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Rahmadi HY, Syukur M, Widodo, Suwarno WB, Wening S, Simamora AN, Nugroho S. 1H NMR analysis of metabolites from leaf tissue of resistant and susceptible oil palm breeding materials against Ganoderma boninense. Metabolomics 2024; 20:89. [PMID: 39095669 DOI: 10.1007/s11306-024-02160-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 07/23/2024] [Indexed: 08/04/2024]
Abstract
INTRODUCTION Breeding for oil palm resistance against basal stem rot caused by Ganoderma boninense is challenging and time-consuming. Advanced oil palm gene pools are very limited, hence it is assumed that parental palms have experienced genetic drift and lost their resistance genes against Ganoderma. High-throughput selection criteria should be developed. Metabolomic analysis using 1H nuclear magnetic resonance (NMR) spectroscopy is easy, and the resulting metabolite can be used as a diagnostic tool for detecting disease in various host-pathogen combinations. OBJECTIVES The objective of this study was to identify metabolite variations in Dura (D) and Pisifera (P) parental palms with different resistance levels against Ganoderma and moderately resistant DxP using 1H NMR analysis. METHODS Leaf tissues of seven different oil palm categories consisting of: resistant, moderate, and susceptible Dura (D); moderate and susceptible Pisifera (P); resistant Tenera/Pisifera (T/P) parental palms; and moderately resistant DxP variety progenies, were sampled and their metabolites were determined using NMR spectroscopy. RESULTS Twenty-nine types of metabolites were identified, and most of the metabolites fall in the monosaccharides, amino acids, and fatty acids compound classes. The PCA, PLS-DA, and heatmap multivariate analysis indicated two identified groups of resistance based on their metabolites. The first group consisted of resistant T/P, moderate P, resistant D, and moderately resistant DxP. In contrast, the second group consisted of susceptible P, moderate D, and susceptible D. Glycerol and ascorbic acid were detected as biomarker candidates by OPLS-DA to differentiate moderately resistant DxP from susceptible D and P. The pathway analysis suggested that glycine, serine, and threonine metabolism and taurine and hypotaurine metabolism were involved in the oil palm defense mechanism against Ganoderma. CONCLUSION A metabolomic study with 1H NMR was able to describe the metabolite composition that could differentiate the characteristics of oil palm resistance against basal stem rot (BSR) caused by G. boninense. These metabolites revealed in this study have enormous potential to become support tools for breeding new oil palm varieties with higher resistance against BSR.
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Affiliation(s)
- Hernawan Yuli Rahmadi
- Agronomy and Horticulture Department, IPB University, Jl. Raya Dramaga, Bogor, West Java, 16680, Indonesia.
- Plant Breeding Department, Indonesian Oil Palm Research Institute, Jl. Brigjend Katamso No.51, Medan, North Sumatera, 20158, Indonesia.
| | - Muhamad Syukur
- Agronomy and Horticulture Department, IPB University, Jl. Raya Dramaga, Bogor, West Java, 16680, Indonesia
| | - Widodo
- Plant Protection Department, IPB University, Jl. Raya Dramaga, Bogor, West Java, 16680, Indonesia
| | - Willy Bayuardi Suwarno
- Agronomy and Horticulture Department, IPB University, Jl. Raya Dramaga, Bogor, West Java, 16680, Indonesia
| | - Sri Wening
- Plant Breeding Department, Indonesian Oil Palm Research Institute, Jl. Brigjend Katamso No.51, Medan, North Sumatera, 20158, Indonesia
| | - Arfan Nazhri Simamora
- Plant Breeding Department, Indonesian Oil Palm Research Institute, Jl. Brigjend Katamso No.51, Medan, North Sumatera, 20158, Indonesia
| | - Syarul Nugroho
- Plant Breeding Department, Indonesian Oil Palm Research Institute, Jl. Brigjend Katamso No.51, Medan, North Sumatera, 20158, Indonesia
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Garg S, Nain P, Kumar A, Joshi S, Punetha H, Sharma PK, Siddiqui S, Alshaharni MO, Algopishi UB, Mittal A. Next generation plant biostimulants & genome sequencing strategies for sustainable agriculture development. Front Microbiol 2024; 15:1439561. [PMID: 39104588 PMCID: PMC11299335 DOI: 10.3389/fmicb.2024.1439561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 06/25/2024] [Indexed: 08/07/2024] Open
Abstract
The best environment for plant growth and development contains certain essential metabolites. A broad category of metabolites known as "plant biostimulants" (PBs) includes biomolecules such as proteins, carbohydrates, lipids, and other secondary metabolites related to groups of terpenes, specific nitrogen-containing compounds, and benzene ring-conjugated compounds. The formation of biomolecules depends on both biotic and abiotic factors, such as the release of PB by plants, animals, and microorganisms, or it can result from the control of temperature, humidity, and pressure in the atmosphere, in the case of humic substances (HSs). Understanding the genomic outputs of the concerned organism (may be plants or others than them) becomes crucial for identifying the underlying behaviors that lead to the synthesis of these complex compounds. For the purposes of achieving the objectives of sustainable agriculture, detailed research on PBs is essential because they aid in increasing yield and other growth patterns of agro-economic crops. The regulation of homeostasis in the plant-soil-microbe system for the survival of humans and other animals is mediated by the action of plant biostimulants, as considered essential for the growth of plants. The genomic size and gene operons for functional and regulation control have so far been revealed through technological implementations, but important gene annotations are still lacking, causing a delay in revealing the information. Next-generation sequencing techniques, such as nanopore, nanoball, and Illumina, are essential in troubleshooting the information gaps. These technical advancements have greatly expanded the candidate gene openings. The secondary metabolites being important precursors need to be studied in a much wider scale for accurate calculations of biochemical reactions, taking place inside and outside the synthesized living cell. The present review highlights the sequencing techniques to provide a foundation of opportunity generation for agricultural sustainability.
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Affiliation(s)
- Shivanshu Garg
- Department of Biochemistry, CBSH-GBPUA&T, Pantnagar, India
| | - Pooja Nain
- Department of Soil Science, College of Agriculture, GBPUA&T, Pantnagar, India
| | - Ashish Kumar
- Department of Microbiology, CBSH-GBPUA&T, Pantnagar, India
| | - Samiksha Joshi
- School of Agriculture, Graphic Era Hill University, Bhimtal, India
| | | | - Pradeep Kumar Sharma
- Department of Environment Science, Graphic Era Deemed to be University, Dehradun, India
| | - Sazada Siddiqui
- Department of Biology, College of Science, King Khalid University, Abha, Saudi Arabia
| | | | | | - Amit Mittal
- School of Allied Sciences, Graphic Era Hill University, Bhimtal, India
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Gentry-Torfer D, Murillo E, Barrington CL, Nie S, Leeming MG, Suwanchaikasem P, Williamson NA, Roessner U, Boughton BA, Kopka J, Martinez-Seidel F. Streamlining Protein Fractional Synthesis Rates Using SP3 Beads and Stable Isotope Mass Spectrometry: A Case Study on the Plant Ribosome. Bio Protoc 2024; 14:e4981. [PMID: 38737506 PMCID: PMC11082790 DOI: 10.21769/bioprotoc.4981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 05/14/2024] Open
Abstract
Ribosomes are an archetypal ribonucleoprotein assembly. Due to ribosomal evolution and function, r-proteins share specific physicochemical similarities, making the riboproteome particularly suited for tailored proteome profiling methods. Moreover, the structural proteome of ribonucleoprotein assemblies reflects context-dependent functional features. Thus, characterizing the state of riboproteomes provides insights to uncover the context-dependent functionality of r-protein rearrangements, as they relate to what has been termed the ribosomal code, a concept that parallels that of the histone code, in which chromatin rearrangements influence gene expression. Compared to high-resolution ribosomal structures, omics methods lag when it comes to offering customized solutions to close the knowledge gap between structure and function that currently exists in riboproteomes. Purifying the riboproteome and subsequent shot-gun proteomics typically involves protein denaturation and digestion with proteases. The results are relative abundances of r-proteins at the ribosome population level. We have previously shown that, to gain insight into the stoichiometry of individual proteins, it is necessary to measure by proteomics bound r-proteins and normalize their intensities by the sum of r-protein abundances per ribosomal complex, i.e., 40S or 60S subunits. These calculations ensure that individual r-protein stoichiometries represent the fraction of each family/paralog relative to the complex, effectively revealing which r-proteins become substoichiometric in specific physiological scenarios. Here, we present an optimized method to profile the riboproteome of any organism as well as the synthesis rates of r-proteins determined by stable isotope-assisted mass spectrometry. Our method purifies the r-proteins in a reversibly denatured state, which offers the possibility for combined top-down and bottom-up proteomics. Our method offers a milder native denaturation of the r-proteome via a chaotropic GuHCl solution as compared with previous studies that use irreversible denaturation under highly acidic conditions to dissociate rRNA and r-proteins. As such, our method is better suited to conserve post-translational modifications (PTMs). Subsequently, our method carefully considers the amino acid composition of r-proteins to select an appropriate protease for digestion. We avoid non-specific protease cleavage by increasing the pH of our standardized r-proteome dilutions that enter the digestion pipeline and by using a digestion buffer that ensures an optimal pH for a reliable protease digestion process. Finally, we provide the R package ProtSynthesis to study the fractional synthesis rates of r-proteins. The package uses physiological parameters as input to determine peptide or protein fractional synthesis rates. Once the physiological parameters are measured, our equations allow a fair comparison between treatments that alter the biological equilibrium state of the system under study. Our equations correct peptide enrichment using enrichments in soluble amino acids, growth rates, and total protein accumulation. As a means of validation, our pipeline fails to find "false" enrichments in non-labeled samples while also filtering out proteins with multiple unique peptides that have different enrichment values, which are rare in our datasets. These two aspects reflect the accuracy of our tool. Our method offers the possibility of elucidating individual r-protein family/paralog abundances, PTM status, fractional synthesis rates, and dynamic assembly into ribosomal complexes if top-down and bottom-up proteomic approaches are used concomitantly, taking one step further into mapping the native and dynamic status of the r-proteome onto high-resolution ribosome structures. In addition, our method can be used to study the proteomes of all macromolecular assemblies that can be purified, although purification is the limiting step, and the efficacy and accuracy of the proteases may be limited depending on the digestion requirements. Key features • Efficient purification of the ribosomal proteome: streamlined procedure for the specific purification of the ribosomal proteome or complex Ome. • Accurate calculation of fractional synthesis rates: robust method for calculating fractional protein synthesis rates in macromolecular complexes under different physiological steady states. • Holistic ribosome methodology focused on plants: comprehensive approach that provides insights into the ribosomes and translational control of plants, demonstrated using cold acclimation [1]. • Tailored strategies for stable isotope labeling in plants: methodology focusing on materials and labeling considerations specific to free and proteinogenic amino acid analysis [2].
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Affiliation(s)
- Dione Gentry-Torfer
- Applied Metabolome Analysis, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- School of Biosciences, The University of Melbourne, Parkville, Australia
| | - Ester Murillo
- Department of Biology, Healthcare and Environment, Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Chloe L. Barrington
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
| | - Shuai Nie
- Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, Australia
| | - Michael G. Leeming
- Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, Australia
- School of Chemistry, The University of Melbourne, Parkville, Australia
| | | | - Nicholas A. Williamson
- Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, Australia
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Australia
| | - Ute Roessner
- School of Biosciences, The University of Melbourne, Parkville, Australia
- Research School of Biology, The Australian National University, Acton, Australia
| | - Berin A. Boughton
- School of Biosciences, The University of Melbourne, Parkville, Australia
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Australia
| | - Joachim Kopka
- Applied Metabolome Analysis, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Federico Martinez-Seidel
- Applied Metabolome Analysis, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- School of Biosciences, The University of Melbourne, Parkville, Australia
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
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Soliman ERS. Preserving the adaptive salt stress response activity of a tissue-specific promoter with modulating activity. J Genet Eng Biotechnol 2024; 22:100354. [PMID: 38494266 PMCID: PMC10941203 DOI: 10.1016/j.jgeb.2024.100354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/17/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND The Arabidopsis "Redox Responsive Transcription Factor1" (RRTF1) promoter is transiently activated by salt stress in roots over 6 h period, followed by an adaptation phase during which its activity returns to baseline levels, even if the salt stress is prolonged. This enables the short-term production of genes that, while initially advantageous to the plant, will have long-term detrimental effects if expressed at high levels indefinitely. RESULTS In this paper, we demonstrate that the RRTF1 promoter salt adaption response is a dominant feature of the promoter, that cannot be overwritten by a strong enhancer. While maintaining the transient activation profile of the RRTF1 promoter, linking it to the 35S enhancer results in a significant boost of salt stress induction in roots. CONCLUSION The RRTF1 promoter's enhanced and still adaptable activity could become a useful tool in plant biotechnology.
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Affiliation(s)
- Elham R S Soliman
- Cytogenetics and Molecular Genetics Unit, Botany and Microbiology Department, Faculty of Science, Helwan University, Helwan, Egypt.
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Xie P, Chen J, Wu P, Cai Z. Spatial Lipidomics Reveals Lipid Changes in the Cotyledon and Plumule of Mung Bean Seeds during Germination. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19879-19887. [PMID: 38018797 PMCID: PMC10722537 DOI: 10.1021/acs.jafc.3c06029] [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: 08/27/2023] [Revised: 11/02/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023]
Abstract
Seed germination is a vital process in plant development involving dynamic biochemical transformations such as lipid metabolism. However, the spatial distribution and dynamic changes of lipids in different seed compartments during germination are poorly understood. In this study, we employed liquid chromatography/mass spectrometry (LC/MS)-based lipidomics and MALDI mass spectrometry imaging (MSI) to investigate lipid changes occurring in the cotyledon and plumule of mung bean seeds during germination. Lipidomic data revealed that the germination process reduced the levels of many glycerolipids (e.g., triglyceride) and phosphatidylglycerols (e.g., phosphatidylcholine) while increased the levels of lysophospholipids (e.g., lysophosphatidylcholine) in both the cotyledon and plumule. Sphingolipids (e.g., sphingomyelin) displayed altered levels solely in the plumule. Sterol levels increased in the cotyledon but decreased in the plumule. Further imaging results revealed that MALDI-MSI could serve as a supplement and validate LC-MS data. These findings enhance our understanding of the metabolic processes underlying seedling development, with potential implications for crop improvement and seed quality control.
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Affiliation(s)
- Peisi Xie
- Ministry
of Education Key Laboratory of Analytical Science for Food Safety
and Biology, Fujian Provincial Key Laboratory of Analysis and Detection
Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Jing Chen
- Ministry
of Education Key Laboratory of Analytical Science for Food Safety
and Biology, Fujian Provincial Key Laboratory of Analysis and Detection
Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Pengfei Wu
- State
Key Laboratory of Environmental and Biological Analysis, Department
of Chemistry, Hong Kong Baptist University, Hong Kong, Special Administrative
Region 999077, China
- College
of Forestry, Nanjing Forestry University, Nanjing, Jiangsu 210018, China
| | - Zongwei Cai
- Ministry
of Education Key Laboratory of Analytical Science for Food Safety
and Biology, Fujian Provincial Key Laboratory of Analysis and Detection
Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
- State
Key Laboratory of Environmental and Biological Analysis, Department
of Chemistry, Hong Kong Baptist University, Hong Kong, Special Administrative
Region 999077, China
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Chan WY, Rudd D, van Oppen MJ. Spatial metabolomics for symbiotic marine invertebrates. Life Sci Alliance 2023; 6:e202301900. [PMID: 37202120 PMCID: PMC10200813 DOI: 10.26508/lsa.202301900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/10/2023] [Accepted: 05/10/2023] [Indexed: 05/20/2023] Open
Abstract
Microbial symbionts frequently localize within specific body structures or cell types of their multicellular hosts. This spatiotemporal niche is critical to host health, nutrient exchange, and fitness. Measuring host-microbe metabolite exchange has conventionally relied on tissue homogenates, eliminating dimensionality and dampening analytical sensitivity. We have developed a mass spectrometry imaging workflow for a soft- and hard-bodied cnidarian animal capable of revealing the host and symbiont metabolome in situ, without the need for a priori isotopic labelling or skeleton decalcification. The mass spectrometry imaging method provides critical functional insights that cannot be gleaned from bulk tissue analyses or other presently available spatial methods. We show that cnidarian hosts may regulate microalgal symbiont acquisition and rejection through specific ceramides distributed throughout the tissue lining the gastrovascular cavity. The distribution pattern of betaine lipids showed that once resident, symbionts primarily reside in light-exposed tentacles to generate photosynthate. Spatial patterns of these metabolites also revealed that symbiont identity can drive host metabolism.
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Affiliation(s)
- Wing Yan Chan
- School of BioSciences, University of Melbourne, Parkville, Australia
- Australian Institute of Marine Science, Townsville, Australia
| | - David Rudd
- Monash Institute of Pharmaceutical Sciences, Parkville, Australia
- Melbourne Centre for Nanofabrication, Clayton, Australia
| | - Madeleine Jh van Oppen
- School of BioSciences, University of Melbourne, Parkville, Australia
- Australian Institute of Marine Science, Townsville, Australia
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Liu H, Micic N, Miller S, Crocoll C, Bjarnholt N. Species-specific dynamics of specialized metabolism in germinating sorghum grain revealed by temporal and tissue-resolved transcriptomics and metabolomics. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:807-820. [PMID: 36863218 DOI: 10.1016/j.plaphy.2023.02.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 06/19/2023]
Abstract
Seed germination is crucial for plant productivity, and the biochemical changes during germination affect seedling survival, plant health and yield. While the general metabolism of germination is extensively studied, the role of specialized metabolism is less investigated. We therefore analyzed the metabolism of the defense compound dhurrin during sorghum (Sorghum bicolor) grain germination and early seedling development. Dhurrin is a cyanogenic glucoside, which is catabolized into different bioactive compounds at other stages of plant development, but its fate and role during germination is unknown. We dissected sorghum grain into three different tissues and investigated dhurrin biosynthesis and catabolism at the transcriptomic, metabolomic and biochemical level. We further analyzed transcriptional signature differences of cyanogenic glucoside metabolism between sorghum and barley (Hordeum vulgare), which produces similar specialized metabolites. We found that dhurrin is de novo biosynthesized and catabolized in the growing embryonic axis as well as the scutellum and aleurone layer, two tissues otherwise mainly acknowledged for their involvement in release and transport of general metabolites from the endosperm to the embryonic axis. In contrast, genes encoding cyanogenic glucoside biosynthesis in barley are exclusively expressed in the embryonic axis. Glutathione transferase enzymes (GSTs) are involved in dhurrin catabolism and the tissue-resolved analysis of GST expression identified new pathway candidate genes and conserved GSTs as potentially important in cereal germination. Our study demonstrates a highly dynamic tissue- and species-specific specialized metabolism during cereal grain germination, highlighting the importance of tissue-resolved analyses and identification of specific roles of specialized metabolites in fundamental plant processes.
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Affiliation(s)
- Huijun Liu
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, 1871, Denmark; Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, 1871, Denmark.
| | - Nikola Micic
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, 1871, Denmark; Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, 1871, Denmark.
| | - Sara Miller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, 1871, Denmark; Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, 1871, Denmark.
| | - Christoph Crocoll
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, 1871, Denmark.
| | - Nanna Bjarnholt
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, 1871, Denmark; Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, 1871, Denmark.
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Bradshaw R. MALDI MS Imaging of Cucumbers. Methods Mol Biol 2023; 2688:63-69. [PMID: 37410284 DOI: 10.1007/978-1-0716-3319-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
There are many different methodologies in the literature for the preparation of plant material for subsequent MALDI MSI analysis. This chapter overviews preparation of cucumbers (Cucumis sativus L.), with emphasis on sample freezing, cryosectioning, and matrix deposition. This should act as a representative example of sample preparation for plant tissue, and due to wide sample variation (e.g., leaves, seeds, and fruit) and analytes of interest, method optimization will be required for different samples.
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Affiliation(s)
- Robert Bradshaw
- Biomolecular Sciences Research Centre (BMRC), Sheffield Hallam University, Sheffield, UK.
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Visualization of Glutamate Decarboxylase Activity in Barley Seeds under Salinity Stress Using Mass Microscope. Metabolites 2022; 12:metabo12121262. [PMID: 36557299 PMCID: PMC9786171 DOI: 10.3390/metabo12121262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
γ-Aminobutyric acid (GABA) accumulates in plants in response to environmental stresses. The activity levels of glutamate decarboxylase (GAD), an enzyme involved in GABA biosynthesis, are reported to increase during germination under salinity stress. However, it is not clear which tissues of the plant seeds are affected by GAD activity in response to salinity stress. In this study, the effects of salinity stress on the distribution of barley seeds GAD activity during germination were investigated. The mass spectrometry imaging (MSI) method was optimized, and the distribution of GAD activity in germinated seeds exposed to salinity stress at different germination stages from 12 to 48 h after imbibition was investigated. In this study, MSI was successfully applied to enzyme histochemistry to visualize the relative GAD activity in germinating barley seeds for the first time. The salinity stress increased the GAD activity, mostly due to the increase in relative GAD activity in the embryo. Higher GAD activity was detected in seeds exposed to salinity stress in the scutellum or aleurone layer, which are difficult to separate for extraction. This method can be used to clarify the role of GABA shunts, including GAD enzyme responses, in barley seeds under stress.
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Genome-Wide Association Study of Salt Tolerance-Related Traits during Germination and Seedling Development in an Intermedium-Spike Barley Collection. Int J Mol Sci 2022; 23:ijms231911060. [PMID: 36232362 PMCID: PMC9569600 DOI: 10.3390/ijms231911060] [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: 07/13/2022] [Revised: 09/07/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022] Open
Abstract
Increased salinity is one of the major consequences of climatic change affecting global crop production. The early stages in the barley (Hordeum vulgare L.) life cycle are considered the most critical phases due to their contributions to final crop yield. Particularly, the germination and seedling development are sensitive to numerous environmental stresses, especially soil salinity. In this study, we aimed to identify SNP markers linked with germination and seedling development at 150 mM NaCl as a salinity treatment. We performed a genome-wide association study (GWAS) using a panel of 208 intermedium-spike barley (H. vulgare convar. intermedium (Körn.) Mansf.) accessions and their genotype data (i.e., 10,323 SNPs) using the genome reference sequence of “Morex”. The phenotypic results showed that the 150 mM NaCl salinity treatment significantly reduced all recorded germination and seedling-related traits compared to the control treatment. Furthermore, six accessions (HOR 11747, HOR 11718, HOR 11640, HOR 11256, HOR 11275 and HOR 11291) were identified as the most salinity tolerant from the intermedium-spike barley collection. GWAS analysis indicated that a total of 38 highly significantly associated SNP markers under control and/or salinity traits were identified. Of these, two SNP markers on chromosome (chr) 1H, two on chr 3H, and one on chr 4H were significantly linked to seedling fresh and dry weight under salinity stress treatment. In addition, two SNP markers on chr 7H were also significantly associated with seedling fresh and dry weight but under control condition. Under salinity stress, one SNP marker on chr 1H, 5H and 7H were detected for more than one phenotypic trait. We found that in most of the accessions exhibiting the highest salinity tolerance, most of the salinity-related QTLs were presented. These results form the basis for detailed studies, leading to improved salt tolerance breeding programs in barley.
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Gupta SVK, Smith PMC, Natera SHA, Roessner U. Biochemical Changes in Two Barley Genotypes Inoculated With a Beneficial Fungus Trichoderma harzianum Rifai T-22 Grown in Saline Soil. FRONTIERS IN PLANT SCIENCE 2022; 13:908853. [PMID: 35982702 PMCID: PMC9379338 DOI: 10.3389/fpls.2022.908853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
One of the most important environmental factors impacting crop plant productivity is soil salinity. Fungal endophytes have been characterised as biocontrol agents that help in plant productivity and induce resistance responses to several abiotic stresses, including salinity. In the salt-tolerant cereal crop barley (Hordeum vulgare L.), there is limited information about the metabolites and lipids that change in response to inoculation with fungal endophytes in saline conditions. In this study, gas chromatography coupled to mass spectrometry (GC-MS) and LC-electrospray ionisation (ESI)-quadrupole-quadrupole time of flight (QqTOF)-MS were used to determine the metabolite and lipid changes in two fungal inoculated barley genotypes with differing tolerance levels to saline conditions. The more salt-tolerant cultivar was Vlamingh and less salt tolerant was Gairdner. Trichoderma harzianum strain T-22 was used to treat these plants grown in soil under control and saline (200 mM NaCl) conditions. For both genotypes, fungus-colonised plants exposed to NaCl had greater root and shoot biomass, and better chlorophyll content than non-colonised plants, with colonised-Vlamingh performing better than uninoculated control plants. The metabolome dataset using GC-MS consisted of a total of 93 metabolites of which 74 were identified in roots of both barley genotypes as organic acids, sugars, sugar acids, sugar alcohols, amino acids, amines, and a small number of fatty acids. LC-QqTOF-MS analysis resulted in the detection of 186 lipid molecular species, classified into three major lipid classes-glycerophospholipids, glycerolipids, and sphingolipids, from roots of both genotypes. In Cultivar Vlamingh both metabolites and lipids increased with fungus and salt treatment while in Gairdner they decreased. The results from this study suggest that the metabolic pathways by which the fungus imparts salt tolerance is different for the different genotypes.
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Affiliation(s)
| | | | - Siria H. A. Natera
- Metabolomics Australia, The University of Melbourne, Parkville, VIC, Australia
| | - Ute Roessner
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
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12
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Dong X, Sun L, Agarwal M, Maker G, Han Y, Yu X, Ren Y. The Effect of Ozone Treatment on Metabolite Profile of Germinating Barley. Foods 2022; 11:foods11091211. [PMID: 35563933 PMCID: PMC9104593 DOI: 10.3390/foods11091211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/11/2022] [Accepted: 04/20/2022] [Indexed: 12/25/2022] Open
Abstract
Ozone is widely used to control pests in grain and impacts seed germination, a crucial stage in crop establishment which involves metabolic alterations. In this study, dormancy was overcome through after-ripening (AR) in dry barley seed storage of more than 4 weeks; alternatively, a 15-min ozone treatment could break the dormancy of barley immediately after harvest, with accelerated germination efficiency remaining around 96% until 4 weeks. Headspace solid-phase microextraction (HS-SPME) and liquid absorption coupled with gas chromatography mass spectrometry (GC-MS) were utilized for metabolite profiling of 2-, 4- and 7-day germinating seeds. Metabolic changes during barley germination are reflected by time-dependent characteristics. Alcohols, fatty acids, and ketones were major contributors to time-driven changes during germination. In addition, greater fatty acids were released at the early germination stage when subjected to ozone treatment.
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Affiliation(s)
- Xue Dong
- College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, Perth 6150, Australia; (X.D.); (L.S.); (M.A.); (G.M.); (Y.H.)
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Litao Sun
- College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, Perth 6150, Australia; (X.D.); (L.S.); (M.A.); (G.M.); (Y.H.)
| | - Manjree Agarwal
- College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, Perth 6150, Australia; (X.D.); (L.S.); (M.A.); (G.M.); (Y.H.)
| | - Garth Maker
- College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, Perth 6150, Australia; (X.D.); (L.S.); (M.A.); (G.M.); (Y.H.)
| | - Yitao Han
- College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, Perth 6150, Australia; (X.D.); (L.S.); (M.A.); (G.M.); (Y.H.)
| | - Xiangyang Yu
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
- Correspondence: (X.Y.); (Y.R.); Tel.: +86-25-8439-1299 (X.Y.); +618-9360-1397 (Y.R.)
| | - Yonglin Ren
- College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, Perth 6150, Australia; (X.D.); (L.S.); (M.A.); (G.M.); (Y.H.)
- Correspondence: (X.Y.); (Y.R.); Tel.: +86-25-8439-1299 (X.Y.); +618-9360-1397 (Y.R.)
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13
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Beasley JT, Bonneau JP, Moreno-Moyano LT, Callahan DL, Howell KS, Tako E, Taylor J, Glahn RP, Appels R, Johnson AAT. Multi-year field evaluation of nicotianamine biofortified bread wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1168-1182. [PMID: 34902177 DOI: 10.1111/tpj.15623] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/27/2021] [Indexed: 06/14/2023]
Abstract
Conventional breeding efforts for iron (Fe) and zinc (Zn) biofortification of bread wheat (Triticum aestivum L.) have been hindered by a lack of genetic variation for these traits and a negative correlation between grain Fe and Zn concentrations and yield. We have employed genetic engineering to constitutively express (CE) the rice (Oryza sativa) nicotianamine synthase 2 (OsNAS2) gene and upregulate biosynthesis of two metal chelators - nicotianamine (NA) and 2'-deoxymugineic acid (DMA) - in bread wheat, resulting in increased Fe and Zn concentrations in wholemeal and white flour. Here we describe multi-location confined field trial (CFT) evaluation of a low-copy transgenic CE-OsNAS2 wheat event (CE-1) over 3 years and demonstrate higher concentrations of NA, DMA, Fe, and Zn in CE-1 wholemeal flour, white flour, and white bread and higher Fe bioavailability in CE-1 white flour relative to a null segregant (NS) control. Multi-environment models of agronomic and grain nutrition traits revealed a negative correlation between grain yield and grain Fe, Zn, and total protein concentrations, yet no correlation between grain yield and grain NA and DMA concentrations. White flour Fe bioavailability was positively correlated with white flour NA concentration, suggesting that NA-chelated Fe should be targeted in wheat Fe biofortification efforts.
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Affiliation(s)
- Jesse T Beasley
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Julien P Bonneau
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Laura T Moreno-Moyano
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Damien L Callahan
- School of Life and Environmental Sciences, Deakin University, Melbourne, Victoria, 3125, Australia
| | - Kate S Howell
- School of Agriculture and Food, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Elad Tako
- Department of Food Science, Cornell University, Stocking Hall, Ithaca, NY, 14853-7201, USA
| | - Julian Taylor
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, South Australia, 5064, Australia
| | - Raymond P Glahn
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Ithaca, NY, 14853, USA
| | - Rudi Appels
- School of Agriculture and Food, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Alexander A T Johnson
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
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14
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Ashraf MF, Hou D, Hussain Q, Imran M, Pei J, Ali M, Shehzad A, Anwar M, Noman A, Waseem M, Lin X. Entailing the Next-Generation Sequencing and Metabolome for Sustainable Agriculture by Improving Plant Tolerance. Int J Mol Sci 2022; 23:651. [PMID: 35054836 PMCID: PMC8775971 DOI: 10.3390/ijms23020651] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/23/2021] [Accepted: 12/29/2021] [Indexed: 02/07/2023] Open
Abstract
Crop production is a serious challenge to provide food for the 10 billion individuals forecasted to live across the globe in 2050. The scientists' emphasize establishing an equilibrium among diversity and quality of crops by enhancing yield to fulfill the increasing demand for food supply sustainably. The exploitation of genetic resources using genomics and metabolomics strategies can help generate resilient plants against stressors in the future. The innovation of the next-generation sequencing (NGS) strategies laid the foundation to unveil various plants' genetic potential and help us to understand the domestication process to unmask the genetic potential among wild-type plants to utilize for crop improvement. Nowadays, NGS is generating massive genomic resources using wild-type and domesticated plants grown under normal and harsh environments to explore the stress regulatory factors and determine the key metabolites. Improved food nutritional value is also the key to eradicating malnutrition problems around the globe, which could be attained by employing the knowledge gained through NGS and metabolomics to achieve suitability in crop yield. Advanced technologies can further enhance our understanding in defining the strategy to obtain a specific phenotype of a crop. Integration among bioinformatic tools and molecular techniques, such as marker-assisted, QTLs mapping, creation of reference genome, de novo genome assembly, pan- and/or super-pan-genomes, etc., will boost breeding programs. The current article provides sequential progress in NGS technologies, a broad application of NGS, enhancement of genetic manipulation resources, and understanding the crop response to stress by producing plant metabolites. The NGS and metabolomics utilization in generating stress-tolerant plants/crops without deteriorating a natural ecosystem is considered a sustainable way to improve agriculture production. This highlighted knowledge also provides useful research that explores the suitable resources for agriculture sustainability.
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Affiliation(s)
- Muhammad Furqan Ashraf
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
| | - Dan Hou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
| | - Quaid Hussain
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
| | - Muhammad Imran
- Colleges of Agriculture and Horticulture, South China Agricultural University, Guangzhou 510642, China; (M.I.); (M.W.)
| | - Jialong Pei
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
| | - Mohsin Ali
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Aamar Shehzad
- Maize Research Station, AARI, Faisalabad 38000, Pakistan;
| | - Muhammad Anwar
- Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China;
| | - Ali Noman
- Department of Botany, Government College University, Faisalabad 38000, Pakistan;
| | - Muhammad Waseem
- Colleges of Agriculture and Horticulture, South China Agricultural University, Guangzhou 510642, China; (M.I.); (M.W.)
| | - Xinchun Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Lin’An, Hangzhou 311300, China; (M.F.A.); (D.H.); (Q.H.); (J.P.)
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15
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Gupta S, Smith PMC, Boughton BA, Rupasinghe TWT, Natera SHA, Roessner U. Inoculation of barley with Trichoderma harzianum T-22 modifies lipids and metabolites to improve salt tolerance. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7229-7246. [PMID: 34279634 DOI: 10.1093/jxb/erab335] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/17/2021] [Indexed: 05/23/2023]
Abstract
Soil salinity has a serious impact on plant growth and agricultural yield. Inoculation of crop plants with fungal endophytes is a cost-effective way to improve salt tolerance. We used metabolomics to study how Trichoderma harzianum T-22 alleviates NaCl-induced stress in two barley (Hordeum vulgare L.) cultivars, Gairdner and Vlamingh, with contrasting salinity tolerance. GC-MS was used to analyse polar metabolites and LC-MS to analyse lipids in roots during the early stages of interaction with Trichoderma. Inoculation reversed the severe effects of salt on root length in sensitive cv. Gairdner and, to a lesser extent, improved root growth in more tolerance cv. Vlamingh. Biochemical changes showed a similar pattern in inoculated roots after salt treatment. Sugars increased in both cultivars, with ribulose, ribose, and rhamnose specifically increased by inoculation. Salt stress caused large changes in lipids in roots but inoculation with fungus greatly reduced the extent of these changes. Many of the metabolic changes in inoculated cv. Gairdner after salt treatment mirror the response of uninoculated cv. Vlamingh, but there are some metabolites that changed in both cultivars only after fungal inoculation. Further study is required to determine how these metabolic changes are induced by fungal inoculation.
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Affiliation(s)
- Sneha Gupta
- School of BioSciences, University of Melbourne, Parkville, Victoria, Australia
| | - Penelope M C Smith
- School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Berin A Boughton
- School of BioSciences, University of Melbourne, Parkville, Victoria, Australia
- Australian National Phenome Centre, Murdoch University, Murdoch, Western Australia, Australia
| | - Thusitha W T Rupasinghe
- School of BioSciences, University of Melbourne, Parkville, Victoria, Australia
- SCIEX, Mulgrave, Victoria, Australia
| | - Siria H A Natera
- Metabolomics Australia, The University of Melbourne, Parkville, Victoria, Australia
| | - Ute Roessner
- School of BioSciences, University of Melbourne, Parkville, Victoria, Australia
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16
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Dermendjiev G, Schnurer M, Weiszmann J, Wilfinger S, Ott E, Gebert C, Weckwerth W, Ibl V. Tissue-Specific Proteome and Subcellular Microscopic Analyses Reveal the Effect of High Salt Concentration on Actin Cytoskeleton and Vacuolization in Aleurone Cells during Early Germination of Barley. Int J Mol Sci 2021; 22:ijms22179642. [PMID: 34502558 PMCID: PMC8431815 DOI: 10.3390/ijms22179642] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 01/03/2023] Open
Abstract
Cereal grain germination provides the basis for crop production and requires a tissue-specific interplay between the embryo and endosperm during heterotrophic germination involving signalling, protein secretion, and nutrient uptake until autotrophic growth is possible. High salt concentrations in soil are one of the most severe constraints limiting the germination of crop plants, affecting the metabolism and redox status within the tissues of germinating seed. However, little is known about the effect of salt on seed storage protein mobilization, the endomembrane system, and protein trafficking within and between these tissues. Here, we used mass spectrometry analyses to investigate the protein dynamics of the embryo and endosperm of barley (Hordeum vulgare, L.) at five different early points during germination (0, 12, 24, 48, and 72 h after imbibition) in germinated grains subjected to salt stress. The expression of proteins in the embryo as well as in the endosperm was temporally regulated. Seed storage proteins (SSPs), peptidases, and starch-digesting enzymes were affected by salt. Additionally, microscopic analyses revealed an altered assembly of actin bundles and morphology of protein storage vacuoles (PSVs) in the aleurone layer. Our results suggest that besides the salt-induced protein expression, intracellular trafficking and actin cytoskeleton assembly are responsible for germination delay under salt stress conditions.
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Affiliation(s)
- Georgi Dermendjiev
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria; (G.D.); (M.S.); (J.W.); (S.W.); (E.O.); (C.G.); (W.W.)
| | - Madeleine Schnurer
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria; (G.D.); (M.S.); (J.W.); (S.W.); (E.O.); (C.G.); (W.W.)
| | - Jakob Weiszmann
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria; (G.D.); (M.S.); (J.W.); (S.W.); (E.O.); (C.G.); (W.W.)
| | - Sarah Wilfinger
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria; (G.D.); (M.S.); (J.W.); (S.W.); (E.O.); (C.G.); (W.W.)
| | - Emanuel Ott
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria; (G.D.); (M.S.); (J.W.); (S.W.); (E.O.); (C.G.); (W.W.)
| | - Claudia Gebert
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria; (G.D.); (M.S.); (J.W.); (S.W.); (E.O.); (C.G.); (W.W.)
| | - Wolfram Weckwerth
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria; (G.D.); (M.S.); (J.W.); (S.W.); (E.O.); (C.G.); (W.W.)
- Vienna Metabolomics Center (VIME), University of Vienna, Djerassiplatz 1, 1030 Wien, Austria
| | - Verena Ibl
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria; (G.D.); (M.S.); (J.W.); (S.W.); (E.O.); (C.G.); (W.W.)
- Correspondence:
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17
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Hamany Djande CY, Piater LA, Steenkamp PA, Tugizimana F, Dubery IA. A Metabolomics Approach and Chemometric Tools for Differentiation of Barley Cultivars and Biomarker Discovery. Metabolites 2021; 11:metabo11090578. [PMID: 34564394 PMCID: PMC8466441 DOI: 10.3390/metabo11090578] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/04/2021] [Accepted: 08/20/2021] [Indexed: 12/15/2022] Open
Abstract
One of the ultimate goals of plant breeding is the development of new crop cultivars capable of withstanding increasing environmental stresses, to sustain the constantly growing population and economic demands. Investigating the chemical composition of the above and underground tissues of cultivars is crucial for the understanding of common and specific traits thereof. Using an untargeted metabolomics approach together with appropriate chemometrics tools, the differential metabolite profiles of leaf and root extracts from five cultivars of barley (‘Erica’, ‘Elim’, ‘Hessekwa’, ‘S16’ and ‘Agulhas’) were explored and potential signatory biomarkers were revealed. The study was conducted on seedlings grown for 21 days under identical controlled conditions. An ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS) was employed to analyse hydromethanolic leaf and root extracts of barley cultivars. Furthermore, unsupervised and supervised learning algorithms were applied to mine the generated data and to pinpoint cultivar-specific metabolites. Among all the classes of metabolites annotated, phenolic acids and derivatives formed the largest group and also represented the most discriminatory metabolites. In roots, saponarin, an important allelochemical differentially distributed across cultivars, was the only flavonoid annotated. The application of an untargeted metabolomics approach in phenotyping grain crops such as barley was demonstrated, and the metabolites responsible for differentiating between the selected cultivars were revealed. The study provides insights into the chemical architecture of barley, an agro-economically relevant cereal crop; and reiterates the importance of metabolomics tools in plant breeding practices for crop improvement.
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18
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Hu W, Han Y, Sheng Y, Wang Y, Pan Q, Nie H. Mass spectrometry imaging for direct visualization of components in plants tissues. J Sep Sci 2021; 44:3462-3476. [PMID: 34245221 DOI: 10.1002/jssc.202100138] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/09/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022]
Abstract
Mass spectrometry is considered the most informative technique for components identification and has been widely adopted in plant sciences. However, the spatial distribution of compounds in the plant, which is vital for the exploration of plant physiological mechanisms, is missed in MS analysis. In recent years, mass spectrometry imaging has brought a great breakthrough in plant analysis because it can determine both the molecular compositions and spatial distributions, which is conducive to understand functions and regulation pathways of specific components in plants. Mass spectrometry imaging analysis of plant tissue is toward high sensitivity, high spatial resolution, and even single-cell analysis. Despite many challenges and technical barriers, such as difficulties of sample pretreatment caused by morphological diversity of plant tissues, obstacles for high spatial resolution imaging, and so on, lots of researches have contributed to remarkable progress, including improvement in tissue preparation, matrix innovation, and ionization mode development. This review focuses on the advances of mass spectrometry imaging analysis of plants in the last 5 years, including commonly used ionization techniques, technical advances, and recent applications of mass spectrometry imaging in plants.
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Affiliation(s)
- Wenya Hu
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, P. R. China
| | - Yehua Han
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, P. R. China
| | - Yiqi Sheng
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, P. R. China
| | - Yinghao Wang
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, P. R. China
| | - Qiong Pan
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering and Environment, China University of Petroleum-Beijing, Beijing, P. R. China
| | - Honggang Nie
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
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19
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The Chemistry of Stress: Understanding the 'Cry for Help' of Plant Roots. Metabolites 2021; 11:metabo11060357. [PMID: 34199628 PMCID: PMC8228326 DOI: 10.3390/metabo11060357] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 12/17/2022] Open
Abstract
Plants are faced with various biotic and abiotic stresses during their life cycle. To withstand these stresses, plants have evolved adaptive strategies including the production of a wide array of primary and secondary metabolites. Some of these metabolites can have direct defensive effects, while others act as chemical cues attracting beneficial (micro)organisms for protection. Similar to aboveground plant tissues, plant roots also appear to have evolved “a cry for help” response upon exposure to stress, leading to the recruitment of beneficial microorganisms to help minimize the damage caused by the stress. Furthermore, emerging evidence indicates that microbial recruitment to the plant roots is, at least in part, mediated by quantitative and/or qualitative changes in root exudate composition. Both volatile and water-soluble compounds have been implicated as important signals for the recruitment and activation of beneficial root-associated microbes. Here we provide an overview of our current understanding of belowground chemical communication, particularly how stressed plants shape its protective root microbiome.
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20
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Martinez-Seidel F, Suwanchaikasem P, Nie S, Leeming MG, Pereira Firmino AA, Williamson NA, Kopka J, Roessner U, Boughton BA. Membrane-Enriched Proteomics Link Ribosome Accumulation and Proteome Reprogramming With Cold Acclimation in Barley Root Meristems. FRONTIERS IN PLANT SCIENCE 2021; 12:656683. [PMID: 33995454 PMCID: PMC8121087 DOI: 10.3389/fpls.2021.656683] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/22/2021] [Indexed: 05/17/2023]
Abstract
Due to their sessile nature, plants rely on root systems to mediate many biotic and abiotic cues. To overcome these challenges, the root proteome is shaped to specific responses. Proteome-wide reprogramming events are magnified in meristems due to their active protein production. Using meristems as a test system, here, we study the major rewiring that plants undergo during cold acclimation. We performed tandem mass tag-based bottom-up quantitative proteomics of two consecutive segments of barley seminal root apexes subjected to suboptimal temperatures. After comparing changes in total and ribosomal protein (RP) fraction-enriched contents with shifts in individual protein abundances, we report ribosome accumulation accompanied by an intricate translational reprogramming in the distal apex zone. Reprogramming ranges from increases in ribosome biogenesis to protein folding factors and suggests roles for cold-specific RP paralogs. Ribosome biogenesis is the largest cellular investment; thus, the vast accumulation of ribosomes and specific translation-related proteins during cold acclimation could imply a divergent ribosomal population that would lead to a proteome shift across the root. Consequently, beyond the translational reprogramming, we report a proteome rewiring. First, triggered protein accumulation includes spliceosome activity in the root tip and a ubiquitous upregulation of glutathione production and S-glutathionylation (S-GSH) assemblage machineries in both root zones. Second, triggered protein depletion includes intrinsically enriched proteins in the tip-adjacent zone, which comprise the plant immune system. In summary, ribosome and translation-related protein accumulation happens concomitantly to a proteome reprogramming in barley root meristems during cold acclimation. The cold-accumulated proteome is functionally implicated in feedbacking transcript to protein translation at both ends and could guide cold acclimation.
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Affiliation(s)
- Federico Martinez-Seidel
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Shuai Nie
- Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, VIC, Australia
| | - Michael G. Leeming
- Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, VIC, Australia
- School of Chemistry, The University of Melbourne, Parkville, VIC, Australia
| | | | - Nicholas A. Williamson
- Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, VIC, Australia
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Joachim Kopka
- Willmitzer Department, Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Ute Roessner
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Berin A. Boughton
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
- Australian National Phenome Centre, Murdoch University, Murdoch, WA, Australia
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21
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Abulfaraj AA. Stepwise signal transduction cascades under salt stress in leaves of wild barley (Hordeum spontaneum). BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1807408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Aala Abdulaziz Abulfaraj
- Department of Biological Sciences, Science and Arts College, King Abdulaziz University, Jeddah, Saudi Arabia
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22
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Feng X, Zhang H, Yu P. X-ray fluorescence application in food, feed, and agricultural science: a critical review. Crit Rev Food Sci Nutr 2020; 61:2340-2350. [PMID: 32543214 DOI: 10.1080/10408398.2020.1776677] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Recently X-ray fluorescence techniques have been widely used in food and agricultural science areas. Minimal sample preparation, nondestructive analysis, high spatial resolution, and multiple elements measurements within a single sample are among its advantages. In this review, literature of X-ray fluorescence are extensively researched and summarized from food and agricultural science areas focusing on food safety inspection, food nutrition, plant science, soil science, and Ca-related problems in horticultural crops. In addition, the advantages and disadvantages of X-ray fluorescence comparing with traditional analytical techniques of elements are also discussed. The more advanced technology such as developments of detector, scanning system, beamline capability among others would significantly increase future application of X-ray fluorescence techniques. Combination use of XRF with other tools such as chemometrics or data analytics would greatly improve its prediction performance. These further improvements offer exciting perspectives for the application of X-ray fluorescence in the food and agricultural science areas.
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Affiliation(s)
- Xin Feng
- School of Life Science and Engineering, Foshan University, Foshan, China.,Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Canada
| | - Huihua Zhang
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Peiqiang Yu
- Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Canada
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23
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Metabolomics: A Tool for Cultivar Phenotyping and Investigation of Grain Crops. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10060831] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The quality of plants is often enhanced for diverse purposes such as improved resistance to environmental pressures, better taste, and higher yields. Considering the world’s dependence on plants (nutrition, medicine, or biofuel), developing new cultivars with superior characteristics is of great importance. As part of the ‘omics’ approaches, metabolomics has been employed to investigate the large number of metabolites present in plant systems under well-defined environmental conditions. Recent advances in the metabolomics field have greatly expanded our understanding of plant metabolism, largely driven by potential application to agricultural systems. The current review presents the workflow for plant metabolome analyses, current knowledge, and future directions of such research as determinants of cultivar phenotypes. Furthermore, the value of metabolome analyses in contemporary crop science is illustrated. Here, metabolomics has provided valuable information in research on grain crops and identified significant biomarkers under different conditions and/or stressors. Moreover, the value of metabolomics has been redefined from simple biomarker identification to a tool for discovering active drivers involved in biological processes. We illustrate and conclude that the rapid advances in metabolomics are driving an explosion of information that will advance modern breeding approaches for grain crops and address problems associated with crop productivity and sustainable agriculture.
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24
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Yukihiro Y, Zaima N. Application of Mass Spectrometry Imaging for Visualizing Food Components. Foods 2020; 9:foods9050575. [PMID: 32375379 PMCID: PMC7278736 DOI: 10.3390/foods9050575] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 04/15/2020] [Accepted: 04/24/2020] [Indexed: 02/07/2023] Open
Abstract
Consuming food is essential for survival, maintaining health, and triggering positive emotions like pleasure. One of the factors that drive us toward such behavior is the presence of various compounds in foods. There are many methods to analyze these molecules in foods; however, it is difficult to analyze the spatial distribution of these compounds using conventional techniques, such as mass spectrometry combined with high-performance liquid chromatography or gas chromatography. Mass spectrometry imaging (MSI) is a two-dimensional ionization technology that enables detection of compounds in tissue sections without extraction, purification, separation, or labeling. There are many methods for ionization of analytes, including secondary ion mass spectrometry, matrix-assisted laser desorption/ionization, and desorption electrospray ionization. Such MSI technologies can provide spatial information on the location of a specific analyte in food. The number of studies utilizing MSI technologies in food science has been increasing in the past decade. This review provides an overview of some of the recent applications of MSI in food science and related fields. In the future, MSI will become one of the most promising technologies for visualizing the distribution of food components and for identifying food-related factors by their molecular weights to improve quality, quality assurance, food safety, nutritional analysis, and to locate administered food factors.
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Affiliation(s)
- Yoshimura Yukihiro
- Department of Nutrition, Kobe Gakuin University, 518 Arise, Ikawadani-cho, Nishi-ku, Kobe City 651-2180, Japan
| | - Nobuhiro Zaima
- Department of Applied Biological Chemistry, Graduate School of Agriculture, Kindai University, 204-3327 Nakamachi, Nara City 631-8505, Japan
- Agricultural Technology and Innovation Research Institute, Kindai University,204-3327 Nakamachi, Nara City 631-8505, Japan
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25
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Mwando E, Han Y, Angessa TT, Zhou G, Hill CB, Zhang XQ, Li C. Genome-Wide Association Study of Salinity Tolerance During Germination in Barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2020; 11:118. [PMID: 32153619 PMCID: PMC7047234 DOI: 10.3389/fpls.2020.00118] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 01/27/2020] [Indexed: 05/21/2023]
Abstract
Barley seeds need to be able to germinate and establish seedlings in saline soils in Mediterranean-type climates. Despite being a major cereal crop, barley has few reported quantitative trait loci (QTL) and candidate genes underlying salt tolerance at the germination stage. Breeding programs targeting salinity tolerance at germination require an understanding of genetic loci and alleles in the current germplasm. In this study, we investigated seed-germination-related traits under control and salt stress conditions in 350 diverse barley accessions. A genome-wide association study, using ~24,000 genetic markers, was undertaken to detect marker-trait associations (MTA) and the underlying candidate genes for salinity tolerance during germination. We detected 19 loci containing 52 significant salt-tolerance-associated markers across all chromosomes, and 4 genes belonging to 4 family functions underlying the predicted MTAs. Our results provide new genetic resources and information to improve salt tolerance at germination in future barley varieties via genomic and marker-assisted selection and to open up avenues for further functional characterization of the identified candidate genes.
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Affiliation(s)
- Edward Mwando
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia
| | - Yong Han
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia
| | - Tefera Tolera Angessa
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia
- Department of Primary Industries and Regional Development Government of Western Australia, Perth, WA, Australia
| | - Gaofeng Zhou
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- Department of Primary Industries and Regional Development Government of Western Australia, Perth, WA, Australia
| | - Camilla Beate Hill
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia
| | - Chengdao Li
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia
- Department of Primary Industries and Regional Development Government of Western Australia, Perth, WA, Australia
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26
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Yu D, Boughton BA, Hill CB, Feussner I, Roessner U, Rupasinghe TWT. Insights Into Oxidized Lipid Modification in Barley Roots as an Adaptation Mechanism to Salinity Stress. FRONTIERS IN PLANT SCIENCE 2020; 11:1. [PMID: 32117356 PMCID: PMC7011103 DOI: 10.3389/fpls.2020.00001] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/01/2020] [Indexed: 05/18/2023]
Abstract
Lipidomics is an emerging technology, which aims at the global characterization and quantification of lipids within biological matrices including biofluids, cells, whole organs and tissues. The changes in individual lipid molecular species in stress treated plant species and different cultivars can indicate the functions of genes affecting lipid metabolism or lipid signaling. Mass spectrometry-based lipid profiling has been used to track the changes of lipid levels and related metabolites in response to salinity stress. We have developed a comprehensive lipidomics platform for the identification and direct qualification and/or quantification of individual lipid species, including oxidized lipids, which enables a more systematic investigation of peroxidation of individual lipid species in barley roots under salinity stress. This new lipidomics approach has improved with an advantage of analyzing the composition of acyl chains at the molecular level, which facilitates to profile precisely the 18:3-containing diacyl-glycerophosphates and allowed individual comparison of lipids across varieties. Our findings revealed a general decrease in most of the galactolipids in plastid membranes, and an increase of glycerophospholipids and acylated steryl glycosides, which indicate that plastidial and extraplastidial membranes in barley roots ubiquitously tend to form a hexagonal II (HII) phase under salinity stress. In addition, salt-tolerant and salt-sensitive cultivars showed contrasting changes in the levels of oxidized membrane lipids. These results support the hypothesis that salt-induced oxidative damage to membrane lipids can be used as an indication of salt stress tolerance in barley.
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Affiliation(s)
- Dingyi Yu
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
- St. Vincent’s Institute of Medical Research, University of Melbourne, Fitzroy, VIC, Australia
| | - Berin A. Boughton
- Metabolomics Australia, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
| | - Camilla B. Hill
- School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia
| | - Ivo Feussner
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, University of Goettingen, Goettingen, Germany
- Goettingen Center for Molecular Biosciences, Department of Plant Biochemistry, University of Goettingen, Goettingen, Germany
| | - Ute Roessner
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
- Metabolomics Australia, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
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