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Gao Q, Zeng Z, Hao T, Zhang Z, Liang D, Xia C, Gao H, Liu L. Transcriptional and post-transcriptional regulation of chloroplast development by nuclear-localized XAP5 CIRCADIAN TIMEKEEPER. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 343:112081. [PMID: 38579979 DOI: 10.1016/j.plantsci.2024.112081] [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: 01/09/2024] [Revised: 03/08/2024] [Accepted: 04/01/2024] [Indexed: 04/07/2024]
Abstract
Chlorophyll biosynthesis and breakdown, important cellular processes for photosynthesis, occur in the chloroplast. As a semi-autonomous organelle, chloroplast development is mainly regulated by nuclear-encoded chloroplast proteins and proteins encoded by itself. However, the knowledge of chloroplast development regulated by other organelles is limited. Here, we report that the nuclear-localized XAP5 CIRCADIAN TIMEKEEPER (XCT) is essential for chloroplast development in Arabidopsis. In this study, significantly decreased chlorophyll content phenotypes of cotyledons and subsequently emerging organs from shoot apical meristem were observed in xct-2. XCT is constitutively expressed in various tissues and localized in the nuclear with speckle patterns. RNA-seq analysis identified 207 differently spliced genes and 1511 differently expressed genes, in which chloroplast development-, chlorophyll metabolism- and photosynthesis-related genes were enriched. Further biochemical assays suggested that XCT was co-purified with the well-known splicing factors and transcription machinery, suggesting dual functions of XCT in gene transcription and splicing. Interestingly, we also found that the chlorophyll contents in xct-2 significantly decreased under high temperature and high light condition, indicating XCT integrates temperature and light signals to fine-tune the chlorophyll metabolism in Arabidopsis. Therefore, our results provide new insights into chloroplast development regulation by XCT, a nuclear-localized protein, at the transcriptional and post-transcriptional level.
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Affiliation(s)
- Qian Gao
- Jiangsu Key Laboratory for Eco-agriculture Biotechnology around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huaian 223300, China
| | - Ziyang Zeng
- Jiangsu Key Laboratory for Eco-agriculture Biotechnology around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huaian 223300, China
| | - Tianqi Hao
- Jiangsu Key Laboratory for Eco-agriculture Biotechnology around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huaian 223300, China
| | - Ziru Zhang
- Jiangsu Key Laboratory for Eco-agriculture Biotechnology around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huaian 223300, China
| | - Daan Liang
- Jiangsu Key Laboratory for Eco-agriculture Biotechnology around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huaian 223300, China
| | - Congcong Xia
- Jiangsu Key Laboratory for Eco-agriculture Biotechnology around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huaian 223300, China
| | - Hui Gao
- College of Marine Resources and Environment, Hebei Normal University of Science and Technology, Qinhuangdao 066600, China.
| | - Lei Liu
- Jiangsu Key Laboratory for Eco-agriculture Biotechnology around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huaian 223300, China.
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Duan X, Zhang Y, Huang X, Ma X, Gao H, Wang Y, Xiao Z, Huang C, Wang Z, Li B, Yang W, Wang Y. GreenPhos, a universal method for in-depth measurement of plant phosphoproteomes with high quantitative reproducibility. MOLECULAR PLANT 2024; 17:199-213. [PMID: 38018035 DOI: 10.1016/j.molp.2023.11.010] [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: 07/28/2023] [Revised: 11/08/2023] [Accepted: 11/25/2023] [Indexed: 11/30/2023]
Abstract
Protein phosphorylation regulates a variety of important cellular and physiological processes in plants. In-depth profiling of plant phosphoproteomes has been more technically challenging than that of animal phosphoproteomes. This is largely due to the need to improve protein extraction efficiency from plant cells, which have a dense cell wall, and to minimize sample loss resulting from the stringent sample clean-up steps required for the removal of a large amount of biomolecules interfering with phosphopeptide purification and mass spectrometry analysis. To this end, we developed a method with a streamlined workflow for highly efficient purification of phosphopeptides from tissues of various green organisms including Arabidopsis, rice, tomato, and Chlamydomonas reinhardtii, enabling in-depth identification with high quantitative reproducibility of about 11 000 phosphosites, the greatest depth achieved so far with single liquid chromatography-mass spectrometry (LC-MS) runs operated in a data-dependent acquisition (DDA) mode. The mainstay features of the method are the minimal sample loss achieved through elimination of sample clean-up before protease digestion and of desalting before phosphopeptide enrichment and hence the dramatic increases of time- and cost-effectiveness. The method, named GreenPhos, combined with single-shot LC-MS, enabled in-depth quantitative identification of Arabidopsis phosphoproteins, including differentially phosphorylated spliceosomal proteins, at multiple time points during salt stress and a number of kinase substrate motifs. GreenPhos is expected to serve as a universal method for purification of plant phosphopeptides, which, if samples are further fractionated and analyzed by multiple LC-MS runs, could enable measurement of plant phosphoproteomes with an unprecedented depth using a given mass spectrometry technology.
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Affiliation(s)
- Xiaoxiao Duan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanya Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiao Ma
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Gao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Xiao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengcheng Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongshu Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bolong Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenqiang Yang
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Shen F, Hu C, Huang X, He H, Yang D, Zhao J, Yang X. Advances in alternative splicing identification: deep learning and pantranscriptome. FRONTIERS IN PLANT SCIENCE 2023; 14:1232466. [PMID: 37790793 PMCID: PMC10544900 DOI: 10.3389/fpls.2023.1232466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/28/2023] [Indexed: 10/05/2023]
Abstract
In plants, alternative splicing is a crucial mechanism for regulating gene expression at the post-transcriptional level, which leads to diverse proteins by generating multiple mature mRNA isoforms and diversify the gene regulation. Due to the complexity and variability of this process, accurate identification of splicing events is a vital step in studying alternative splicing. This article presents the application of alternative splicing algorithms with or without reference genomes in plants, as well as the integration of advanced deep learning techniques for improved detection accuracy. In addition, we also discuss alternative splicing studies in the pan-genomic background and the usefulness of integrated strategies for fully profiling alternative splicing.
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Affiliation(s)
- Fei Shen
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chenyang Hu
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Shanxi Key Lab of Chinese Jujube, College of Life Science, Yan’an University, Yan’an, Shanxi, China
| | - Xin Huang
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Hao He
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Deng Yang
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jirong Zhao
- Shanxi Key Lab of Chinese Jujube, College of Life Science, Yan’an University, Yan’an, Shanxi, China
| | - Xiaozeng Yang
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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Zheng J, Wen S, Yu Z, Luo K, Rong J, Ding M. Alternative Splicing during Fiber Development in G. hirsutum. Int J Mol Sci 2023; 24:11812. [PMID: 37511571 PMCID: PMC10380772 DOI: 10.3390/ijms241411812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/12/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Cotton is a valuable cash crop in many countries. Cotton fiber is a trichome that develops from a single epidermal cell and serves as an excellent model for understanding cell differentiation and other life processes. Alternative splicing (AS) of genes is a common post-transcriptional regulatory process in plants that is essential for plant growth and development. The process of AS during cotton fiber formation, on the other hand, is mainly unknown. A substantial number of multi-exon genes were discovered to be alternatively spliced during cotton fiber formation in this study, accounting for 23.31% of the total number of genes in Gossypium hirsutum. Retention intron (RI) is not necessarily the most common AS type, indicating that AS genes and processes during fiber development are very temporal and tissue-specific. When compared to fiber samples, AS is more prevalent at the fiber initiation stages and in the ovule, indicating that development stages and tissues use different AS strategies. Genes involved in fiber development have gone through stage-specific AS, demonstrating that AS regulates cotton fiber development. Furthermore, AS can be regulated by trans-regulation elements such as splicing factor and cis-regulation elements such as gene length, exon numbers, and GC content, particularly at exon-intron junction sites. Our findings also suggest that increased DNA methylation may aid in the efficiency of AS, and that gene body methylation is key in AS control. Finally, our research will provide useful information about the roles of AS during the cotton fiber development process.
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Affiliation(s)
- Jing Zheng
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China
| | - Shuhan Wen
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China
| | - Zhipeng Yu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China
| | - Keyan Luo
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China
| | - Junkang Rong
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China
| | - Mingquan Ding
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou 311300, China
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Liu L, Wu D, Gu Y, Liu F, Liu B, Mao F, Yi X, Tang T, Zhao X. Comprehensive profiling of alternative splicing landscape during secondary dormancy in oilseed rape ( Brassica napus L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:44. [PMID: 37313517 PMCID: PMC10248609 DOI: 10.1007/s11032-022-01314-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Alternative splicing is a general mechanism that regulates gene expression at the post-transcriptional level, which increases the transcriptomic diversity. Oilseed rape (Brassica napus L.), one of the main oil crops worldwide, is prone to secondary dormancy. However, how alternative splicing landscape of oilseed rape seed changes in response to secondary dormancy is unknown. Here, we analyzed twelve RNA-seq libraries from varieties "Huaiyou-SSD-V1" and "Huaiyou-WSD-H2" which exhibited high (> 95%) and low (< 5%) secondary dormancy potential, respectively, and demonstrated that alternative splicing changes led to a significant increase with the diversity of the transcripts in response to secondary dormancy induction via polyethylene glycol 6000 (PEG6000) treatment. Among the four basic alternative splicing types, intron retention dominates, and exon skipping shows the rarest frequency. A total of 8% of expressed genes had two or more transcripts after PEG treatment. Further analysis revealed that global isoform expression percentage variations in alternative splicing in differently expressed genes (DEGs) is more than three times as much as those in non-DEGs, suggesting alternative splicing change is associated with the transcriptional activity change in response to secondary dormancy induction. Eventually, 342 differently spliced genes (DSGs) associated with secondary dormancy were identified, five of which were validated by RT-PCR. The number of the overlapped genes between DSGs and DEGs associated with secondary dormancy was much less than that of either DSGs or DEGs, suggesting that DSGs and DEGs may independently regulates secondary dormancy. Functional annotation analysis of DSGs revealed that spliceosome components are overrepresented among the DSGs, including small nuclear ribonucleoprotein particles (snRNPs), serine/arginine-rich (SR) proteins, and other splicing factors. Thus, it is proposed that the spliceosome components could be exploited to reduce secondary dormancy potential in oilseed rape. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01314-8.
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Affiliation(s)
- Lei Liu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, 223300 China
| | - Depeng Wu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, 223300 China
| | - Yujuan Gu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
- College of Marine Resources and Environment, Hebei Normal University of Science and Technology, Qinghuangdao, Hebei 066600 China
| | - Fuxia Liu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, 223300 China
| | - Bin Liu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
| | - Feng Mao
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
| | - Xin Yi
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, 223300 China
| | - Tang Tang
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, 223300 China
| | - Xiangxiang Zhao
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai’an, 223300 China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, 223300 China
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Alternative Splicing and Its Roles in Plant Metabolism. Int J Mol Sci 2022; 23:ijms23137355. [PMID: 35806361 PMCID: PMC9266299 DOI: 10.3390/ijms23137355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 01/02/2023] Open
Abstract
Plant metabolism, including primary metabolism such as tricarboxylic acid cycle, glycolysis, shikimate and amino acid pathways as well as specialized metabolism such as biosynthesis of phenolics, alkaloids and saponins, contributes to plant survival, growth, development and interactions with the environment. To this end, these metabolic processes are tightly and finely regulated transcriptionally, post-transcriptionally, translationally and post-translationally in response to different growth and developmental stages as well as the constantly changing environment. In this review, we summarize and describe the current knowledge of the regulation of plant metabolism by alternative splicing, a post-transcriptional regulatory mechanism that generates multiple protein isoforms from a single gene by using alternative splice sites during splicing. Numerous genes in plant metabolism have been shown to be alternatively spliced under different developmental stages and stress conditions. In particular, alternative splicing serves as a regulatory mechanism to fine-tune plant metabolism by altering biochemical activities, interaction and subcellular localization of proteins encoded by splice isoforms of various genes.
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Liu L, Li X, Yuan L, Zhang G, Gao H, Xu X, Zhao H. XAP5 CIRCADIAN TIMEKEEPER specifically modulates 3' splice site recognition and is important for circadian clock regulation partly by alternative splicing of LHY and TIC. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 172:151-157. [PMID: 35065375 DOI: 10.1016/j.plaphy.2022.01.013] [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: 09/29/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 06/14/2023]
Abstract
Pre-mRNA splicing is an essential step during gene expression, which takes place in the spliceosome, a large dynamic ribonucleoprotein complex assembled in a stepwise manner. During the last decade, several spliceosomal mutants were functionally identified to cause a lengthened circadian period by introducing intron retention defects into circadian clock genes in Arabidopsis. However, the spliceosomal components that play opposite roles in the circadian period via alternative 3' splice site (Alt 3'ss) are largely unknown. Here, we demonstrated that XCT (XAP5 CIRCADIAN TIMEKEEPER) is a key spliceosomal component associated with multiple splicing factors. Moreover, genome-wide analysis revealed that inactivation of XCT particularly results in defects in Alt 3'ss recognition by RNA sequencing. Further analysis indicated that a strong alteration in the 3' splice sites of LHY and TIC partly accounts for the shortened circadian period of the xct mutant. Therefore, our results demonstrated that mutations in XCT shortened the circadian period partly by alternative splicing of LHY and TIC particularly in 3' splice site recognition, which provides new insight into the link between alternative splicing and the circadian clock.
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Affiliation(s)
- Lei Liu
- Jiangsu Key Laboratory for Eco-agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai'an, 223300, China.
| | - Xiaoyun Li
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Li Yuan
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Guofang Zhang
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Hui Gao
- College of Marine Resources and Environment, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, China
| | - Xiaodong Xu
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Hongtao Zhao
- College of Life Science, Hebei Normal University, Hebei, 050024, China.
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Liu L, Zhou Y, Mao F, Gu Y, Tang Z, Xin Y, Liu F, Tang T, Gao H, Zhao X. Fine-Tuning of the Grain Size by Alternative Splicing of GS3 in Rice. RICE (NEW YORK, N.Y.) 2022; 15:4. [PMID: 35015162 PMCID: PMC8752655 DOI: 10.1186/s12284-022-00549-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
Grain size is subtly regulated by multiple signaling pathways in rice. Alternative splicing is a general mechanism that regulates gene expression at the post-transcriptional level. However, to our knowledge, the molecular mechanism underlying grain size regulation by alternative splicing is largely unknown. GS3, the first identified QTL for grain size in rice, is regulated at the transcriptional and post-translational level. In this study, we identified that GS3 is subject to alternative splicing. GS3.1 and GS3.2, two dominant isoforms, accounts for about 50% and 40% of total transcripts, respectively. GS3.1 encodes the full-length protein, while GS3.2 generated a truncated proteins only containing OSR domain due to a 14 bp intronic sequence retention. Genetic analysis revealed that GS3.1 overexpressors decreased grain size, but GS3.2 showed no significant effect on grain size. Furthermore, we demonstrated that GS3.2 disrupts GS3.1 signaling by competitive occupation of RGB1. Therefore, we draw a conclusion that the alternative splicing of GS3 decreases the amount of GS3.1 and GS3.2 disrupts the GS3.1 signaling to inhibit the negative effects of GS3.1 to fine-tune grain size. Moreover, the mechanism is conserved in cereals rather than in Cruciferae, which is associated with its effects on grain size. The results provide a novel, conserved and important mechanism underlying grain size regulation at the post-transcriptional level in cereals.
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Affiliation(s)
- Lei Liu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai'an, 223300, China.
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai'an, 223300, China.
| | - Ying Zhou
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai'an, 223300, China
| | - Feng Mao
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai'an, 223300, China
| | - Yujuan Gu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai'an, 223300, China
- College of Marine Resources and Environment, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, China
| | - Ziwei Tang
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai'an, 223300, China
| | - Yi Xin
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai'an, 223300, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai'an, 223300, China
| | - Fuxia Liu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai'an, 223300, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai'an, 223300, China
| | - Tang Tang
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai'an, 223300, China
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai'an, 223300, China
| | - Hui Gao
- College of Marine Resources and Environment, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, China
| | - Xiangxiang Zhao
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Huaiyin Normal University, Huai'an, 223300, China.
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai'an, 223300, China.
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