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Liu L, Chen Y, Wu W, Chen Q, Tian Z, Huang J, Ren H, Zhang J, Du X, Zhuang M, Wang P. A multilevel investigation to reveal the regulatory mechanism of lignin accumulation in juice sac granulation of pomelo. BMC PLANT BIOLOGY 2024; 24:390. [PMID: 38730367 PMCID: PMC11088010 DOI: 10.1186/s12870-024-05095-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/02/2024] [Indexed: 05/12/2024]
Abstract
Granulation of juice sacs is a physiological disorder, which affects pomelo fruit quality. Here, the transcriptome and ubiquitinome of the granulated juice sacs were analyzed in Guanxi pomelo. We found that lignin accumulation in the granulated juice sacs was regulated at transcription and protein modification levels. In transcriptome data, we found that the genes in lignin biosynthesis pathway and antioxidant enzyme system of the granulated juice sacs were significantly upregulated. However, in ubiquitinome data, we found that ubiquitinated antioxidant enzymes increased in abundance but the enzyme activities decreased after the modification, which gave rise to reactive oxygen species (ROS) contents in granulated juice sacs. This finding suggests that ubiquitination level of the antioxidant enzymes is negatively correlated with the enzyme activities. Increased H2O2 is considered to be a signaling molecule to activate the key gene expressions in lignin biosynthesis pathway, which leads to the lignification in granulated juice sacs of pomelo. This regulatory mechanism in juice sac granulation of pomelo was further confirmed through the verification experiment using tissue culture by adding H2O2 or dimethylthiourea (DMTU). Our findings suggest that scavenging H2O2 and other ROS are important for reducing lignin accumulation, alleviating juice sac granulation and improving pomelo fruit quality.
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Affiliation(s)
- Luning Liu
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yiran Chen
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weilin Wu
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qiuyou Chen
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhijiao Tian
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiakang Huang
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huaqing Ren
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiacheng Zhang
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xi Du
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mulai Zhuang
- Bureau of Agriculture and Rural Affairs of Pinghe County, Pinghe, China
| | - Ping Wang
- Insititute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China.
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Gao C, Peng X, Zhang L, Zhao Q, Ma L, Yu Q, Lian X, Gao L, Xiong L, Li S. Proteome and Ubiquitylome Analyses of Maize Endoplasmic Reticulum under Heat Stress. Genes (Basel) 2023; 14:genes14030749. [PMID: 36981020 PMCID: PMC10047965 DOI: 10.3390/genes14030749] [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: 02/07/2023] [Revised: 03/12/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
High temperatures severely affect plant growth and pose a threat to global crop production. Heat causes the accumulation of misfolded proteins in the endoplasmic reticulum(ER), as well as triggering the heat-shock response (HSR) in the cytosol and the unfolded protein response (UPR) in the ER. Excessive misfolded proteins undergo further degradation through ER-associated degradation (ERAD). Although much research on the plant heat stress response has been conducted, the regulation of ER-localized proteins has not been well-studied thus far. We isolated the microsome fraction from heat-treated and untreated maize seedlings and performed proteome and ubiquitylome analyses. Of the 8306 total proteins detected in the proteomics analysis, 1675 proteins were significantly up-regulated and 708 proteins were significantly down-regulated. Global ubiquitination analysis revealed 1780 proteins with at least one ubiquitination site. Motif analysis revealed that alanine and glycine are the preferred amino acids upstream and downstream of ubiquitinated lysine sites. ERAD components were found to be hyper-ubiquitinated after heat treatment, implying the feedback regulation of ERAD activity through protein degradation.
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Affiliation(s)
- Chunyan Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaohui Peng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Luoying Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qi Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Liguo Ma
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qi Yu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuechun Lian
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lei Gao
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Langyu Xiong
- Institute of Advanced Studies in Humanities and Social Sciences, Beijing Normal University, Zhuhai 519087, China
| | - Shengben Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
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Kausar R, Wang X, Komatsu S. Crop Proteomics under Abiotic Stress: From Data to Insights. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11212877. [PMID: 36365330 PMCID: PMC9657731 DOI: 10.3390/plants11212877] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/09/2022] [Accepted: 10/22/2022] [Indexed: 06/09/2023]
Abstract
Food security is a major challenge in the present world due to erratic weather and climatic changes. Environmental stress negatively affects plant growth and development which leads to reduced crop yields. Technological advancements have caused remarkable improvements in crop-breeding programs. Proteins have an indispensable role in developing stress resilience and tolerance in crops. Genomic and biotechnological advancements have made the process of crop improvement more accurate and targeted. Proteomic studies provide the information required for such targeted approaches. The crosstalk among cellular components is being analyzed by subcellular proteomics. Additionally, the functional diversity of proteins is being unraveled by post-translational modifications during abiotic stress. The exploration of precise cellular responses and the networking among different cellular organelles help in the prediction of signaling pathways and protein-protein interactions. High-throughput mass-spectrometry-based protein studies are now possible due to incremental advancements in mass-spectrometry techniques, sample protocols, and bioinformatic tools as well as the increasing availability of plant genome sequence information for multiple species. In this review, the key role of proteomic analysis in identifying the abiotic-stress-responsive mechanisms in various crops was summarized. The development and availability of advanced computational tools were discussed in detail. The highly variable protein responses among different crops have provided a wide avenue for molecular-marker-assisted genetic buildup studies to develop smart, high-yielding, and stress-tolerant varieties to cope with food-security challenges.
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Affiliation(s)
- Rehana Kausar
- Department of Botany, University of Azad Jammu and Kashmir, Muzaffarabad 13100, Pakistan
| | - Xin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
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Jiang C, Jiang T, Deng S, Yuan C, Liang Y, Li S, Ma C, Gao Y. Integrative analysis of transcriptome, proteome, and ubiquitome changes during rose petal abscission. FRONTIERS IN PLANT SCIENCE 2022; 13:1041141. [PMID: 36340335 PMCID: PMC9627506 DOI: 10.3389/fpls.2022.1041141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Plant organ abscission is regulated by multiple physiological and biochemical processes. However, the transcriptional, translational, and post-translational modifications occurring during organ abscission have not been systematically investigated. In this study, we report transcriptome, proteome, and ubiquitome data for the abscission zone (AZ) of rose petals collected during petal shedding. We quantified 40,506 genes, 6,595 proteins, and 2,720 ubiquitinated proteins in rose petal AZ. Our results showed that during petal abscission, 1,496 genes were upregulated and 2,199 were downregulated; 271 proteins were upregulated and 444 were downregulated; and 139 ubiquitination sites in 100 proteins were upregulated and 55 ubiquitination sites in 48 proteins were downregulated. Extracellular levels of cell component proteins were significantly increased, while levels within protoplasts were significantly decreased. During petal abscission, transcript levels of genes involved in defense response, transport, and metabolism changed significantly. Levels of proteins involved in the starch and sucrose metabolism and phenylpropanoid biosynthesis pathways were significantly altered at both the transcript and protein levels. The transcriptional and translational upregulation of peroxidase (POD), in the phenylpropanoid biosynthesis, pathway may be associated with deposition of lignin, which forms a protective layer during petal abscission. Overall, our data provide a comprehensive assessment of the translational and post-translational changes that occur during rose petal abscission.
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Affiliation(s)
- Chuyan Jiang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Tianhua Jiang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Shuning Deng
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Chaoli Yuan
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Yue Liang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Susu Li
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Chao Ma
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Yuerong Gao
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
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The molecular basis of cereal grain proteostasis. Essays Biochem 2022; 66:243-253. [PMID: 35818971 PMCID: PMC9400069 DOI: 10.1042/ebc20210041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/07/2022] [Accepted: 06/27/2022] [Indexed: 11/17/2022]
Abstract
Storage proteins deposited in the endosperm of cereal grains are both a nitrogen reserve for seed germination and seedling growth and a primary protein source for human nutrition. Detailed surveys of the patterns of storage protein accumulation in cereal grains during grain development have been undertaken, but an in-depth understanding of the molecular mechanisms that regulate these patterns is still lacking. Accumulation of storage proteins in cereal grains involves a series of subcellular compartments, a set of energy-dependent events that compete with other cellular processes, and a balance of protein synthesis and protein degradation rates at different times during the developmental process. In this review, we focus on the importance of rates in cereal grain storage protein accumulation during grain development and outline the potential implications and applications of this information to accelerate modern agriculture breeding programmes and optimize energy use efficiency in proteostasis.
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