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Wang Y, Jiang Y, Xu Y, Tan F. Effects of uptake pathways on the accumulation, translocation, and metabolism of OPEs in rice: An emphasis on foliar uptake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170562. [PMID: 38307293 DOI: 10.1016/j.scitotenv.2024.170562] [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: 12/19/2023] [Revised: 01/27/2024] [Accepted: 01/28/2024] [Indexed: 02/04/2024]
Abstract
The often-overlooked importance of foliar absorption on the plant uptake of organic pollutants was investigated by an exposure chamber test. Rice seedlings were exposed to organophosphate esters (OPEs) through 8 scenarios arranged from 3 major uptake pathways: root uptake via solution, foliar uptake via gas, and foliar uptake via particles, to identify the contributions of these 3 uptake pathways and their influences on the translocation and metabolism of OPEs in rice. The concentration of OPEs in rice tissues showed an "additive effect" with the increase of exposure pathways. OPEs in rice shoots mainly originated from foliar uptake through particle (29.6 %-63.5 %) and gaseous (28.5 %-49.4 %) absorptions rather than root uptake (7.86 %-24.2 %) under the exposure condition. In comparison with stomal absorption, wax layer penetration was the main pathway for most OPEs to enter into leaves, especially for those compounds with high octanol-air partition coefficients. Although the subcellular distributions of OPEs in the rice tissues of the foliar exposure were slightly different from those of the root exposure, hydrophobic OPEs were mainly stored in the cell wall with hydrophilic OPEs mainly in the cytosol. The translocation of OPEs from the exposed tissue to the unexposed tissue were significantly negatively correlated with their octanol-water partition coefficients, but their basipetal translocation were limited. The result suggested that the translocation of OPEs within rice is prioritized over their degradation. This study deepens our understanding of the processes behind OPE uptake by rice and highlights the importance of foliar uptake, especially for those via particle absorption.
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Affiliation(s)
- Yan Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Yingying Jiang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yue Xu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Feng Tan
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
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Zhou H, Deng XW, He H. Gene expression variations and allele-specific expression of two rice and their hybrid in caryopses at single-nucleus resolution. FRONTIERS IN PLANT SCIENCE 2023; 14:1171474. [PMID: 37287712 PMCID: PMC10242081 DOI: 10.3389/fpls.2023.1171474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/26/2023] [Indexed: 06/09/2023]
Abstract
Seeds are an indispensable part of the flowering plant life cycle and a critical determinant of agricultural production. Distinct differences in the anatomy and morphology of seeds separate monocots and dicots. Although some progress has been made with respect to understanding seed development in Arabidopsis, the transcriptomic features of monocotyledon seeds at the cellular level are much less understood. Since most important cereal crops, such as rice, maize, and wheat, are monocots, it is essential to study transcriptional differentiation and heterogeneity during seed development at a finer scale. Here, we present single-nucleus RNA sequencing (snRNA-seq) results of over three thousand nuclei from caryopses of the rice cultivars Nipponbare and 9311 and their intersubspecies F1 hybrid. A transcriptomics atlas that covers most of the cell types present during the early developmental stage of rice caryopses was successfully constructed. Additionally, novel specific marker genes were identified for each nuclear cluster in the rice caryopsis. Moreover, with a focus on rice endosperm, the differentiation trajectory of endosperm subclusters was reconstructed to reveal the developmental process. Allele-specific expression (ASE) profiling in endosperm revealed 345 genes with ASE (ASEGs). Further pairwise comparisons of the differentially expressed genes (DEGs) in each endosperm cluster among the three rice samples demonstrated transcriptional divergence. Our research reveals differentiation in rice caryopsis from the single-nucleus perspective and provides valuable resources to facilitate clarification of the molecular mechanism underlying caryopsis development in rice and other monocots.
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Affiliation(s)
- Han Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
- Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
- Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, China
| | - Hang He
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
- Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, China
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Badoni S, Parween S, Henry RJ, Sreenivasulu N. Systems seed biology to understand and manipulate rice grain quality and nutrition. Crit Rev Biotechnol 2022:1-18. [PMID: 35723584 DOI: 10.1080/07388551.2022.2058460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Rice is one of the most essential crops since it meets the calorific needs of 3 billion people around the world. Rice seed development initiates upon fertilization, leading to the establishment of two distinct filial tissues, the endosperm and embryo, which accumulate distinct seed storage products, such as starch, storage proteins, and lipids. A range of systems biology tools deployed in dissecting the spatiotemporal dynamics of transcriptome data, methylation, and small RNA based regulation operative during seed development, influencing the accumulation of storage products was reviewed. Studies of other model systems are also considered due to the limited information on the rice transcriptome. This review highlights key genes identified through a holistic view of systems biology targeted to modify biochemical composition and influence rice grain quality and nutritional value with the target of improving rice as a functional food.
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Affiliation(s)
- Saurabh Badoni
- Consumer-Driven Grain Quality and Nutrition Unit, International Rice Research Institute (IRRI), Manila, Philippines
| | - Sabiha Parween
- Consumer-Driven Grain Quality and Nutrition Unit, International Rice Research Institute (IRRI), Manila, Philippines
| | - Robert J Henry
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Nese Sreenivasulu
- Consumer-Driven Grain Quality and Nutrition Unit, International Rice Research Institute (IRRI), Manila, Philippines
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Sampaio M, Rocha M, Dias O. Exploring synergies between plant metabolic modelling and machine learning. Comput Struct Biotechnol J 2022; 20:1885-1900. [PMID: 35521559 PMCID: PMC9052043 DOI: 10.1016/j.csbj.2022.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 11/03/2022] Open
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Schaarschmidt S, Glaubitz U, Erban A, Kopka J, Zuther E. Differentiation of the High Night Temperature Response in Leaf Segments of Rice Cultivars with Contrasting Tolerance. Int J Mol Sci 2021; 22:ijms221910451. [PMID: 34638787 PMCID: PMC8508630 DOI: 10.3390/ijms221910451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/15/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022] Open
Abstract
High night temperatures (HNT) affect rice yield in the field and induce chlorosis symptoms in leaves in controlled chamber experiments. However, little is known about molecular changes in leaf segments under these conditions. Transcript and metabolite profiling were performed for leaf segments of six rice cultivars with different HNT sensitivity. The metabolite profile of the sheath revealed a lower metabolite abundance compared to segments of the leaf blade. Furthermore, pre-adaptation to stress under control conditions was detected in the sheath, whereas this segment was only slightly affected by HNT. No unique significant transcriptomic changes were observed in the leaf base, including the basal growth zone at HNT conditions. Instead, selected metabolites showed correlations with HNT sensitivity in the base. The middle part and the tip were most highly affected by HNT in sensitive cultivars on the transcriptomic level with higher expression of jasmonic acid signaling related genes, genes encoding enzymes involved in flavonoid metabolism and a gene encoding galactinol synthase. In addition, gene expression of expansins known to improve stress tolerance increased in tolerant and sensitive cultivars. The investigation of the different leaf segments indicated highly segment specific responses to HNT. Molecular key players for HNT sensitivity were identified.
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Zeng D, Cui J, Yin Y, Xiong Y, Liu M, Guan S, Cheng D, Sun Y, Lu W. Metabolomics Analysis in Different Development Stages on SP0 Generation of Rice Seeds After Spaceflight. FRONTIERS IN PLANT SCIENCE 2021; 12:700267. [PMID: 34276752 PMCID: PMC8278407 DOI: 10.3389/fpls.2021.700267] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 05/28/2021] [Indexed: 06/13/2023]
Abstract
Spaceflight is a special abiotic stress condition. In recent years, it has been confirmed that the spaceflight caused the stress response of rice seeds, and the protein level, transcription level, and methylation level will change during the planting process after returning to the ground. However, the changes at the metabolome level are not very clear. In this study, two kinds of rice seeds, Dongnong423 (DN3) and Dongnong416 (DN6), were carried on the ShiJian-10 retractable satellite (SJ-10) for 12.5 days in orbit, returned to the ground and planted in the field until the three-leaf (TLP) and tillering stage (TS). The results of antioxidant enzyme activity, soluble sugar, and electron leakage rate revealed that the spaceflight caused the stress response of rice. The TLP and TS of DN3 identified 110 and 57 different metabolites, respectively, while the TLP and TS of DN6 identified 104 and 74 different metabolites, respectively. These metabolites included amino acids, sugars, fatty acids, organic acids and secondary metabolites. We used qRT-PCR technology to explore the changes of enzyme genes in the tricarboxylic acid cycle (TCA) and amino acid metabolism pathway. Combined with the results of metabolomics, we determined that during the TLP, the TCA cycle rate of DN3 was inhibited and amino acid metabolism was activated, while the TCA cycle rate of DN6 was activated and amino acid metabolism was inhibited. In TS, the TCA cycle rate of DN3 was inhibited, and amino acid metabolism was not significantly changed, while the TCA cycle rate of DN6 was activated and amino acid metabolism was inhibited. These results suggested that the response mechanisms of the two different rice strains to spaceflight stress are different, and these differences may be reflected in energy consumption and compound biosynthesis of rice in different growth and development stages. This study provided new insights for further exploring the effects of spaceflight.
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Affiliation(s)
- Deyong Zeng
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin Institute of Technology, Harbin, China
| | - Jie Cui
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin Institute of Technology, Harbin, China
| | - YiShu Yin
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin Institute of Technology, Harbin, China
| | - Yi Xiong
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin Institute of Technology, Harbin, China
| | - Mengyao Liu
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin Institute of Technology, Harbin, China
| | - Shuanghong Guan
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin Institute of Technology, Harbin, China
| | - Dayou Cheng
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin Institute of Technology, Harbin, China
| | - Yeqing Sun
- Dalian Maritime University, Environmental Systems Biology Institute, Dalian, China
| | - Weihong Lu
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin Institute of Technology, Harbin, China
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Transcriptome integrated metabolic modeling of carbon assimilation underlying storage root development in cassava. Sci Rep 2021; 11:8758. [PMID: 33888810 PMCID: PMC8062692 DOI: 10.1038/s41598-021-88129-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 04/08/2021] [Indexed: 02/02/2023] Open
Abstract
The existing genome-scale metabolic model of carbon metabolism in cassava storage roots, rMeCBM, has proven particularly resourceful in exploring the metabolic basis for the phenotypic differences between high and low-yield cassava cultivars. However, experimental validation of predicted metabolic fluxes by carbon labeling is quite challenging. Here, we incorporated gene expression data of developing storage roots into the basic flux-balance model to minimize infeasible metabolic fluxes, denoted as rMeCBMx, thereby improving the plausibility of the simulation and predictive power. Three different conceptual algorithms, GIMME, E-Flux, and HPCOF were evaluated. The rMeCBMx-HPCOF model outperformed others in predicting carbon fluxes in the metabolism of storage roots and, in particular, was highly consistent with transcriptome of high-yield cultivars. The flux prediction was improved through the oxidative pentose phosphate pathway in cytosol, as has been reported in various studies on root metabolism, but hardly captured by simple FBA models. Moreover, the presence of fluxes through cytosolic glycolysis and alanine biosynthesis pathways were predicted with high consistency with gene expression levels. This study sheds light on the importance of prediction power in the modeling of complex plant metabolism. Integration of multi-omics data would further help mitigate the ill-posed problem of constraint-based modeling, allowing more realistic simulation.
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Chen J, Le XC, Zhu L. Metabolomics and transcriptomics reveal defense mechanism of rice (Oryza sativa) grains under stress of 2,2',4,4'-tetrabromodiphenyl ether. ENVIRONMENT INTERNATIONAL 2019; 133:105154. [PMID: 31521816 DOI: 10.1016/j.envint.2019.105154] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/03/2019] [Accepted: 09/03/2019] [Indexed: 06/10/2023]
Abstract
2,2',4,4'-Tetrabromodiphenyl ether (BDE-47), a predominant polybrominated diphenyl ether (PBDE), has received extensive attention for its potential environmental impact. An integrated study of metabolomics and transcriptomics was conducted on two rice (Oryza sativa) cultivars, Lianjing-7 (LJ-7) and Yongyou-9 (YY-9), which have been identified as tolerant and sensitive cultivars to BDE-47, respectively. The objective was to investigate the molecular mechanisms of their different ability to tolerate BDE-47. Both rice plants were cultivated to maturity in soils containing three concentrations of BDE-47 (10, 20, and 50 mg/kg). Metabolomic analyses of rice grains identified 65 metabolites in LJ-7 and 45 metabolites in YY-9, including amino acids, saccharides, organic acids, fatty acids, and secondary metabolites. In the tolerant cultivar LJ-7 exposed to 50 mg/kg BDE-47, concentrations of most of the metabolites increased significantly, with α-ketoglutaric acid increased by 20-fold and stigmastanol increased by 12-fold. In the sensitive cultivar YY-9, the concentrations of most metabolites increased after the plant was exposed to 1 and 10 mg/kg BDE-47 but decreased after the plant was exposed to 50 mg/kg BDE-47. Transcriptomic data demonstrated that regulation of gene expressions was affected most in LJ-7 exposed to 50 mg/kg BDE-47 (966 genes up-regulated and 620 genes down-regulated) and in YY-9 exposed to 10 mg/kg BDE-47 (85 genes up-regulated and 291 genes down-regulated), in good accordance with the observed metabolic alternation in the two cultivars. Analyses of metabolic pathways and KEGG enrichment revealed that many biological processes, including energy consumption and biosynthesis, were perturbed in the two rice cultivars by BDE-47. A majority of metabolites and genes involved in dominating pathways of energy consumption (e.g., tricarboxylic acid cycle) and the biosynthesis (e.g., metabolism of saccharides and amino acids) were enhanced in LJ-7 by BDE-47. In contrast, energy consumption was increased while biosynthetic processes were inhibited in YY-9 by BDE-47, which could lead to the sensitivity of YY-9 to BDE-47. The combined results suggest that the different defensive abilities of these two rice cultivars in response to BDE-47 could be attributed to their differences in energy-consumption strategy and biosynthesis of nutritional components in grains. This study provides a useful reference for rice cultivation in PBDE-polluted areas.
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Affiliation(s)
- Jie Chen
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - X Chris Le
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Lizhong Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China.
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