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Wang Q, Shi J, Liu J, Zhang P, Li L, Xie H, Li H, Wang H, Liu C, Qin P. Integration of transcriptome and metabolome reveals the accumulation of related metabolites and gene regulation networks during quinoa seed development. PLANT MOLECULAR BIOLOGY 2024; 114:10. [PMID: 38319430 DOI: 10.1007/s11103-023-01402-z] [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: 07/12/2023] [Accepted: 11/15/2023] [Indexed: 02/07/2024]
Abstract
Quinoa seeds are gluten- and cholesterol-free, contain all amino acids required by the human body, have a high protein content, provide endocrine regulation, protein supplementation, and cardiovascular protection effects. However, metabolite accumulation and transcriptional regulatory networks in quinoa seed development are not well understood. Four key stages of seed development in Dianli-3260 and Dianli-557 were thus analyzed and 849 metabolites were identified, among which sugars, amino acids, and lipids were key for developmental processes, and their accumulation showed a gradual decrease. Transcriptome analysis identified 40,345 genes, of which 20,917 were differential between the M and F phases, including 8279 and 12,638 up- and down-regulated genes, respectively. Grain development processes were mainly enriched in galactose metabolism, pentose and glucuronate interconversions, the biosynthesis of amino acids, and carbon metabolism pathways, in which raffinose, phosphoenolpyruvate, series and other metabolites are significantly enriched, gene-LOC110689372, Gene-LOC110710556 and gene-LOC110714584 are significantly expressed, and these metabolites and genes play an important role in carbohydrate metabolism, lipid and Amino acid synthesis of quinoa. This study provides a theoretical basis to expand our understanding of the molecular and metabolic development of quinoa grains.
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Affiliation(s)
- Qianchao Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Jirong Shi
- Food Crop Research Institute, Zhaotong Academy of Agricultural Sciences, Zhaotong, 657000, China
| | - Junna Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Ping Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Li Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Heng Xie
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Hanxue Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Hongxin Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Chenghong Liu
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106, China
| | - Peng Qin
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China.
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Zhu M, Zang Y, Zhang X, Shang S, Xue S, Chen J, Tang X. Insights into the regulation of energy metabolism during the seed-to-seedling transition in marine angiosperm Zostera marina L.: Integrated metabolomic and transcriptomic analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1130292. [PMID: 36968358 PMCID: PMC10036900 DOI: 10.3389/fpls.2023.1130292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Seed development is a crucial phase in the life cycle of seed-propagated plants. As the only group of angiosperms that evolved from terrestrial plants to complete their life cycle submerged in marine environments, the mechanisms underlying seed development in seagrasses are still largely unknown. In the present study, we attempted to combine transcriptomic, metabolomic, and physiological data to comprehensively analyze the molecular mechanism that regulates energy metabolism in Zostera marina seeds at the four major developmental stages. Our results demonstrated that seed metabolism was reprogrammed with significant alteration of starch and sucrose metabolism, glycolysis, the tricarboxylic acid cycle (TCA cycle), and the pentose phosphate pathway during the transition from seed formation to seedling establishment. The interconversion of starch and sugar provided energy storage substances in mature seeds and further acted as energy sources to support seed germination and seedling growth. The glycolysis pathway was active during Z. marina germination and seedling establishment, which provided pyruvate for TCA cycle by decomposing soluble sugar. Notably, the biological processes of glycolysis were severely inhibited during Z. marina seed maturation may have a positive effect on seed germination, maintaining a low level of metabolic activity during seed maturation to preserve seed viability. Increased acetyl-CoA and ATP contents were accompanied with the higher TCA cycle activity during seed germination and seedling establishment, indicating that the accumulations of precursor and intermediates metabolite that can strengthen the TCA cycle and facilitate energy supply for Z. marina seed germination and seedling growth. The large amount of oxidatively generated sugar phosphate promotes fructose 1,6-bisphosphate synthesis to feed back to glycolysis during seed germination, indicating that the pentose phosphate pathway not only provides energy for germination, but also complements the glycolytic pathway. Collectively, our findings suggest these energy metabolism pathways cooperate with each other in the process of seed transformation from maturity to seedling establishment, transforming seed from storage tissue to highly active metabolic tissue to meet the energy requirement seed development. These findings provide insights into the roles of the energy metabolism pathway in the complete developmental process of Z. marina seeds from different perspectives, which could facilitate habitat restoration of Z. marina meadows via seeds.
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Affiliation(s)
- Meiling Zhu
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
| | - Yu Zang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, Shandong, China
| | - Xuelei Zhang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, Shandong, China
| | - Shuai Shang
- College of Biological and Environmental Engineering, Binzhou University, Binzhou, Shandong, China
| | - Song Xue
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
| | - Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
| | - Xuexi Tang
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
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3
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Zheng Z, Chen S, Wei P, Guo S, Yu G, Wu J. The proteomics and metabolomics studies of GZU001 on promoting the Merisis of maize (Zea mays L.) roots. BMC PLANT BIOLOGY 2023; 23:103. [PMID: 36803498 PMCID: PMC9942296 DOI: 10.1186/s12870-023-04130-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Plant growth regulators are chemicals that regulate plant growth and development, which can regulate hormonal balance and affect plant growth, thereby increasing crop yield and improving crop quality. Our studies have revealed a new compound, GZU001, which could be used as a plant growth regulator. This compound has been observed to affect root elongation in maize significantly. However, the exact mechanism of this phenomenon is still being investigated. RESULTS Metabolomics and proteomics were used in unison in this study to explore the response pathway and regulation mechanism of GZU001 in promoting maize root elongation. From the appearance, we can see that both roots and plants of maize treated with GZU001 are significantly improved. Maize root metabolism revealed 101 differentially abundant proteins and 79 differentially expressed metabolites. The current study identified altered proteins and metabolites associated with physiological and biochemical processes. GZU001 treatment has been demonstrated to promote primary metabolism, essential for carbohydrates, amino acids, energy, and secondary metabolism. The result suggests that the stimulation of primary metabolism is beneficial for the growth and development of maize and plays a significant role in sustaining metabolism and growth. CONCLUSIONS This study recorded the changes of related proteins and metabolites in maize roots after GZU001 treatment and provided evidence for this compound's action mode and mechanism in plants.
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Affiliation(s)
- Zhiguo Zheng
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education/Guizhou University, Huaxi District, Guiyang, 550025, People's Republic of China
| | - Shunhong Chen
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education/Guizhou University, Huaxi District, Guiyang, 550025, People's Republic of China
| | - Panpan Wei
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education/Guizhou University, Huaxi District, Guiyang, 550025, People's Republic of China
| | - Shengxin Guo
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education/Guizhou University, Huaxi District, Guiyang, 550025, People's Republic of China
| | - Gang Yu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education/Guizhou University, Huaxi District, Guiyang, 550025, People's Republic of China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guizhou Provincial Engineering Research Center for Natural Drugs, Guiyang, 550014, China
| | - Jian Wu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education/Guizhou University, Huaxi District, Guiyang, 550025, People's Republic of China.
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Singh DP, Bisen MS, Shukla R, Prabha R, Maurya S, Reddy YS, Singh PM, Rai N, Chaubey T, Chaturvedi KK, Srivastava S, Farooqi MS, Gupta VK, Sarma BK, Rai A, Behera TK. Metabolomics-Driven Mining of Metabolite Resources: Applications and Prospects for Improving Vegetable Crops. Int J Mol Sci 2022; 23:ijms232012062. [PMID: 36292920 PMCID: PMC9603451 DOI: 10.3390/ijms232012062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/13/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
Vegetable crops possess a prominent nutri-metabolite pool that not only contributes to the crop performance in the fields, but also offers nutritional security for humans. In the pursuit of identifying, quantifying and functionally characterizing the cellular metabolome pool, biomolecule separation technologies, data acquisition platforms, chemical libraries, bioinformatics tools, databases and visualization techniques have come to play significant role. High-throughput metabolomics unravels structurally diverse nutrition-rich metabolites and their entangled interactions in vegetable plants. It has helped to link identified phytometabolites with unique phenotypic traits, nutri-functional characters, defense mechanisms and crop productivity. In this study, we explore mining diverse metabolites, localizing cellular metabolic pathways, classifying functional biomolecules and establishing linkages between metabolic fluxes and genomic regulations, using comprehensive metabolomics deciphers of the plant’s performance in the environment. We discuss exemplary reports covering the implications of metabolomics, addressing metabolic changes in vegetable plants during crop domestication, stage-dependent growth, fruit development, nutri-metabolic capabilities, climatic impacts, plant-microbe-pest interactions and anthropogenic activities. Efforts leading to identify biomarker metabolites, candidate proteins and the genes responsible for plant health, defense mechanisms and nutri-rich crop produce are documented. With the insights on metabolite-QTL (mQTL) driven genetic architecture, molecular breeding in vegetable crops can be revolutionized for developing better nutritional capabilities, improved tolerance against diseases/pests and enhanced climate resilience in plants.
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Affiliation(s)
- Dhananjaya Pratap Singh
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
- Correspondence:
| | - Mansi Singh Bisen
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Renu Shukla
- Indian Council of Agricultural Research (ICAR), Krishi Bhawan, Dr. Rajendra Prasad Road, New Delhi 110001, India
| | - Ratna Prabha
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Sudarshan Maurya
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Yesaru S. Reddy
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Prabhakar Mohan Singh
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Nagendra Rai
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Tribhuwan Chaubey
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
| | - Krishna Kumar Chaturvedi
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Sudhir Srivastava
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Mohammad Samir Farooqi
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Centre, Scotland’s Rural College, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK
| | - Birinchi K. Sarma
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, Centre for Agricultural Bioinformatics, Library Avenue, Pusa, New Delhi 110012, India
| | - Tusar Kanti Behera
- ICAR-Indian Institute of Vegetable Research, Jakhini, Shahanshahpur, Varanasi 221305, India
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5
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Studies on Lotus Genomics and the Contribution to Its Breeding. Int J Mol Sci 2022; 23:ijms23137270. [PMID: 35806274 PMCID: PMC9266308 DOI: 10.3390/ijms23137270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 02/01/2023] Open
Abstract
Lotus (Nelumbo nucifera), under the Nelumbonaceae family, is one of the relict plants possessing important scientific research and economic values. Because of this, much attention has been paid to this species on both its biology and breeding among the scientific community. In the last decade, the genome of lotus has been sequenced, and several high-quality genome assemblies are available, which have significantly facilitated functional genomics studies in lotus. Meanwhile, re-sequencing of the natural and genetic populations along with different levels of omics studies have not only helped to classify the germplasm resources but also to identify the domestication of selected regions and genes controlling different horticultural traits. This review summarizes the latest progress of all these studies on lotus and discusses their potential application in lotus breeding.
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6
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Song H, Liu Y, Dong G, Zhang M, Wang Y, Xin J, Su Y, Sun H, Yang M. Genome-Wide Characterization and Comprehensive Analysis of NAC Transcription Factor Family in Nelumbo nucifera. Front Genet 2022; 13:901838. [PMID: 35754820 PMCID: PMC9214227 DOI: 10.3389/fgene.2022.901838] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/17/2022] [Indexed: 11/18/2022] Open
Abstract
NAC (NAM, ATAF, and CUC) is a ubiquitously expressed plant-specific transcription factor (TF) family which is involved in the regulation of various biological processes. However, a systematic characterization of NAC gene family is yet to be reported in lotus. Here, 82 NnNAC genes which included five predicted membrane-bound NAC proteins were identified in the lotus genome. Phylogenetic analysis revealed seven-subfamily clusters (I–VII) of NnNAC proteins, with homologous gene pairs displaying similar conserved motifs and gene structure characteristics. Transactivation assay of NnNAC proteins revealed an extensive transcriptional activation capacity which is mediated by the highly divergent C-terminal activation domain (AD). Expression analysis of NnNAC genes in lotus tissues showed high transcript levels in root, stamen, petal and seed coat. In addition, 30 and 29 differentially expressed NnNAC candidate genes putatively involved in lotus seed development and response to complete submergence stress, respectively, were identified. Overall, our study provides potentially useful candidate gene resources for future molecular breeding of lotus varieties with novel agronomic traits.
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Affiliation(s)
- Heyun Song
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yanling Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | | | - Minghua Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuxin Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jia Xin
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yanyan Su
- Amway (China) Botanical R&D Centre, Wuxi, China
| | - Heng Sun
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Mei Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
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7
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Sun H, Song H, Deng X, Liu J, Yang D, Zhang M, Wang Y, Xin J, Chen L, Liu Y, Yang M. Transcriptome-Wide Characterization of Alkaloids and Chlorophyll Biosynthesis in Lotus Plumule. FRONTIERS IN PLANT SCIENCE 2022; 13:885503. [PMID: 35677240 PMCID: PMC9168470 DOI: 10.3389/fpls.2022.885503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
Lotus plumule is a green tissue in the middle of seeds that predominantly accumulates bisbenzylisoquinoline alkaloids (bis-BIAs) and chlorophyll (Chl). However, the biosynthetic mechanisms of these two metabolites remain largely unknown in lotus. This study used physiological and RNA sequencing (RNA-Seq) approaches to characterize the development and molecular mechanisms of bis-BIAs and Chl biosynthesis in lotus plumule. Physiological analysis revealed that exponential plumule growth occurred between 9 and 15 days after pollination (DAP), which coincided with the onset of bis-BIAs biosynthesis and its subsequent rapid accumulation. Transcriptome analysis of lotus plumule identified a total of 8,725 differentially expressed genes (DEGs), representing ~27.7% of all transcripts in the lotus genome. Sixteen structural DEGs, potentially associated with bis-BIAs biosynthesis, were identified. Of these, 12 encoded O-methyltransferases (OMTs) are likely involved in the methylation and bis-BIAs diversity in lotus. In addition, functionally divergent paralogous and redundant homologous gene members of the BIAs biosynthesis pathway, as well as transcription factors co-expressed with bis-BIAs and Chl biosynthesis genes, were identified. Twenty-two genes encoding 16 conserved enzymes of the Chl biosynthesis pathway were identified, with the majority being significantly upregulated by Chl biosynthesis. Photosynthesis and Chl biosynthesis pathways were simultaneously activated during lotus plumule development. Moreover, our results showed that light-driven Pchlide reduction is essential for Chl biosynthesis in the lotus plumule. These results will be useful for enhancing our understanding of alkaloids and Chl biosynthesis in plants.
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Affiliation(s)
- Heng Sun
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Heyun Song
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xianbao Deng
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Juan Liu
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Dong Yang
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Minghua Zhang
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuxin Wang
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jia Xin
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lin Chen
- Center of Applied Biotechnology, Wuhan Institute of Bioengineering, Wuhan, China
| | - Yanling Liu
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Mei Yang
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
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8
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Sun J, Guo H, Liu M, Chen M, Zhu M, Liu D, Tao J. Histology and transcriptomic profiling reveal the dynamics of seed coat and endosperm formation in tree peony ( Paeonia ostii). HORTICULTURE RESEARCH 2022; 9:uhac106. [PMID: 35873729 PMCID: PMC9297151 DOI: 10.1093/hr/uhac106] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 04/23/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Jing Sun
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Haixia Guo
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Mi Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Ming Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Mengyuan Zhu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Datong Liu
- Key Laboratory of Wheat Biology and Genetic Improvement for the Low & Middle Yangtze Valley, Ministry of Agriculture/Lixiahe Agricultural Institute of Jiangsu Province, Yangzhou 225007, China
| | - Jun Tao
- Corresponding author. E-mail:
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9
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Raza A. Metabolomics: a systems biology approach for enhancing heat stress tolerance in plants. PLANT CELL REPORTS 2022; 41:741-763. [PMID: 33251564 DOI: 10.1007/s00299-020-02635-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/09/2020] [Indexed: 05/22/2023]
Abstract
Comprehensive metabolomic investigations provide a large set of stress-related metabolites and metabolic pathways, advancing crops under heat stress conditions. Metabolomics-assisted breeding, including mQTL and mGWAS boosted our understanding of improving numerous quantitative traits under heat stress. During the past decade, metabolomics has emerged as a fascinating scientific field that includes documentation, evaluation of metabolites, and chemical methods for cell monitoring programs in numerous plant species. A comprehensive metabolome profiling allowed the investigator to handle the comprehensive data groups of metabolites and the equivalent metabolic pathways in an extraordinary manner. Metabolomics, together with transcriptomics, plays an influential role in discovering connections between stress and genes/metabolite, phenotyping, and biomarkers documentation. Further, it helps to decode several metabolic systems connected with heat stress (HS) tolerance in plants. Heat stress is a critical environmental factor that is globally affecting the growth and productivity of plants. Thus, there is an urgent need to exploit modern breeding and biotechnological tools like metabolomics to develop cultivars with improved HS tolerance. Several studies have reported that amino acids, carbohydrates, nitrogen metabolisms, etc. and metabolites involved in the biosynthesis and catalyzing actions play a game-changing role in HS response and help plants to cope with the HS. The use of metabolomics-assisted breeding (MAB) allows a well-organized transmission of higher yield and HS tolerance at the metabolome level with specific properties. Progressive metabolomics systematic techniques have accelerated metabolic profiling. Nonetheless, continuous developments in bioinformatics, statistical tools, and databases are allowing us to produce ever-progressing, comprehensive insights into the biochemical configuration of plants and by what means this is inclined by genetic and environmental cues. Currently, assimilating metabolomics with post-genomic platforms has allowed a significant division of genetic-phenotypic connotation in several plant species. This review highlights the potential of a state-of-the-art plant metabolomics approach for the improvement of crops under HS. The development of plants with specific properties using integrated omics (metabolomics and transcriptomics) and MAB can provide new directions for future research to enhance HS tolerance in plants to achieve a goal of "zero hunger".
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Affiliation(s)
- Ali Raza
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China.
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10
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Zhang D, Liu T, Sheng J, Lv S, Ren L. TMT-Based Quantitative Proteomic Analysis Reveals the Physiological Regulatory Networks of Embryo Dehydration Protection in Lotus ( Nelumbo nucifera). FRONTIERS IN PLANT SCIENCE 2021; 12:792057. [PMID: 34975978 PMCID: PMC8718645 DOI: 10.3389/fpls.2021.792057] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/19/2021] [Indexed: 06/14/2023]
Abstract
Lotus is an aquatic plant that is sensitive to water loss, but its seeds are longevous after seed embryo dehydration and maturation. The great difference between the responses of vegetative organs and seeds to dehydration is related to the special protective mechanism in embryos. In this study, tandem mass tags (TMT)-labeled proteomics and parallel reaction monitoring (PRM) technologies were used to obtain novel insights into the physiological regulatory networks during lotus seed dehydration process. Totally, 60,266 secondary spectra and 32,093 unique peptides were detected. A total of 5,477 proteins and 815 differentially expressed proteins (DEPs) were identified based on TMT data. Of these, 582 DEPs were continuously downregulated and 228 proteins were significantly up-regulated during the whole dehydration process. Bioinformatics and protein-protein interaction network analyses indicated that carbohydrate metabolism (including glycolysis/gluconeogenesis, galactose, starch and sucrose metabolism, pentose phosphate pathway, and cell wall organization), protein processing in ER, DNA repair, and antioxidative events had positive responses to lotus embryo dehydration. On the contrary, energy metabolism (metabolic pathway, photosynthesis, pyruvate metabolism, fatty acid biosynthesis) and secondary metabolism (terpenoid backbone, steroid, flavonoid biosynthesis) gradually become static status during lotus embryo water loss and maturation. Furthermore, non-enzymatic antioxidants and pentose phosphate pathway play major roles in antioxidant protection during dehydration process in lotus embryo. Abscisic acid (ABA) signaling and the accumulation of oligosaccharides, late embryogenesis abundant proteins, and heat shock proteins may be the key factors to ensure the continuous dehydration and storage tolerance of lotus seed embryo. Stress physiology detection showed that H2O2 was the main reactive oxygen species (ROS) component inducing oxidative stress damage, and glutathione and vitamin E acted as the major antioxidant to maintain the REDOX balance of lotus embryo during the dehydration process. These results provide new insights to reveal the physiological regulatory networks of the protective mechanism of embryo dehydration in lotus.
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Affiliation(s)
- Di Zhang
- School of Design, Shanghai Jiao Tong University, Shanghai, China
| | - Tao Liu
- School of Design, Shanghai Jiao Tong University, Shanghai, China
| | - Jiangyuan Sheng
- School of Design, Shanghai Jiao Tong University, Shanghai, China
| | - Shan Lv
- School of Design, Shanghai Jiao Tong University, Shanghai, China
| | - Li Ren
- Institute for Agri-Food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
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11
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Zhang S, Ghatak A, Bazargani MM, Bajaj P, Varshney RK, Chaturvedi P, Jiang D, Weckwerth W. Spatial distribution of proteins and metabolites in developing wheat grain and their differential regulatory response during the grain filling process. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:669-687. [PMID: 34227164 PMCID: PMC9291999 DOI: 10.1111/tpj.15410] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/06/2021] [Accepted: 06/25/2021] [Indexed: 05/03/2023]
Abstract
Grain filling and grain development are essential biological processes in the plant's life cycle, eventually contributing to the final seed yield and quality in all cereal crops. Studies of how the different wheat (Triticum aestivum L.) grain components contribute to the overall development of the seed are very scarce. We performed a proteomics and metabolomics analysis in four different developing components of the wheat grain (seed coat, embryo, endosperm, and cavity fluid) to characterize molecular processes during early and late grain development. In-gel shotgun proteomics analysis at 12, 15, 20, and 26 days after anthesis (DAA) revealed 15 484 identified and quantified proteins, out of which 410 differentially expressed proteins were identified in the seed coat, 815 in the embryo, 372 in the endosperm, and 492 in the cavity fluid. The abundance of selected protein candidates revealed spatially and temporally resolved protein functions associated with development and grain filling. Multiple wheat protein isoforms involved in starch synthesis such as sucrose synthases, starch phosphorylase, granule-bound and soluble starch synthase, pyruvate phosphate dikinase, 14-3-3 proteins as well as sugar precursors undergo a major tissue-dependent change in abundance during wheat grain development suggesting an intimate interplay of starch biosynthesis control. Different isoforms of the protein disulfide isomerase family as well as glutamine levels, both involved in the glutenin macropolymer pattern, showed distinct spatial and temporal abundance, revealing their specific role as indicators of wheat gluten quality. Proteins binned into the functional category of cell growth/division and protein synthesis/degradation were more abundant in the early stages (12 and 15 DAA). At the metabolome level all tissues and especially the cavity fluid showed highly distinct metabolite profiles. The tissue-specific data are integrated with biochemical networks to generate a comprehensive map of molecular processes during grain filling and developmental processes.
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Affiliation(s)
- Shuang Zhang
- Department of Functional and Evolutionary EcologyMolecular Systems Biology Lab (MOSYS)University of ViennaAlthanstrasse 14ViennaA‐1090Austria
| | - Arindam Ghatak
- Department of Functional and Evolutionary EcologyMolecular Systems Biology Lab (MOSYS)University of ViennaAlthanstrasse 14ViennaA‐1090Austria
| | | | - Prasad Bajaj
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)Hyderabad502324India
| | - Rajeev K. Varshney
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)Hyderabad502324India
- State Agricultural Biotechnology CentreCentre for Crop and Food InnovationMurdoch UniversityMurdochWA6150Australia
| | - Palak Chaturvedi
- Department of Functional and Evolutionary EcologyMolecular Systems Biology Lab (MOSYS)University of ViennaAlthanstrasse 14ViennaA‐1090Austria
| | - Dong Jiang
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop EcophysiologyMinistry of Agriculture/Nanjing Agricultural UniversityNanjing210095China
| | - Wolfram Weckwerth
- Department of Functional and Evolutionary EcologyMolecular Systems Biology Lab (MOSYS)University of ViennaAlthanstrasse 14ViennaA‐1090Austria
- Vienna Metabolomics Center (VIME)University of ViennaAlthanstrasse 14ViennaA‐1090Austria
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12
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Comparative transcriptomic and physiological analyses of weedy rice and cultivated rice to identify vital differentially expressed genes and pathways regulating the ABA response. Sci Rep 2021; 11:12881. [PMID: 34145345 PMCID: PMC8213743 DOI: 10.1038/s41598-021-92504-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 06/03/2021] [Indexed: 01/15/2023] Open
Abstract
Weedy rice is a valuable germplasm resource characterized by its high tolerance to both abiotic and biotic stresses. Abscisic acid (ABA) serves as a regulatory signal in plant cells as part of their adaptive response to stress. However, a global understanding of the response of weedy rice to ABA remains to be elucidated. In the present study, the sensitivity to ABA of weedy rice (WR04-6) was compared with that of temperate japonica Shennong9816 (SN9816) in terms of seed germination and post-germination growth via the application of exogenous ABA and diniconazole, an inhibitor of ABA catabolism. Physiological analysis and a transcriptomic comparison allowed elucidation of the molecular and physiological mechanisms associated with continuous ABA and diniconazole treatment. WR04-6 was found to display higher ABA sensitivity than SN9816, resulting in the rapid promotion of antioxidant enzyme activity. Comparative transcriptomic analyses indicated that the number of differentially expressed genes (DEGs) in WR04-6 seedlings treated with 2 μM ABA or 10 μM diniconazole was greater than that in SN9816 seedlings. Genes involved in stress defense, hormone signal transduction, and glycolytic and citrate cycle pathways were highly expressed in WR04-6 in response to ABA and diniconazole. These findings provide new insight into key processes mediating the ABA response between weedy and cultivated rice.
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Matamoros V, Rendón-Mera AM, Piña B, Tadić Đ, Cañameras N, Carazo N, Bayona JM. Metabolomic and phenotypic implications of the application of fertilization products containing microcontaminants in lettuce (Lactuca sativa). Sci Rep 2021; 11:9701. [PMID: 33958645 PMCID: PMC8102503 DOI: 10.1038/s41598-021-89058-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 04/12/2021] [Indexed: 11/17/2022] Open
Abstract
Cultivation practice using organic amendments is plausible to ensure global food security. However, plant abiotic stress due to the presence of metals and organic microcontaminants (OMCs) in fertilization products cannot be overlooked. In this study, we monitored lettuce metabolism and phenotypic response following the application of either sewage sludge (SS), the organic fraction of municipal solid waste, swine manure (SM), chemical fertilizers (CF), or no amendment (C) in a greenhouse facility. The experimental set-up consisted of five treatments with five replicates (25 experimental units randomly distributed). All fertilizers were supplied at the equivalent agronomic total nitrogen dose, but the occurrence of trace metals and/or OMCs was greater in the SS and SM than the rest. Non-target metabolomic analysis (high-resolution mass spectrometry coupled with partial least squares regression) identified more than 300 plant metabolites (amino acids, organic acids, sugar alcohols, and sugars), 55 of which showed significant changes in their relative abundances depending on the type of amendment. Functional analysis indicated that the use of CF or SS increased the levels of metabolites involved in carbohydrate and nitrogen metabolism. Therefore, although SS and SM fertilizers had a greater presence of heavy metals and/or OMCs, our results indicate that they did not induce measurable adverse effects in the lettuce phenotype or metabolism. Metabolic changes between fertilizers (CF and SS vs. C and SM) were mainly due to nitrogen availability.
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Affiliation(s)
- Víctor Matamoros
- Department of Environmental Chemistry, Institute of Environmental, Assessment and Water Research (IDAEA), Spanish National Research Council (CSIC), c/Jordi Girona, 18-26, 08034, Barcelona, Spain.
| | - Alicia María Rendón-Mera
- Grupo GDCON, Facultad de Ingeniería, Sede de Investigación Universitaria (SIU), Universidad de Antioquia, Calle 70 # 52-21, Medellín, 050010, Colombia
| | - Benjamí Piña
- Department of Environmental Chemistry, Institute of Environmental, Assessment and Water Research (IDAEA), Spanish National Research Council (CSIC), c/Jordi Girona, 18-26, 08034, Barcelona, Spain
| | - Đorđe Tadić
- Department of Environmental Chemistry, Institute of Environmental, Assessment and Water Research (IDAEA), Spanish National Research Council (CSIC), c/Jordi Girona, 18-26, 08034, Barcelona, Spain
| | - Núria Cañameras
- Department of Agri-Food Engineering and Biotechnology (DEAB), Polytechnic University of Catalonia (UPC), Esteve Terrades 8, Building 4, Castelldefels, Spain
| | - Nuria Carazo
- Department of Agri-Food Engineering and Biotechnology (DEAB), Polytechnic University of Catalonia (UPC), Esteve Terrades 8, Building 4, Castelldefels, Spain
| | - J M Bayona
- Department of Environmental Chemistry, Institute of Environmental, Assessment and Water Research (IDAEA), Spanish National Research Council (CSIC), c/Jordi Girona, 18-26, 08034, Barcelona, Spain
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Metabolomics Analyses of Cotyledon and Plumule Showing the Potential Domestic Selection in Lotus Breeding. Molecules 2021; 26:molecules26040913. [PMID: 33572231 PMCID: PMC7915064 DOI: 10.3390/molecules26040913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/01/2021] [Accepted: 02/06/2021] [Indexed: 11/23/2022] Open
Abstract
Lotus (Nelumbo nucifera) seeds are widely consumed as functional food or herbal medicine, of which cotyledon (CL) is the main edible part, and lotus plumule (LP) is commonly utilized in traditional Chinese medicine. However, few studies have been conducted to investigate the chemical components of CL and LP in dry lotus seeds, not to mention the comparison between wild and domesticated varieties. In this study, a widely targeted metabolomics approach based on Ultra Performance Liquid Chromatography-electrospray ionization-Tandem mass spectrometry (UPLC-ESI-MS/MS) was utilized to analyze the metabolites in CL and LP of China Antique (“CA”, a wild variety) and Jianxuan-17 (“JX”, a popular cultivar). A total of 402 metabolites were identified, which included flavonoids (23.08% to 27.84%), amino acids and derivatives (14.18–16.57%), phenolic acids (11.49–12.63%), and lipids (9.14–10.95%). These metabolites were classified into ten clusters based on their organ or cultivar-specific characters. Most of these metabolites were more abundant in LP than in CL for both varieties, except for metabolites belonging to organic acids and lipids. The analysis of differentially accumulated metabolites (DAMs) demonstrated that more than 25% of metabolites detected in our study were DAMs in CL and LP comparing “JX” with “CA”, most of which were less abundant in “JX”, including 35 flavonoids in LP, 23 amino acids and derivatives in CL, 7 alkaloids in CL, and 10 nucleotides and derivatives in LP, whereas all of 11 differentially accumulated lipids in LP were more abundant in “JX”. Together with the fact that the seed yield of “JX” is much higher than that of “CA”, these results indicated that abundant metabolites, especially the functional secondary metabolites (mainly flavonoids and alkaloids), were lost during the process of breeding selection.
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Liu YL, Zheng HL. Physiological and Proteomic Analyses of Two Acanthus Species to Tidal Flooding Stress. Int J Mol Sci 2021; 22:ijms22031055. [PMID: 33494455 PMCID: PMC7865619 DOI: 10.3390/ijms22031055] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/16/2021] [Accepted: 01/18/2021] [Indexed: 12/16/2022] Open
Abstract
The mangrove plant Acanthus ilicifolius and its relative, Acanthus mollis, have been previously proved to possess diverse pharmacological effects. Therefore, evaluating the differentially expressed proteins of these species under tidal flooding stress is essential to fully exploit and benefit from their medicinal values. The roots of A. ilicifolius and A. mollis were exposed to 6 h of flooding stress per day for 10 days. The dry weight, hydrogen peroxide (H2O2) content, anatomical characteristics, carbon and energy levels, and two-dimensional electrophoresis coupled with MALDI-TOF/TOF MS technology were used to reveal the divergent flooding resistant strategies. A. ilicifolius performed better under tidal flooding stress, which was reflected in the integrity of the morphological structure, more efficient use of carbon and energy, and a higher percentage of up-regulated proteins associated with carbon and energy metabolism. A. mollis could not survive in flooding conditions for a long time, as revealed by disrupting cell structures of the roots, less efficient use of carbon and energy, and a higher percentage of down-regulated proteins associated with carbon and energy metabolism. Energy provision and flux balance played a role in the flooding tolerance of A. ilicifolius and A. mollis.
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The Establishment of an Efficient Callus Induction System for Lotus ( Nelumbo nucifera). PLANTS 2020; 9:plants9111436. [PMID: 33113801 PMCID: PMC7693671 DOI: 10.3390/plants9111436] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 11/16/2022]
Abstract
The lotus (Nelumbo nucifera) is one of the most popular aquatic plants in Asia, and has emerged as a novel model for studying flower and rhizome development, and primary and secondary metabolite accumulation. Here, we developed a highly efficient callus induction system for the lotus by optimizing a series of key factors that affect callus formation. The highest efficient callus production was induced on immature cotyledon and embryo explants grown on Murashige and Skoog (MS) basal medium containing an optimized combination of 3 mg/L 2,4-dichlorophenoxyacetic acid (2,4-D) and 0.5 mg/L 6-benzylaminopurine (6-BA). In addition, lotus callus induction was proven to be influenced by lotus genotypes, light conditions, the developmental stages of explants and the time of explant sampling. Collecting immature cotyledons from seeds of the genotype “Shilihe 1”, at 9 days post pollination, and to culture the explants in darkness, are proposed as the optimum conditions for lotus callus induction. Interestingly, highly efficient callus induction was also observed in explants of immature embryo derived aseptic seedlings; and a small amount of lotus benzylisoquinoline alkaloid (BIA) and obvious expression of BIA biosynthetic genes were detected in lotus callus.
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Sun H, Li J, Song H, Yang D, Deng X, Liu J, Wang Y, Ma J, Xiong Y, Liu Y, Yang M. Comprehensive analysis of AGPase genes uncovers their potential roles in starch biosynthesis in lotus seed. BMC PLANT BIOLOGY 2020; 20:457. [PMID: 33023477 PMCID: PMC7541243 DOI: 10.1186/s12870-020-02666-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/23/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Starch in the lotus seed contains a high proportion of amylose, which endows lotus seed a promising property in the development of hypoglycemic and low-glycemic index functional food. Currently, improving starch content is one of the major goals for seed-lotus breeding. ADP-glucose pyrophosphorylase (AGPase) plays an essential role in regulating starch biosynthesis in plants, but little is known about its characterization in lotus. RESULTS We describe the nutritional compositions of lotus seed among 30 varieties with starch as a major component. Comparative transcriptome analysis showed that AGPase genes were differentially expressed in two varieties (CA and JX) with significant different starch content. Seven putative AGPase genes were identified in the lotus genome (Nelumbo nucifera Gaertn.), which could be grouped into two subfamilies. Selective pressure analysis indicated that purifying selection acted as a vital force in the evolution of AGPase genes. Expression analysis revealed that lotus AGPase genes have varying expression patterns, with NnAGPL2a and NnAGPS1a as the most predominantly expressed, especially in seed and rhizome. NnAGPL2a and NnAGPS1a were co-expressed with a number of starch and sucrose metabolism pathway related genes, and their expressions were accompanied by increased AGPase activity and starch content in lotus seed. CONCLUSIONS Seven AGPase genes were characterized in lotus, with NnAGPL2a and NnAGPS1a, as the key genes involved in starch biosynthesis in lotus seed. These results considerably extend our understanding on lotus AGPase genes and provide theoretical basis for breeding new lotus varieties with high-starch content.
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Affiliation(s)
- Heng Sun
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Juanjuan Li
- Hubei Province Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000 Hubei China
| | - Heyun Song
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049 China
| | - Dong Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Xianbao Deng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Juan Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Yunmeng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049 China
| | - Junyu Ma
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049 China
| | - Yaqian Xiong
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049 China
| | - Yanling Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
| | - Mei Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074 China
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Yuan J, Sun N, Du H, Yin S, Kang H, Umair M, Liu C. Roles of metabolic regulation in developing Quercus variabilis acorns at contrasting geologically-derived phosphorus sites in subtropical China. BMC PLANT BIOLOGY 2020; 20:389. [PMID: 32842952 PMCID: PMC7449008 DOI: 10.1186/s12870-020-02605-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/16/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUND Phosphorus (P) -rich soils develop in phosphorite residing areas while P-deficient soils are ubiquitous in subtropical regions. Little has been reported that how metabolites participate in the seed development and the processes involved in their coping with contrasting-nutrient environments. RESULTS Here we quantified the metabolites of Quercus variabilis acorns in the early (July), middle (August), late (September) development stages, and determined element (C, H, O, N, P, K, Ca, Mg, S, Fe, Al, Mn, Na, Zn, and Cu) concentrations of acorns in the late stage, at geologically-derived contrasting-P sites in subtropical China. The primary metabolic pathways included sugar metabolism, the TCA cycle, and amino acid metabolism. Most metabolites (especially C- and N-containing metabolites) increased and then decreased from July to September. Acorns between the two sites were significantly discriminated at the three stages, respectively, by metabolites (predominantly sugars and organic acids). Concentrations of P, orthophosphoric acid and most sugars were higher; erythrose was lower in late-stage acorns at P-rich sites than those at P-deficient sites. No significant differences existed in the size and dry mass of individual acorns between oak populations at the two sites. CONCLUSIONS Oak acorns at the two sites formed distinct metabolic phenotypes related to their distinct geologically-derived soil conditions, and the late-stage acorns tended to increase P-use-efficiency in the material synthesis process at P-deficient sites, relative to those at P-rich sites.
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Affiliation(s)
- Jun Yuan
- School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Rd. 800, Shanghai, 200240, China
| | - Ningxiao Sun
- School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Rd. 800, Shanghai, 200240, China
| | - Hongmei Du
- School of Design, Shanghai Jiao Tong University, 800 Dongchuan RD, Shanghai, China
| | - Shan Yin
- School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Rd. 800, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan RD, Shanghai, China
- Shanghai Yangtze River Delta Eco-environmental Change and Management Observation and Research Station, Ministry of Education, P. R. China, 800 Dongchuan RD, Shanghai, China
- Key Laboratory of Urban Agriculture, Ministry of Agriculture, 800 Dongchuan RD., Shanghai, China
| | - Hongzhang Kang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Rd. 800, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan RD, Shanghai, China
- Shanghai Yangtze River Delta Eco-environmental Change and Management Observation and Research Station, Ministry of Education, P. R. China, 800 Dongchuan RD, Shanghai, China
- Key Laboratory of Urban Agriculture, Ministry of Agriculture, 800 Dongchuan RD., Shanghai, China
| | - Muhammad Umair
- School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Rd. 800, Shanghai, 200240, China
| | - Chunjiang Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Rd. 800, Shanghai, 200240, China.
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan RD, Shanghai, China.
- Shanghai Yangtze River Delta Eco-environmental Change and Management Observation and Research Station, Ministry of Education, P. R. China, 800 Dongchuan RD, Shanghai, China.
- Key Laboratory of Urban Agriculture, Ministry of Agriculture, 800 Dongchuan RD., Shanghai, China.
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Dong W, Ma X, Jiang H, Zhao C, Ma H. Physiological and transcriptome analysis of Poa pratensis var. anceps cv. Qinghai in response to cold stress. BMC PLANT BIOLOGY 2020; 20:362. [PMID: 32736517 PMCID: PMC7393922 DOI: 10.1186/s12870-020-02559-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/19/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Low temperature limits the growth and development and geographical distribution of plants. Poa pratensis is a cool-season turfgrass mainly grown in urban areas. However, low winter temperature or cold events in spring and autumn may cause P.pratensis mortality, affecting the appearance of lawns. P.pratensis var. anceps cv. Qinghai (PQ) is widely distributed in the Qinghai-Tibet Plateau above 3000 m. PQ has greater cold tolerance than the commercially cultivated P.pratensis varieties. However, existing studies on the response mechanism of PQ to low temperatures have mainly focused on physiological and biochemical perspectives, while changes in the PQ transcriptome during the response to cold stress have not been reported. RESULTS To investigate the molecular mechanism of the PQ cold response and identify genes to improve the low-temperature tolerance of P.pratensis, we analyzed and compared the transcriptomes of PQ and the cold-sensitive P.pratensis cv. 'Baron' (PB) under cold stress using RNA sequencing. We identified 5996 and 3285 differentially expressed genes (DEGs) between the treatment vs control comparison of PQ and PB, respectively, with 5612 DEGs specific to PQ. Based on the DEGs, important Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, such as "starch and sucrose metabolism", "protein processing in endoplasmic reticulum", "phenylalanine metabolism" and "glycolysis/gluconeogenesis" were significantly enriched in PQ, and "starch and sucrose metabolism", "phenylpropanoid biosynthesis", "galactose metabolism" and "glutathione metabolism" were significantly enriched in PB. In addition, the "glycolysis" and "citrate cycle (TCA cycle)" pathways were identified as involved in cold tolerance of P.pratensis. CONCLUSIONS As we know, this is the first study to explore the transcriptome of P.pratensis var. anceps cv. Qinghai. Our study not noly provides important insights into the molecular mechanisms of P.pratensis var. anceps cv. Qinghai responds to cold stress, but also systematically reveals the changes of key genes and products of glycolysis and TCA cycle in response to cold stress, which is conductive to the breeding of cold-tolerance P.pratensis genotype.
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Affiliation(s)
- Wenke Dong
- Key Laboratory of Grassland Ecosystem of Ministry of Education, College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xiang Ma
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Science and Veterinary Medicine, Xining, 810016, China
| | - Hanyu Jiang
- Department of Physic, Nanjing Normal University, Nanjing, 210097, China
| | - Chunxu Zhao
- Key Laboratory of Grassland Ecosystem of Ministry of Education, College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Huiling Ma
- Key Laboratory of Grassland Ecosystem of Ministry of Education, College of Grassland Science, Gansu Agricultural University, Lanzhou, 730070, China.
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Ouyang S, Zhou Q, Zeng H, Wang Y, Hu X. Natural Nanocolloids Mediate the Phytotoxicity of Graphene Oxide. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:4865-4875. [PMID: 32182041 DOI: 10.1021/acs.est.9b07460] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nanocolloids (Ncs) are ubiquitous in natural surface waters. However, the effects of Ncs on the fate and ecotoxicity of graphene oxide (GO, a popular engineered nanomaterial (ENM)) remain largely unknown. Ncs exhibit strong adsorption affinity (KL = 1.93 L/mg) and high adsorption capacity (176.2 mg/g) for GO. After Ncs hybridization, GO nanosheets became scrolls, and the aggregation rate of GO decreased. The influence of humic acid and Ncs on GO toxicity was compared. Humic acid mitigated the phytotoxicity of GO. However, GO and GO-Ncs were found to have an envelopment effect on algal cells, and both could enter algal cells. GO-Ncs induced higher reactive oxygen species (ROS) generation, stronger DNA damage and plasmolysis, and more obvious inhibition of photosynthesis compared to GO. Proteomic analysis revealed that photosystem I- and II-related proteins (e.g., E1ZQR2 and E1ZPG5) were regulated more significantly in the GO-Ncs groups than in the GO groups. A combined proteomic and metabolomic analysis showed that inhibition of carbohydrate, fatty acid, and amino acid metabolism contributed to ROS generation. Given the high concentrations and activity of Ncs, the above results highlight the need for reconsideration of the Ncs-mediated environmental behaviors and risks of ENMs and other pollutants.
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Affiliation(s)
- Shaohu Ouyang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Qixing Zhou
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Hui Zeng
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Yue Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Xiangang Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
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Li X, Ban Z, Yu F, Hao W, Hu X. Untargeted Metabolic Pathway Analysis as an Effective Strategy to Connect Various Nanoparticle Properties to Nanoparticle-Induced Ecotoxicity. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:3395-3406. [PMID: 32097552 DOI: 10.1021/acs.est.9b06096] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Elucidation of the relationships between nanoparticle properties and ecotoxicity is a fundamental issue for environmental applications and risk assessment of nanoparticles. However, effective strategies to connect the various properties of nanoparticles with their ecotoxicity remain largely unavailable. Herein, an untargeted metabolic pathway analysis was employed to investigate the environmental risk posed by 10 typical nanoparticles (AgNPs, CuNPs, FeNPs, ZnONPs, SiO2NPs, TiO2NPs, GO, GOQDs, SWCNTs, and C60) to rice (a staple food for half of the world's population). Downregulation of carbohydrate metabolism and upregulation of amino acid metabolism were the two dominant metabolic effects induced by all tested nanoparticles. Partial least-squares regression analysis indicated that a zerovalent metal and high specific surface area positively contributed to the downregulation of carbohydrate metabolism, indicating strong abiotic stress. In contrast, the carbon type, the presence of a spherical or sheet shape, and the absence of oxygen functional groups in the nanoparticles positively contributed to the upregulation of amino acid metabolism, indicating adaptation to abiotic stress. Moreover, network relationships among five properties of nanoparticles were established for these metabolic pathways. The results of the present study will aid in the understanding and prediction of environmental risks and in the design of environmentally friendly nanoparticles.
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Affiliation(s)
- Xiaokang Li
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, People's Republic of China
| | - Zhan Ban
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, People's Republic of China
| | - Fubo Yu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, People's Republic of China
| | - Weidan Hao
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, People's Republic of China
| | - Xiangang Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, People's Republic of China
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Genome-Wide DNA Methylation Profiling in the Lotus ( Nelumbo nucifera) Flower Showing its Contribution to the Stamen Petaloid. PLANTS 2019; 8:plants8050135. [PMID: 31137487 PMCID: PMC6572404 DOI: 10.3390/plants8050135] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 01/06/2023]
Abstract
DNA methylation is a vital epigenetic modification. Methylation has a significant effect on the gene expression influencing the regulation of different physiological processes. Current studies on DNA methylation have been conducted on model plants. Lotus (Nelumbo nucifera) is a basic eudicot exhibiting variations during development, especially in flower formation. DNA methylation profiling was conducted on different flower tissues of lotuses through whole genome bisulfite sequencing (WGBS) to investigate the effects of DNA methylation on its stamen petaloid. A map of methylated cytosines at the single base pair resolution for the lotus was constructed. When the stamen was compared with the stamen petaloid, the DNA methylation exhibited a global decrease. Genome-wide relationship analysis between DNA methylation and gene expression identified 31 different methylation region (DMR)-associated genes, which might play crucial roles in floral organ formation, especially in the stamen petaloid. One out of 31 DMR-associated genes, NNU_05638 was homolog with Plant U-box 33 (PUB33). The DNA methylation status of NNU_05638 promoter was distinct in three floral organs, which was confirmed by traditional bisulfite sequencing. These results provide further insights about the regulation of stamen petaloids at the epigenetic level in lotus.
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Jia XM, Zhu YF, Hu Y, Zhang R, Cheng L, Zhu ZL, Zhao T, Zhang X, Wang YX. Integrated physiologic, proteomic, and metabolomic analyses of Malus halliana adaptation to saline-alkali stress. HORTICULTURE RESEARCH 2019; 6:91. [PMID: 31645949 PMCID: PMC6804568 DOI: 10.1038/s41438-019-0172-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/15/2019] [Accepted: 06/04/2019] [Indexed: 05/19/2023]
Abstract
Saline-alkali stress is a severely adverse abiotic stress limiting plant growth. Malus halliana Koehne is an apple rootstock that is tolerant to saline-alkali stress. To understand the molecular mechanisms underlying the tolerance of M. halliana to saline-alkali stress, an integrated metabolomic and proteomic approach was used to analyze the plant pathways involved in the stress response of the plant and its regulatory mechanisms. A total of 179 differentially expressed proteins (DEPs) and 140 differentially expressed metabolites (DEMs) were identified. We found that two metabolite-related enzymes (PPD and PAO) were associated with senescence and involved in porphyrin and chlorophyll metabolism; six photosynthesis proteins (PSAH2, PSAK, PSBO2, PSBP1, and PSBQ2) were significantly upregulated, especially PSBO2, and could act as regulators of photosystem II (PSII) repair. Sucrose, acting as a signaling molecule, directly mediated the accumulation of D-phenylalanine, tryptophan, and alkaloid (vindoline and ecgonine) and the expression of proteins related to aspartate and glutamate (ASP3, ASN1, NIT4, and GLN1-1). These responses play a central role in maintaining osmotic balance and removing reactive oxygen species (ROS). In addition, sucrose signaling induced flavonoid biosynthesis by activating the expression of CYP75B1 to regulate the homeostasis of ROS and promoted auxin signaling by activating the expression of T31B5_170 to enhance the resistance of M. halliana to saline-alkali stress. The decrease in peroxidase superfamily protein (PER) and ALDH2C4 during lignin synthesis further triggered a plant saline-alkali response. Overall, this study provides an important starting point for improving saline-alkali tolerance in M. halliana via genetic engineering.
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Affiliation(s)
- Xu-mei Jia
- College of Horticulture, Gansu Agricultural University, 730070 Lanzhou, China
| | - Yan-fang Zhu
- College of Horticulture, Gansu Agricultural University, 730070 Lanzhou, China
| | - Ya Hu
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Science, 730000 Lanzhou, China
| | - Rui Zhang
- College of Horticulture, Gansu Agricultural University, 730070 Lanzhou, China
| | - Li Cheng
- College of Horticulture, Gansu Agricultural University, 730070 Lanzhou, China
| | - Zu-lei Zhu
- College of Horticulture, Gansu Agricultural University, 730070 Lanzhou, China
| | - Tong Zhao
- College of Horticulture, Gansu Agricultural University, 730070 Lanzhou, China
| | - Xiayi Zhang
- College of Horticulture, Gansu Agricultural University, 730070 Lanzhou, China
| | - Yan-xiu Wang
- College of Horticulture, Gansu Agricultural University, 730070 Lanzhou, China
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Hurtado C, Parastar H, Matamoros V, Piña B, Tauler R, Bayona JM. Linking the morphological and metabolomic response of Lactuca sativa L exposed to emerging contaminants using GC × GC-MS and chemometric tools. Sci Rep 2017; 7:6546. [PMID: 28747703 PMCID: PMC5529569 DOI: 10.1038/s41598-017-06773-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/16/2017] [Indexed: 02/05/2023] Open
Abstract
The occurrence of contaminants of emerging concern (CECs) in irrigation waters (up to low μg L-1) and irrigated crops (ng g-1 in dry weight) has been reported, but the linkage between plant morphological changes and plant metabolomic response has not yet been addressed. In this study, a non-targeted metabolomic analysis was performed on lettuce (Lactuca sativa L) exposed to 11 CECs (pharmaceuticals, personal care products, anticorrosive agents and surfactants) by irrigation. The plants were watered with different CEC concentrations (0-50 µg L-1) for 34 days under controlled conditions and then harvested, extracted, derivatised and analysed by comprehensive two-dimensional gas chromatography coupled to a time-of-flight mass spectrometer (GC × GC-TOFMS). The resulting raw data were analysed using multivariate curve resolution (MCR) and partial least squares (PLS) methods. The metabolic response indicates that exposure to CECs at environmentally relevant concentrations (0.05 µg L-1) can cause significant metabolic alterations in plants (carbohydrate metabolism, the citric acid cycle, pentose phosphate pathway and glutathione pathway) linked to changes in morphological parameters (leaf height, stem width) and chlorophyll content.
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Affiliation(s)
- Carlos Hurtado
- Department of Environmental Chemistry, IDAEA-CSIC, c/Jordi Girona, 18-26, E-08034, Barcelona, Spain
| | - Hadi Parastar
- Department of Chemistry, Sharif University of Technology, Tehran, Iran
| | - Víctor Matamoros
- Department of Environmental Chemistry, IDAEA-CSIC, c/Jordi Girona, 18-26, E-08034, Barcelona, Spain
| | - Benjamín Piña
- Department of Environmental Chemistry, IDAEA-CSIC, c/Jordi Girona, 18-26, E-08034, Barcelona, Spain
| | - Romà Tauler
- Department of Environmental Chemistry, IDAEA-CSIC, c/Jordi Girona, 18-26, E-08034, Barcelona, Spain
| | - Josep M Bayona
- Department of Environmental Chemistry, IDAEA-CSIC, c/Jordi Girona, 18-26, E-08034, Barcelona, Spain.
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A Quantitative Acetylomic Analysis of Early Seed Development in Rice (Oryza sativa L.). Int J Mol Sci 2017; 18:ijms18071376. [PMID: 28654018 PMCID: PMC5535869 DOI: 10.3390/ijms18071376] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 06/23/2017] [Accepted: 06/23/2017] [Indexed: 11/20/2022] Open
Abstract
PKA (protein lysine acetylation) is a critical post-translational modification that regulates various developmental processes, including seed development. However, the acetylation events and dynamics on a proteomic scale in this process remain largely unknown, especially in rice early seed development. We report the first quantitative acetylproteomic study focused on rice early seed development by employing a mass spectral-based (MS-based), label-free approach. A total of 1817 acetylsites on 1688 acetylpeptides from 972 acetylproteins were identified in pistils and seeds at three and seven days after pollination, including 268 acetyproteins differentially acetylated among the three stages. Motif-X analysis revealed that six significantly enriched motifs, such as (DxkK), (kH) and (kY) around the acetylsites of the identified rice seed acetylproteins. Differentially acetylated proteins among the three stages, including adenosine diphosphate (ADP) -glucose pyrophosphorylases (AGPs), PDIL1-1 (protein disulfide isomerase like 1-1), hexokinases, pyruvate dehydrogenase complex (PDC) and numerous other regulators that are extensively involved in the starch and sucrose metabolism, glycolysis/gluconeogenesis, tricarboxylic acid (TCA) cycle and photosynthesis pathways during early seed development. This study greatly expanded the rice acetylome dataset, and shed novel insight into the regulatory roles of PKA in rice early seed development.
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Ghatak A, Chaturvedi P, Weckwerth W. Cereal Crop Proteomics: Systemic Analysis of Crop Drought Stress Responses Towards Marker-Assisted Selection Breeding. FRONTIERS IN PLANT SCIENCE 2017; 8:757. [PMID: 28626463 PMCID: PMC5454074 DOI: 10.3389/fpls.2017.00757] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Sustainable crop production is the major challenge in the current global climate change scenario. Drought stress is one of the most critical abiotic factors which negatively impact crop productivity. In recent years, knowledge about molecular regulation has been generated to understand drought stress responses. For example, information obtained by transcriptome analysis has enhanced our knowledge and facilitated the identification of candidate genes which can be utilized for plant breeding. On the other hand, it becomes more and more evident that the translational and post-translational machinery plays a major role in stress adaptation, especially for immediate molecular processes during stress adaptation. Therefore, it is essential to measure protein levels and post-translational protein modifications to reveal information about stress inducible signal perception and transduction, translational activity and induced protein levels. This information cannot be revealed by genomic or transcriptomic analysis. Eventually, these processes will provide more direct insight into stress perception then genetic markers and might build a complementary basis for future marker-assisted selection of drought resistance. In this review, we survey the role of proteomic studies to illustrate their applications in crop stress adaptation analysis with respect to productivity. Cereal crops such as wheat, rice, maize, barley, sorghum and pearl millet are discussed in detail. We provide a comprehensive and comparative overview of all detected protein changes involved in drought stress in these crops and have summarized existing knowledge into a proposed scheme of drought response. Based on a recent proteome study of pearl millet under drought stress we compare our findings with wheat proteomes and another recent study which defined genetic marker in pearl millet.
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Affiliation(s)
- Arindam Ghatak
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
- Vienna Metabolomics Center, University of ViennaVienna, Austria
- *Correspondence: Wolfram Weckwerth
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Wang L, Sun X, Weiszmann J, Weckwerth W. System-Level and Granger Network Analysis of Integrated Proteomic and Metabolomic Dynamics Identifies Key Points of Grape Berry Development at the Interface of Primary and Secondary Metabolism. FRONTIERS IN PLANT SCIENCE 2017; 8:1066. [PMID: 28713396 PMCID: PMC5491621 DOI: 10.3389/fpls.2017.01066] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 06/02/2017] [Indexed: 05/19/2023]
Abstract
Grapevine is a fruit crop with worldwide economic importance. The grape berry undergoes complex biochemical changes from fruit set until ripening. This ripening process and production processes define the wine quality. Thus, a thorough understanding of berry ripening is crucial for the prediction of wine quality. For a systemic analysis of grape berry development we applied mass spectrometry based platforms to analyse the metabolome and proteome of Early Campbell at 12 stages covering major developmental phases. Primary metabolites involved in central carbon metabolism, such as sugars, organic acids and amino acids together with various bioactive secondary metabolites like flavonols, flavan-3-ols and anthocyanins were annotated and quantified. At the same time, the proteomic analysis revealed the protein dynamics of the developing grape berries. Multivariate statistical analysis of the integrated metabolomic and proteomic dataset revealed the growth trajectory and corresponding metabolites and proteins contributing most to the specific developmental process. K-means clustering analysis revealed 12 highly specific clusters of co-regulated metabolites and proteins. Granger causality network analysis allowed for the identification of time-shift correlations between metabolite-metabolite, protein- protein and protein-metabolite pairs which is especially interesting for the understanding of developmental processes. The integration of metabolite and protein dynamics with their corresponding biochemical pathways revealed an energy-linked metabolism before veraison with high abundances of amino acids and accumulation of organic acids, followed by protein and secondary metabolite synthesis. Anthocyanins were strongly accumulated after veraison whereas other flavonoids were in higher abundance at early developmental stages and decreased during the grape berry developmental processes. A comparison of the anthocyanin profile of Early Campbell to other cultivars revealed similarities to Concord grape and indicates the strong effect of genetic background on metabolic partitioning in primary and secondary metabolism.
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Affiliation(s)
- Lei Wang
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Xiaoliang Sun
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Jakob Weiszmann
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
- Vienna Metabolomics Center, University of ViennaVienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
- Vienna Metabolomics Center, University of ViennaVienna, Austria
- *Correspondence: Wolfram Weckwerth
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