiao Feng Mi‐Jeong Yoo Ruth Davenport J. Lucas Boatwright Jin Koh Sixue Chen W. Brad Barbazuk Jasmonate induced alternative splicing responses in Arabidopsis Plant Direct alternative splicing gene network jasmonate signaling miRNA splicing factor transcription factor |
| title | Jasmonate induced alternative splicing responses in Arabidopsis |
| title_full | Jasmonate induced alternative splicing responses in Arabidopsis |
| title_fullStr | Jasmonate induced alternative splicing responses in Arabidopsis |
| title_full_unstemmed | Jasmonate induced alternative splicing responses in Arabidopsis |
| title_short | Jasmonate induced alternative splicing responses in Arabidopsis |
| title_sort | jasmonate induced alternative splicing responses in arabidopsis |
| topic | alternative splicing gene network jasmonate signaling miRNA splicing factor transcription factor |
| url | https://doi.org/10.1002/pld3.245 |
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