Transcriptomic, proteomic, and phosphoproteomic analyses reveal dynamic signaling networks influencing long-grain rice development
The LGS1 (Large grain size 1) gene, also known as GS2/GL2/OsGRF4, is involved in regulating grain size and quality in rice, but the mechanism governing grain size has not been elucidated. We performed transcriptomic, proteomic, and phosphoproteomic analyses of young rice panicles in Samba (a wild-ty...
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| Format: | Article |
| Language: | English |
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KeAi Communications Co., Ltd.
2022-06-01
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| Series: | Crop Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2214514121002257 |
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| author | Fangyu Chen Yongsheng Wang Zesen Zhang Xiaolong Chen Jinpeng Huang Zhiming Chen Jingsheng Zheng Liangrong Jiang Yumin Huang Houcong Wang Rongyu Huang |
| author_facet | Fangyu Chen Yongsheng Wang Zesen Zhang Xiaolong Chen Jinpeng Huang Zhiming Chen Jingsheng Zheng Liangrong Jiang Yumin Huang Houcong Wang Rongyu Huang |
| author_sort | Fangyu Chen |
| collection | DOAJ |
| description | The LGS1 (Large grain size 1) gene, also known as GS2/GL2/OsGRF4, is involved in regulating grain size and quality in rice, but the mechanism governing grain size has not been elucidated. We performed transcriptomic, proteomic, and phosphoproteomic analyses of young rice panicles in Samba (a wild-type cultivar with extra-small grain) and NIL-LGS1 (a nearly isogenic line of LGS1 with large grain in the Samba genetic background) at three developmental stages (4–6) to identify internal dynamic functional networks determining grain size that are mediated by LGS1. Differentially expressed proteins formed seven highly functionally correlated clusters. The concordant regulation of multiple functional clusters may be key features of the development of grain length in rice. In stage 5, 16 and 24 phosphorylated proteins were significantly up-regulated and down-regulated, and dynamic phosphorylation events may play accessory roles in determining rice grain size by participating in protein–protein interaction networks. Transcriptomic analysis in stage 5 showed that differentially expressed alternative splicing events and dynamic gene regulatory networks based on 39 transcription factors and their highly correlated target genes might contribute to rice grain development. Integrative multilevel omics analysis suggested that the regulatory network at the transcriptional and posttranscriptional levels could be directly manifested at the translational level, and this analysis also suggested a regulatory mechanism, regulation of protein translation levels, in the biological process that extends from transcript to protein to the development of grain. Functional analysis suggested that biological processes including MAPK signaling, calcium signaling, cell proliferation, cell wall, energy metabolism, hormone pathway, and ubiquitin-proteasome pathway might be involved in LGS1-mediated regulation of grain length. Thus, LGS1-mediated regulation of grain size is affected by dynamic transcriptional, posttranscriptional, translational and posttranslational changes. |
| first_indexed | 2024-04-13T15:40:29Z |
| format | Article |
| id | doaj.art-0ab834b513744390bbec788823ab1b7d |
| institution | Directory Open Access Journal |
| issn | 2214-5141 |
| language | English |
| last_indexed | 2024-04-13T15:40:29Z |
| publishDate | 2022-06-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Crop Journal |
| spelling | doaj.art-0ab834b513744390bbec788823ab1b7d2022-12-22T02:41:10ZengKeAi Communications Co., Ltd.Crop Journal2214-51412022-06-01103716728Transcriptomic, proteomic, and phosphoproteomic analyses reveal dynamic signaling networks influencing long-grain rice developmentFangyu Chen0Yongsheng Wang1Zesen Zhang2Xiaolong Chen3Jinpeng Huang4Zhiming Chen5Jingsheng Zheng6Liangrong Jiang7Yumin Huang8Houcong Wang9Rongyu Huang10Key Laboratory of Ministry of Education for Genetic Improvement and Comprehensive Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, ChinaPostdoctoral Station of Biology, School of Life Sciences, Hebei University, Baoding 071000, Hebei, ChinaSchool of Life Sciences, Xiamen University, Xiamen 361102, Fujian, ChinaSchool of Life Sciences, Xiamen University, Xiamen 361102, Fujian, ChinaSchool of Life Sciences, Xiamen University, Xiamen 361102, Fujian, ChinaKey Laboratory of Ministry of Education for Genetic Improvement and Comprehensive Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, ChinaSchool of Life Sciences, Xiamen University, Xiamen 361102, Fujian, ChinaSchool of Life Sciences, Xiamen University, Xiamen 361102, Fujian, ChinaSchool of Life Sciences, Xiamen University, Xiamen 361102, Fujian, ChinaSchool of Life Sciences, Xiamen University, Xiamen 361102, Fujian, ChinaSchool of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China; Corresponding author.The LGS1 (Large grain size 1) gene, also known as GS2/GL2/OsGRF4, is involved in regulating grain size and quality in rice, but the mechanism governing grain size has not been elucidated. We performed transcriptomic, proteomic, and phosphoproteomic analyses of young rice panicles in Samba (a wild-type cultivar with extra-small grain) and NIL-LGS1 (a nearly isogenic line of LGS1 with large grain in the Samba genetic background) at three developmental stages (4–6) to identify internal dynamic functional networks determining grain size that are mediated by LGS1. Differentially expressed proteins formed seven highly functionally correlated clusters. The concordant regulation of multiple functional clusters may be key features of the development of grain length in rice. In stage 5, 16 and 24 phosphorylated proteins were significantly up-regulated and down-regulated, and dynamic phosphorylation events may play accessory roles in determining rice grain size by participating in protein–protein interaction networks. Transcriptomic analysis in stage 5 showed that differentially expressed alternative splicing events and dynamic gene regulatory networks based on 39 transcription factors and their highly correlated target genes might contribute to rice grain development. Integrative multilevel omics analysis suggested that the regulatory network at the transcriptional and posttranscriptional levels could be directly manifested at the translational level, and this analysis also suggested a regulatory mechanism, regulation of protein translation levels, in the biological process that extends from transcript to protein to the development of grain. Functional analysis suggested that biological processes including MAPK signaling, calcium signaling, cell proliferation, cell wall, energy metabolism, hormone pathway, and ubiquitin-proteasome pathway might be involved in LGS1-mediated regulation of grain length. Thus, LGS1-mediated regulation of grain size is affected by dynamic transcriptional, posttranscriptional, translational and posttranslational changes.http://www.sciencedirect.com/science/article/pii/S2214514121002257ProteomePhosphoproteomeTranscriptomeLGS1/GS2/GL2/OsGRF4Young panicleRice (Oryza sativa L.) |
| spellingShingle | Fangyu Chen Yongsheng Wang Zesen Zhang Xiaolong Chen Jinpeng Huang Zhiming Chen Jingsheng Zheng Liangrong Jiang Yumin Huang Houcong Wang Rongyu Huang Transcriptomic, proteomic, and phosphoproteomic analyses reveal dynamic signaling networks influencing long-grain rice development Crop Journal Proteome Phosphoproteome Transcriptome LGS1/GS2/GL2/OsGRF4 Young panicle Rice (Oryza sativa L.) |
| title | Transcriptomic, proteomic, and phosphoproteomic analyses reveal dynamic signaling networks influencing long-grain rice development |
| title_full | Transcriptomic, proteomic, and phosphoproteomic analyses reveal dynamic signaling networks influencing long-grain rice development |
| title_fullStr | Transcriptomic, proteomic, and phosphoproteomic analyses reveal dynamic signaling networks influencing long-grain rice development |
| title_full_unstemmed | Transcriptomic, proteomic, and phosphoproteomic analyses reveal dynamic signaling networks influencing long-grain rice development |
| title_short | Transcriptomic, proteomic, and phosphoproteomic analyses reveal dynamic signaling networks influencing long-grain rice development |
| title_sort | transcriptomic proteomic and phosphoproteomic analyses reveal dynamic signaling networks influencing long grain rice development |
| topic | Proteome Phosphoproteome Transcriptome LGS1/GS2/GL2/OsGRF4 Young panicle Rice (Oryza sativa L.) |
| url | http://www.sciencedirect.com/science/article/pii/S2214514121002257 |
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