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Qing D, Chen W, Huang S, Li J, Pan Y, Zhou W, Liang Q, Yuan J, Gan D, Chen L, Chen L, Huang J, Zhou Y, Dai G, Deng G. Editing of rice (Oryza sativa L.) OsMKK3 gene using CRISPR/Cas9 decreases grain length by modulating the expression of photosystem components. Proteomics 2023; 23:e2200538. [PMID: 37376803 DOI: 10.1002/pmic.202200538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023]
Abstract
Grain size is one of the most important agronomic traits for grain yield determination in rice. To better understand the proteins that are regulated by the grain size regulatory gene OsMKK3, this gene was knocked out using the CRISPR/Cas9 system, and tandem mass tag (TMT) labeling combined with liquid chromatograph-tandem mass spectrometry analysis was performed to study the regulation of proteins in the panicle. Quantitative proteomic screening revealed a total of 106 differentially expressed proteins (DEPs) via comparison of the OsMKK3 mutant line to the wild-type YexiangB, including 15 and 91 up-regulated and down-regulated DEPs, respectively. Pathway analysis revealed that DEPs were enriched in metabolic pathways, biosynthesis of secondary metabolites, phenylpropanoid biosynthesis, and photosynthesis. Strong interactions were detected among seven down-regulated proteins related to photosystem components in the protein-protein interaction network, and photosynthetic rate was decreased in mutant plants. The results of the liquid chromatography-parallel reaction monitoring/mass spectromery analysis and western blot analysis were consistent with the results of the proteomic analysis, and the results of the quantitative reverse transcription polymerase chain reaction analysis revealed that the expression levels of most candidate genes were consistent with protein levels. Overall, OsMKK3 controls grain size by regulating the protein content in cells. Our findings provide new candidate genes that will aid the study of grain size regulatory mechanisms associated with the mitogen-activated protein kinase (MAPK) signaling pathway.
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Affiliation(s)
- Dongjin Qing
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Weiwei Chen
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Suosheng Huang
- Guangxi Academy of Agricultural Sciences, Plant Protection Research Institute, Nanning, China
| | - Jingcheng Li
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Yinghua Pan
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Weiyong Zhou
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Qiongyue Liang
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Jinghua Yuan
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Dongmei Gan
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Li Chen
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Lei Chen
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Juan Huang
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Yan Zhou
- Key Laboratory of Chemistry and Engineering of Forest Products, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning, China
| | - Gaoxing Dai
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
| | - Guofu Deng
- Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Nanning, China
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Qing D, Zhou Y, Pan Y, Yang X, Li J, Zhou W, Liang H, Chen W, Chen L, Lu C, Dai G, Deng G. TMT-based quantitative proteomic analysis of indica rice cultivars reveals that novel components of the signaling pathways might play a role in grain length regulation. J Proteomics 2023; 270:104745. [PMID: 36220543 DOI: 10.1016/j.jprot.2022.104745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
Grain length is one of the most important rice grain appearance components. To better understand the protein regulated by grain length in indica rice, the tandem mass tag (TMT) labeling combined with LC-MS/MS analysis was used for quantitative identification of differentially regulated proteins by comparing six long-grain cultivars (MeiB, LongfengB, YexiangB, FengtianB, WantaiB, and DingxiangB) to the short-grain cultivar BoB, respectively. A total of 6622 proteins were detected for quantitative analysis by comparing protein content of six long-grain cultivars to the short-grain cultivar, and 715 proteins were significantly regulated, consisting of 336 uniquely over-accumulated proteins and 355 uniquely down-accumulated proteins. KEGG pathway analysis revealed that most of accumulated proteins are involved in metabolic pathways, biosynthesis of secondary metabolites and phenylpropanoid biosynthesis. Four down-accumulated proteins maybe involved in the signaling pathways for grain length regulation. LC-PRM/MS quantitative analysis was used to analyze 10 differentially expressed proteins. The results were almost consistent with the TMT quantitative analysis. qRT-PCR analysis results showed that the transcription level was not always parallel to the protein content. This study identified many novel grain length accumulated proteins through the quantitative proteomics approach, providing candidate genes for further study of grain size regulatory mechanisms. SIGNIFICANCE: Rice grain length is one of the most important characteristics influencing appearance and yield. Six long-grain cultivars (MeiB, LongfengB, YexiangB, FengtianB, WantaiB, and DingxiangB obtained in Guangxi province of China from the 2000s to 2020s) and one short-grain cultivar (BoB obtained in Guangxi province of China in 1980s) were used for comparative analyses. Totally, 715 differentially expressed proteins (DEPs) were identified using TMT-base proteomic analysis. The numbers of DEPs increased as the grain length increased. 4 DEPs may be related to rice's signaling pathways for grain size regulation. A total of 85 DEPs regulated in at least four long-grain cultivars compared with the short-grain cultivar BoB, and 7 proteins were over-accumulated, and 3 proteins were down-accumulated in six long-grain cultivars. These findings provide valuable information to better understand the mechanisms of protein regulation by grain length in rice.
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Affiliation(s)
- Dongjin Qing
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Yan Zhou
- School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China; Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Nanning 530006, China; Key Laboratory of Guangxi Colleges, Universities for Food Safety and Pharmaceutical Analytical Chemistry, Nanning 530006, China
| | - Yinghua Pan
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Xinghai Yang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Jingcheng Li
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Weiyong Zhou
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Haifu Liang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Weiwei Chen
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Lei Chen
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Chunju Lu
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China
| | - Gaoxing Dai
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China.
| | - Guofu Deng
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, China.
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