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Advances in Plant Metabolomics and Its Applications in Stress and Single-Cell Biology. Int J Mol Sci 2022; 23:ijms23136985. [PMID: 35805979 PMCID: PMC9266571 DOI: 10.3390/ijms23136985] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/19/2022] [Accepted: 06/19/2022] [Indexed: 02/04/2023] Open
Abstract
In the past two decades, the post-genomic era envisaged high-throughput technologies, resulting in more species with available genome sequences. In-depth multi-omics approaches have evolved to integrate cellular processes at various levels into a systems biology knowledge base. Metabolomics plays a crucial role in molecular networking to bridge the gaps between genotypes and phenotypes. However, the greater complexity of metabolites with diverse chemical and physical properties has limited the advances in plant metabolomics. For several years, applications of liquid/gas chromatography (LC/GC)-mass spectrometry (MS) and nuclear magnetic resonance (NMR) have been constantly developed. Recently, ion mobility spectrometry (IMS)-MS has shown utility in resolving isomeric and isobaric metabolites. Both MS and NMR combined metabolomics significantly increased the identification and quantification of metabolites in an untargeted and targeted manner. Thus, hyphenated metabolomics tools will narrow the gap between the number of metabolite features and the identified metabolites. Metabolites change in response to environmental conditions, including biotic and abiotic stress factors. The spatial distribution of metabolites across different organs, tissues, cells and cellular compartments is a trending research area in metabolomics. Herein, we review recent technological advancements in metabolomics and their applications in understanding plant stress biology and different levels of spatial organization. In addition, we discuss the opportunities and challenges in multiple stress interactions, multi-omics, and single-cell metabolomics.
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Lu D, Liu B, Ren M, Wu C, Ma J, Shen Y. Light Deficiency Inhibits Growth by Affecting Photosynthesis Efficiency as well as JA and Ethylene Signaling in Endangered Plant Magnolia sinostellata. PLANTS (BASEL, SWITZERLAND) 2021; 10:2261. [PMID: 34834626 PMCID: PMC8618083 DOI: 10.3390/plants10112261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/13/2021] [Accepted: 10/13/2021] [Indexed: 12/27/2022]
Abstract
The endangered plant Magnolia sinostellata largely grows in the understory of forest and suffers light deficiency stress. It is generally recognized that the interaction between plant development and growth environment is intricate; however, the underlying molecular regulatory pathways by which light deficiency induced growth inhibition remain obscure. To understand the physiological and molecular mechanisms of plant response to shading caused light deficiency, we performed photosynthesis efficiency analysis and comparative transcriptome analysis in M. sinostellata leaves, which were subjected to shading treatments of different durations. Most of the parameters relevant to the photosynthesis systems were altered as the result of light deficiency treatment, which was also confirmed by the transcriptome analysis. Gene Ontology and KEGG pathway enrichment analyses illustrated that most of differential expression genes (DEGs) were enriched in photosynthesis-related pathways. Light deficiency may have accelerated leaf abscission by impacting the photosynthesis efficiency and hormone signaling. Further, shading could repress the expression of stress responsive transcription factors and R-genes, which confer disease resistance. This study provides valuable insight into light deficiency-induced molecular regulatory pathways in M. sinostellata and offers a theoretical basis for conservation and cultivation improvements of Magnolia and other endangered woody plants.
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Affiliation(s)
- Danying Lu
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China; (D.L.); (M.R.); (C.W.)
- College of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Bin Liu
- Department of Plant Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, 08193 Bellaterra, Spain;
| | - Mingjie Ren
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China; (D.L.); (M.R.); (C.W.)
- College of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Chao Wu
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China; (D.L.); (M.R.); (C.W.)
- College of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Jingjing Ma
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China; (D.L.); (M.R.); (C.W.)
- College of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Yamei Shen
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China; (D.L.); (M.R.); (C.W.)
- College of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
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Cai D, Xu Y, Zhao F, Zhang Y, Duan H, Guo X. Improved salt tolerance of Chenopodium quinoa Willd. contributed by Pseudomonas sp. strain M30-35. PeerJ 2021; 9:e10702. [PMID: 33520465 PMCID: PMC7811290 DOI: 10.7717/peerj.10702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/14/2020] [Indexed: 11/20/2022] Open
Abstract
Background Plant-growth-promoting rhizobacteria (PGPR) can promote plant growth and enhance plant tolerance to salt stress. Pseudomonas sp. strain M30-35 might confer abiotic stress tolerance to its host plants. We evaluated the effects of M30-35 inoculation on the growth and metabolite accumulation of Chenopodium quinoa Willd. during salt stress growth conditions. Methods The effects of M30-35 on the growth of C. quinoa seedlings were tested under salt stress. Seedling growth parameters measured included chlorophyll content, root activity, levels of plant- phosphorus (P), and saponin content. Results M30-35 increased biomass production and root activity compared to non-inoculated plants fertilized with rhizobia and plants grown under severe salt stress conditions. The photosynthetic pigment content of chlorophyll a and b were higher in M30-35-inoculated C. quinoa seedlings under high salt stress conditions compared to non-inoculated seedlings. The stability of P content was also maintained. The content of saponin, an important secondary metabolite in C. quinoa, was increased by the inoculation of M30-35 under 300 mM NaCl conditions. Conclusion Inoculation of M30-35 rescues the growth diminution of C. quinoa seedlings under salt stress.
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Affiliation(s)
- Deyu Cai
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, China.,China-Malaysia National Joint Laboratory, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Ying Xu
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, China
| | - Fei Zhao
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Yan Zhang
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, China
| | - Huirong Duan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xiaonong Guo
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, China.,China-Malaysia National Joint Laboratory, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
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Guillamón JG, Prudencio ÁS, Yuste JE, Dicenta F, Sánchez-Pérez R. Ascorbic acid and prunasin, two candidate biomarkers for endodormancy release in almond flower buds identified by a nontargeted metabolomic study. HORTICULTURE RESEARCH 2020; 7:203. [PMID: 33328455 PMCID: PMC7705690 DOI: 10.1038/s41438-020-00427-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 10/16/2020] [Accepted: 10/20/2020] [Indexed: 05/13/2023]
Abstract
Temperate fruit trees belonging to Prunus species have the ability to suspend (induce dormancy) and resume growth periodically in response to environmental and seasonal conditions. Endodormancy release requires the long-term accumulation of chill. Upon accumulation of cultivar-specific chill requirements, plants enter the state of ecodormancy, which means the ability to grow has been restored, depending on the fulfilment of heat requirements. As many different metabolic pathways are implicated in endodormancy release, we have performed a metabolomic analysis, using the ultra-high-performance liquid chromatography-quadrupole time-of-flying (UPLC-QToF) technique. We assayed flower buds in different stages of endodormancy in four almond cultivars with different flowering times: the extra-early Desmayo Largueta, the late Antoñeta, the extra-late Penta, and the ultra-late Tardona. An orthogonal projection to latent-structure discriminant-analysis model was created to observe differences between endodormant and ecodormant flower buds. The metabolites showing the most significant variation were searched against the Metlin, HMDB, and KEGG libraries, which allowed us to identify 87 metabolites. These metabolites were subsequently assigned to specific pathways, such as abscisic acid biosynthesis, phenylpropanoid biosynthesis, and D-sorbitol metabolism, among others. The two metabolites that exhibited the most significant variations in all the cultivars studied with fold changes of up to 6.49 were ascorbic acid and prunasin. For the first time, these two metabolites have been proposed as potential biomarkers for endodormancy release in almond. Given the high synteny present between the Rosaceae species, these results could be extrapolated to other important crops like peach, plum, cherry, or apricot, among others.
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Affiliation(s)
- Jesús Guillamón Guillamón
- Department of Plant Breeding. CEBAS-CSIC, Campus Universitario de Espinardo, 30100, Espinardo, Spain
| | - Ángela Sánchez Prudencio
- Department of Plant Breeding. CEBAS-CSIC, Campus Universitario de Espinardo, 30100, Espinardo, Spain
| | - José Enrique Yuste
- Metabolomics Platform of CEBAS-CSIC, Campus Universitario de Espinardo, 30100, Espinardo, Spain
| | - Federico Dicenta
- Department of Plant Breeding. CEBAS-CSIC, Campus Universitario de Espinardo, 30100, Espinardo, Spain
| | - Raquel Sánchez-Pérez
- Department of Plant Breeding. CEBAS-CSIC, Campus Universitario de Espinardo, 30100, Espinardo, Spain.
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Zhang H, Wang R, Wang H, Liu B, Xu M, Guan Y, Yang Y, Qin L, Chen E, Li F, Huang R, Zhou Y. Heterogeneous root zone salinity mitigates salt injury to Sorghum bicolor (L.) Moench in a split-root system. PLoS One 2019; 14:e0227020. [PMID: 31887166 PMCID: PMC6936808 DOI: 10.1371/journal.pone.0227020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/10/2019] [Indexed: 01/24/2023] Open
Abstract
The heterogeneous distribution of soil salinity across the rhizosphere can moderate salt injury and improve sorghum growth. However, the essential molecular mechanisms used by sorghum to adapt to such environmental conditions remain uncharacterized. The present study evaluated physiological parameters such as the photosynthetic rate, antioxidative enzyme activities, leaf Na+ and K+ contents, and osmolyte contents and investigated gene expression patterns via RNA sequencing (RNA-seq) analysis under various conditions of nonuniformly distributed salt. Totals of 5691 and 2047 differentially expressed genes (DEGs) in the leaves and roots, respectively, were identified by RNA-seq under nonuniform (NaCl-free and 200 mmol·L-1 NaCl) and uniform (100 mmol·L-1 and 100 mmol·L-1 NaCl) salinity conditions. The expression of genes related to photosynthesis, Na+ compartmentalization, phytohormone metabolism, antioxidative enzymes, and transcription factors (TFs) was enhanced in leaves under nonuniform salinity stress compared with uniform salinity stress. Similarly, the expression of the majority of aquaporins and essential mineral transporters was upregulated in the NaCl-free root side in the nonuniform salinity treatment, whereas abscisic acid (ABA)-related and salt stress-responsive TF transcripts were more abundant in the high-saline root side in the nonuniform salinity treatment. In contrast, the expression of the DEGs identified in the nonuniform salinity treatment remained virtually unaffected and was even downregulated in the uniform salinity treatment. The transcriptome findings might be supportive of the increased photosynthetic rate, reduced Na+ levels, increased antioxidative capability in the leaves and, consequently, the growth recovery of sorghum under nonuniform salinity stress as well as the inhibited sorghum growth under uniform salinity conditions. The increased expression of salt resistance genes activated in response to the nonuniform salinity distribution implied that the cross-talk between the nonsaline and high-saline sides of the roots exposed to nonuniform salt stress is potentially regulated.
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Affiliation(s)
- Huawen Zhang
- Agronomy College, Shenyang Agricultural University, Shenyang, Liaoning, China
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Shandong Engineering Laboratory for Featured Crops, Jinan, Shandong, China
| | - Runfeng Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Shandong Engineering Laboratory for Featured Crops, Jinan, Shandong, China
| | - Hailian Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Shandong Engineering Laboratory for Featured Crops, Jinan, Shandong, China
| | - Bin Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Shandong Engineering Laboratory for Featured Crops, Jinan, Shandong, China
| | - Mengping Xu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Shandong Engineering Laboratory for Featured Crops, Jinan, Shandong, China
| | - Yan’an Guan
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Shandong Engineering Laboratory for Featured Crops, Jinan, Shandong, China
| | - Yanbing Yang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Shandong Engineering Laboratory for Featured Crops, Jinan, Shandong, China
| | - Ling Qin
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Shandong Engineering Laboratory for Featured Crops, Jinan, Shandong, China
| | - Erying Chen
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Shandong Engineering Laboratory for Featured Crops, Jinan, Shandong, China
| | - Feifei Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Shandong Engineering Laboratory for Featured Crops, Jinan, Shandong, China
| | - Ruidong Huang
- Agronomy College, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Yufei Zhou
- Agronomy College, Shenyang Agricultural University, Shenyang, Liaoning, China
- * E-mail:
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Hernández JA. Salinity Tolerance in Plants: Trends and Perspectives. Int J Mol Sci 2019; 20:ijms20102408. [PMID: 31096626 PMCID: PMC6567217 DOI: 10.3390/ijms20102408] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 05/14/2019] [Indexed: 12/30/2022] Open
Abstract
Salinity stress is one of the more prevailing abiotic stresses which results in significant losses in agricultural crop production, particularly in arid and semi-arid areas [...].
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Affiliation(s)
- Jose Antonio Hernández
- Group of Fruit Trees Biotechnology, Dept. Plant Breeding, CEBAS-CSIC, Campus Universitario de Espinardo, 25, 30100 Murcia, Spain.
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