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Cells
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Metabolomics in Plant Research
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Metabolomics in Plant Research

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Plant, Algae and Fungi Cell Biology".

Deadline for manuscript submissions: closed (31 January 2021) | Viewed by 64926

Special Issue Editors

Dr. Sara Rinalducci

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Guest Editor
Department of Ecological and Biological Sciences (DEB), University of Tuscia, 01100 Viterbo, Italy
Interests: proteomics/metabolomics/lipidomics; systems biology; post-translational modifications; plant responses to biotic and abiotic stresses; omics for health and disease
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Stefanie Wienkoop

E-Mail Website
Guest Editor
Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
Interests: plant–microbes interactions; plant molecular ecology; plant proteomics; plant physiology; plant biology
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Mohsen Janmohammadi

E-Mail Website
Guest Editor
Department of Plant Production and Genetics, Faculty of Agriculture, University of Maragheh, P.O. Box 55181-83111, Maragheh, Iran
Interests: plant physiology; metabolome analysis; physiology of crop yield; plant response to environmental stress and climate change

Special Issue Information

Dear Colleagues,

Metabolites are small biological molecules within a cell and represent the phenotypic status of a biological system. Therefore, their exploration provides unique and beneficial information on the metabolic pathways participating in different biological processes and on the state of cell perturbations. Plants represent major metabolite factories on Earth. More than 50,000 compounds have been detected in plants (including amino acids, organic acids, fatty acids, amines, sugars, vitamins, cofactors, pigments, antioxidants, and others), and it is forecasted that the final figure for the plant kingdom will approach or even exceed 200,000. This metabolic affluence not only reflects the availability of corresponding genetic information, but it is also the result of multiple substrate specificities for many enzymes, subcellular compartmentation, and the occurrence of non-enzymatic reactions. The metabolome is highly dynamic, time-dependent, and sensitive to many environmental conditions. Metabolomics is the term coined for essentially comprehensive, non-biased, high-throughput analyses of complex metabolite mixtures typical of plant extracts. Plant metabolomes are generally sub-divided into two categories: primary (or central) metabolites indispensable for plant growth and development, and secondary (or specialized) metabolites that, although not essential, are crucial for plant survival under abiotic or biotic stress conditions as well as for the plant’s communication with their environment. Thus, metabolomics is successful in the area of general plant cell physiology as well as in the field of environmental research. However, metabolite detection and structural identification still represents a considerable challenge for plant scientists. More recently, metabolomics has been gaining ground in studying biogenic volatile organic compounds (BVOCs) that are produced as specialized metabolites contributing to the characteristics of each plant. They are released from leaves, flowers, and fruits into the atmosphere and from roots into the soil, attracting pollinators, seed dispersers, and other beneficial animals and microorganisms, serving as signals in plant–plant communication. Besides their ecological role, BVOCs can determine taste and fragrance. Overall plant metabolomics can therefore allow plant biodiversity screening, but can also be a tool at the service of plant breeding and food/pharmaceutical/cosmeceutical industries.

In this very wide context, we invite investigators to submit contributions that explore all these aspects.

Sara Rinalducci
Stefanie Wienkoop
Mohsen Janmohammadi
Guest Editors

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Keywords

  • biodiversity
  • bioactive compounds of fruits and vegetables
  • crop science
  • plant development
  • response to biotic and abiotic stress
  • root exudation
  • symbiotic plant–microbe interaction
  • volatilome

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Published Papers (15 papers)

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Editorial

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2 pages, 198 KiB  
Editorial
Metabolomics in Plant Research—From Ecometabolomics to Metabolotyping
by Sara Rinalducci and Stefanie Wienkoop
Cells 2023, 12(4), 600; https://doi.org/10.3390/cells12040600 - 13 Feb 2023
Viewed by 1495
Abstract
In this Special Issue, a state-of-the-art review of the current knowledge of sample preparation and LC–MS techniques for the analyses of nucleosides and nucleotides in plants was published [...] Full article
(This article belongs to the Special Issue Metabolomics in Plant Research)

Research

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20 pages, 2697 KiB  
Article
Paraburkholderia phymatum Homocitrate Synthase NifV Plays a Key Role for Nitrogenase Activity during Symbiosis with Papilionoids and in Free-Living Growth Conditions
by Paula Bellés-Sancho, Martina Lardi, Yilei Liu, Sebastian Hug, Marta Adriana Pinto-Carbó, Nicola Zamboni and Gabriella Pessi
Cells 2021, 10(4), 952; https://doi.org/10.3390/cells10040952 - 20 Apr 2021
Cited by 12 | Viewed by 3605
Abstract
Homocitrate is an essential component of the iron-molybdenum cofactor of nitrogenase, the bacterial enzyme that catalyzes the reduction of dinitrogen (N2) to ammonia. In nitrogen-fixing and nodulating alpha-rhizobia, homocitrate is usually provided to bacteroids in root nodules by their plant host. [...] Read more.
Homocitrate is an essential component of the iron-molybdenum cofactor of nitrogenase, the bacterial enzyme that catalyzes the reduction of dinitrogen (N2) to ammonia. In nitrogen-fixing and nodulating alpha-rhizobia, homocitrate is usually provided to bacteroids in root nodules by their plant host. In contrast, non-nodulating free-living diazotrophs encode the homocitrate synthase (NifV) and reduce N2 in nitrogen-limiting free-living conditions. Paraburkholderia phymatum STM815 is a beta-rhizobial strain, which can enter symbiosis with a broad range of legumes, including papilionoids and mimosoids. In contrast to most alpha-rhizobia, which lack nifV, P. phymatum harbors a copy of nifV on its symbiotic plasmid. We show here that P. phymatum nifV is essential for nitrogenase activity both in root nodules of papilionoid plants and in free-living growth conditions. Notably, nifV was dispensable in nodules of Mimosa pudica despite the fact that the gene was highly expressed during symbiosis with all tested papilionoid and mimosoid plants. A metabolome analysis of papilionoid and mimosoid root nodules infected with the P. phymatum wild-type strain revealed that among the approximately 400 measured metabolites, homocitrate and other metabolites involved in lysine biosynthesis and degradation have accumulated in all plant nodules compared to uninfected roots, suggesting an important role of these metabolites during symbiosis. Full article
(This article belongs to the Special Issue Metabolomics in Plant Research)
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16 pages, 5988 KiB  
Article
Allotetraploidization in Brachypodium May Have Led to the Dominance of One Parent’s Metabolome in Germinating Seeds
by Aleksandra Skalska, Elzbieta Wolny, Manfred Beckmann, John H. Doonan, Robert Hasterok and Luis A. J. Mur
Cells 2021, 10(4), 828; https://doi.org/10.3390/cells10040828 - 7 Apr 2021
Cited by 1 | Viewed by 2198
Abstract
Seed germination is a complex process during which a mature seed resumes metabolic activity to prepare for seedling growth. In this study, we performed a comparative metabolomic analysis of the embryo and endosperm using the community standard lines of three annual Brachypodium species, [...] Read more.
Seed germination is a complex process during which a mature seed resumes metabolic activity to prepare for seedling growth. In this study, we performed a comparative metabolomic analysis of the embryo and endosperm using the community standard lines of three annual Brachypodium species, i.e., B. distachyon (Bd) and B. stacei (Bs) and their natural allotetraploid B. hybridum (BdBs) that has wider ecological range than the other two species. We explored how far the metabolomic impact of allotetraploidization would be observable as over-lapping changes at 4, 12, and 24 h after imbibition (HAI) with water when germination was initiated. Metabolic changes during germination were more prominent in Brachypodium embryos than in the endosperm. The embryo and endosperm metabolomes of Bs and BdBs were similar, and those of Bd were distinctive. The Bs and BdBs embryos showed increased levels of sugars and the tricarboxylic acid cycle compared to Bd, which could have been indicative of better nutrient mobilization from the endosperm. Bs and BdBs also showed higher oxalate levels that could aid nutrient transfer through altered cellular events. In Brachypodium endosperm, the thick cell wall, in addition to starch, has been suggested to be a source of nutrients to the embryo. Metabolites indicative of sugar metabolism in the endosperm of all three species were not prominent, suggesting that mobilization mostly occurred prior to 4 HAI. Hydroxycinnamic and monolignol changes in Bs and BdBs were consistent with cell wall remodeling that arose following the release of nutrients to the respective embryos. Amino acid changes in both the embryo and endosperm were broadly consistent across the species. Taking our data together, the formation of BdBs may have maintained much of the Bs metabolome in both the embryo and endosperm during the early stages of germination. In the embryo, this conserved Bs metabolome appeared to include an elevated sugar metabolism that played a vital role in germination. If these observations are confirmed in the future with more Brachypodium accessions, it would substantiate the dominance of the Bs metabolome in BdBs allotetraploidization and the use of metabolomics to suggest important adaptive changes. Full article
(This article belongs to the Special Issue Metabolomics in Plant Research)
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18 pages, 4234 KiB  
Article
Effect of Agroecological Conditions on Biologically Active Compounds and Metabolome in Carrot
by Martin Koudela, Vera Schulzova, Ales Krmela, Hana Chmelarova, Jana Hajslova and Cenek Novotny
Cells 2021, 10(4), 784; https://doi.org/10.3390/cells10040784 - 1 Apr 2021
Cited by 5 | Viewed by 2542
Abstract
Carrot serves as a source of health-beneficial phytochemicals for human diet whose content is affected by agroecological conditions. The effect of conventional, integrated and organic farming on ascorbic acid (AA) and α,β-carotene levels of new carrot cultivars Cortina F1 and Afalon F1 was [...] Read more.
Carrot serves as a source of health-beneficial phytochemicals for human diet whose content is affected by agroecological conditions. The effect of conventional, integrated and organic farming on ascorbic acid (AA) and α,β-carotene levels of new carrot cultivars Cortina F1 and Afalon F1 was investigated and their metabolomic profiles were measured by direct analysis in real time ion source coupled with a high-resolution mass spectrometer (DART-HRMS). Cortina and Afalon exhibited high levels of AA and total carotenes under all agroecological conditions tested that fluctuated in broad ranges of 215–539 and 173–456 mg AA.kg−1 dry biomass and 1069–2165 and 1683–2165 mg carotene.kg−1 dry biomass, respectively. The ratio of β- to α-carotene in both cultivars was about 1.3. The most important variable for the PCA and the partial least squares discriminant analysis (PLS-DA) models for ethyl acetate extracts measured in positive and negative ionization mode was 6-methoxymellein (6-MM). Total carotene content and 6-MM levels were higher in the organic carrot compared to the conventional one and were correlated with a higher level of spontaneous infection. Other important compounds identified were sitosterol, hexose and various organic acids including antioxidant ferulic and coumaric acids. The findings allow comparison of metabolomic profiles and the AA and carotene contents of both cultivars with those of other commercially used carrots. Full article
(This article belongs to the Special Issue Metabolomics in Plant Research)
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15 pages, 5423 KiB  
Article
Metabolomic Variation Aligns with Two Geographically Distinct Subpopulations of Brachypodium Distachyon before and after Drought Stress
by Aleksandra Skalska, Manfred Beckmann, Fiona Corke, Gulsemin Savas Tuna, Metin Tuna, John H. Doonan, Robert Hasterok and Luis A. J. Mur
Cells 2021, 10(3), 683; https://doi.org/10.3390/cells10030683 - 19 Mar 2021
Cited by 10 | Viewed by 3214
Abstract
Brachypodium distachyon (Brachypodium) is a non-domesticated model grass that has been used to assess population level genomic variation. We have previously established a collection of 55 Brachypodium accessions that were sampled to reflect five different climatic regions of Turkey; designated 1a, 1c, 2, [...] Read more.
Brachypodium distachyon (Brachypodium) is a non-domesticated model grass that has been used to assess population level genomic variation. We have previously established a collection of 55 Brachypodium accessions that were sampled to reflect five different climatic regions of Turkey; designated 1a, 1c, 2, 3 and 4. Genomic and methylomic variation differentiated the collection into two subpopulations designated as coastal and central (respectively from regions 1a, 1c and the other from 2, 3 and 4) which were linked to environmental variables such as relative precipitation. Here, we assessed how far genomic variation would be reflected in the metabolomes and if this could be linked to an adaptive trait. Metabolites were extracted from eight-week-old seedlings from each accession and assessed using flow infusion high-resolution mass spectrometry (FIE-HRMS). Principal Component Analysis (PCA) of the derived metabolomes differentiated between samples from coastal and central subpopulations. The major sources of variation between seedling from the coastal and central subpopulations were identified. The central subpopulation was typified by significant increases in alanine, aspartate and glutamate metabolism and the tricarboxylic acid (TCA) cycle. Coastal subpopulation exhibited elevated levels of the auxin, indolacetic acid and rhamnose. The metabolomes of the seedling were also determined following the imposition of drought stress for seven days. The central subpopulation exhibited a metabolomic shift in response to drought, but no significant changes were seen in the coastal one. The drought responses in the central subpopulation were typified by changes in amino acids, increasing the glutamine that could be functioning as a stress signal. There were also changes in sugars that were likely to be an osmotic counter to drought, and changes in bioenergetic metabolism. These data indicate that genomic variation in our Turkish Brachypodium collection is largely reflected as distinctive metabolomes (“metabolotypes”) through which drought tolerance might be mediated. Full article
(This article belongs to the Special Issue Metabolomics in Plant Research)
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18 pages, 5270 KiB  
Article
Highly Species-Specific Foliar Metabolomes of Diverse Woody Species and Relationships with the Leaf Economics Spectrum
by Rabea Schweiger, Eva Castells, Luca Da Sois, Jordi Martínez-Vilalta and Caroline Müller
Cells 2021, 10(3), 644; https://doi.org/10.3390/cells10030644 - 13 Mar 2021
Cited by 11 | Viewed by 3413
Abstract
Plants show an extraordinary diversity in chemical composition and are characterized by different functional traits. However, relationships between the foliar primary and specialized metabolism in terms of metabolite numbers and composition as well as links with the leaf economics spectrum have rarely been [...] Read more.
Plants show an extraordinary diversity in chemical composition and are characterized by different functional traits. However, relationships between the foliar primary and specialized metabolism in terms of metabolite numbers and composition as well as links with the leaf economics spectrum have rarely been explored. We investigated these relationships in leaves of 20 woody species from the Mediterranean region grown as saplings in a common garden, using a comparative ecometabolomics approach that included (semi-)polar primary and specialized metabolites. Our analyses revealed significant positive correlations between both the numbers and relative composition of primary and specialized metabolites. The leaf metabolomes were highly species-specific but in addition showed some phylogenetic imprints. Moreover, metabolomes of deciduous species were distinct from those of evergreens. Significant relationships were found between the primary metabolome and nitrogen content and carbon/nitrogen ratio, important traits of the leaf economics spectrum, ranging from acquisitive (mostly deciduous) to conservative (evergreen) leaves. A comprehensive understanding of various leaf traits and their coordination in different plant species may facilitate our understanding of plant functioning in ecosystems. Chemodiversity is thereby an important component of biodiversity. Full article
(This article belongs to the Special Issue Metabolomics in Plant Research)
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24 pages, 3809 KiB  
Article
Metabolomics and DNA-Based Authentication of Two Traditional Asian Medicinal and Aromatic Species of Salvia subg. Perovskia
by Monika Bielecka, Bartosz Pencakowski, Marta Stafiniak, Klemens Jakubowski, Mehdi Rahimmalek, Shima Gharibi, Adam Matkowski and Sylwester Ślusarczyk
Cells 2021, 10(1), 112; https://doi.org/10.3390/cells10010112 - 9 Jan 2021
Cited by 27 | Viewed by 3870
Abstract
Subgenus Perovskia of the extended genus of Salvia comprises several Central Asian medicinal and aromatic species, of which S. yangii and S. abrotanoides are the most widespread. These plants are cultivated in Europe as robust ornamentals, and several cultivars are available. However, their [...] Read more.
Subgenus Perovskia of the extended genus of Salvia comprises several Central Asian medicinal and aromatic species, of which S. yangii and S. abrotanoides are the most widespread. These plants are cultivated in Europe as robust ornamentals, and several cultivars are available. However, their medicinal potential remains underutilized because of limited information about their phytochemical and genetic diversity. Thus, we combined an ultra-high performance liquid chromatography quadrupole time of flight mass spectrometry (UHPLC-QTOF-MS) based metabolomics with DNA barcoding approach based on trnH-psbA and ITS2 barcodes to clarify the relationships between these two taxa. Metabolomic analysis demonstrated that aerial parts are more similar than roots and none of the major compounds stand out as distinct. Sugiol in S. yangii leaves and carnosic acid quinone in S. abrotanoides were mostly responsible for their chemical differentiation, whereas in roots the distinction was supported by the presence of five norditerpenoids in S. yangii and two flavonoids and one norditerpenoid in S. abrotanoides. To verify the metabolomics-based differentiation, we performed DNA authentication that revealed S. yangii and S. abrotanoides to be very closely related but separate species. We demonstrated that DNA barcoding coupled with parallel LC-MS profiling constitutes a powerful tool in identification of taxonomically close Salvia species. Full article
(This article belongs to the Special Issue Metabolomics in Plant Research)
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11 pages, 5954 KiB  
Article
Metabolite Profiling of Alangium salviifolium Bark Using Advanced LC/MS and GC/Q-TOFTechnology
by Chandranayaka Siddaiah, Anil Kumar BM, Saligrama Adavigowda Deepak, Syed Salman Lateef, Saurabh Nagpal, Kanchugarakoppal S. Rangappa, Chakrabhavi D. Mohan, Shobith Rangappa, Madan Kumar S, Minaxi Sharma and Vijai Kumar Gupta
Cells 2021, 10(1), 1; https://doi.org/10.3390/cells10010001 - 22 Dec 2020
Cited by 6 | Viewed by 3598
Abstract
There is an urge for traditional herbal remedies as an alternative to modern medicine in treating several ailments. Alangium salviifolium is one such plant, used traditionally to treat several diseases. In several reports, there are findings related to the use of this plant [...] Read more.
There is an urge for traditional herbal remedies as an alternative to modern medicine in treating several ailments. Alangium salviifolium is one such plant, used traditionally to treat several diseases. In several reports, there are findings related to the use of this plant extract that demonstrate its therapeutic value. However, very few attempts have been made to identify the extensive metabolite composition of this plant. Here, we performed metabolite profiling and identification from the bark of A. salviifolium by extracting the sample in organic and aqueous solvents. The organic and aqueous extracts were fraction-collected using the Agilent 1260 Analytical Scale Fraction Collection System. Each of the fractions was analyzed on Liquid Chromatogaphy/Quadrupole Time-of-Flight LC/Q-TOF and Gas Chromatography/Quadrupole Time-of-Flight GC/instruments. The Liquid Chromatography/Mass Spectrometry (LC/MS) analyses were performed using Hydrophilic Ineraction Liquid Chromatography (HILIC), as well as reversed-phase chromatography using three separate, orthogonal reverse phase columns. Samples were analyzed using an Agilent Jet Stream (AJS) source in both positive and negative ionization modes. The compounds found were flavonoids, fatty acids, sugars, and terpenes. Eighty-one secondary metabolites were identified as having therapeutic potential. The data produced was against the METLIN database using accurate mass and/or MS/MS library matching. Compounds from Alangium that could not be identified by database or library matching were subsequently searched against the ChemSpider) database of over 30 million structures using MSMS data and Agilent MSC software.In order to identify compounds generated by GC/MS, the data were searched against the AgilentFiehn GCMS Metabolomics Library as well as the Wiley/NIST libraries. Full article
(This article belongs to the Special Issue Metabolomics in Plant Research)
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15 pages, 1457 KiB  
Article
Grapefruit-Derived Micro and Nanovesicles Show Distinct Metabolome Profiles and Anticancer Activities in the A375 Human Melanoma Cell Line
by Christopher Stanly, Mariaevelina Alfieri, Alfredo Ambrosone, Antonietta Leone, Immacolata Fiume and Gabriella Pocsfalvi
Cells 2020, 9(12), 2722; https://doi.org/10.3390/cells9122722 - 21 Dec 2020
Cited by 82 | Viewed by 6152
Abstract
Fruit juice is one of the most easily accessible resources for the isolation of plant-derived vesicles. Here we found that micro- and nano-sized vesicles (MVs and NVs) from four Citrus species, C. sinensis, C. limon, C. paradisi and C. aurantium, [...] Read more.
Fruit juice is one of the most easily accessible resources for the isolation of plant-derived vesicles. Here we found that micro- and nano-sized vesicles (MVs and NVs) from four Citrus species, C. sinensis, C. limon, C. paradisi and C. aurantium, specifically inhibit the proliferation of lung, skin and breast cancer cells, with no substantial effect on the growth of non-cancer cells. Cellular and molecular analyses demonstrate that grapefruit-derived vesicles cause cell cycle arrest at G2/M checkpoint associated with a reduced cyclins B1 and B2 expression levels and the upregulation of cell cycle inhibitor p21. Further data suggest the inhibition of Akt and ERK signalling, reduced intercellular cell adhesion molecule-1 and cathepsins expressions, and the presence of cleaved PARP-1, all associated with the observed changes at the cellular level. Gas chromatography-mass spectrometry-based metabolomics reveals distinct metabolite profiles for the juice and vesicle fractions. NVs exhibit a high relative amount of amino acids and organic acids whereas MVs and fruit juice are characterized by a high percentage of sugars and sugar derivatives. Grapefruit-derived NVs are in particular rich in alpha–hydroxy acids and leucine/isoleucine, myo-inositol and doconexent, while quininic acid was detected in MVs. Our findings reveal the metabolite signatures of grapefruit-derived vesicles and substantiate their potential use in new anticancer strategies. Full article
(This article belongs to the Special Issue Metabolomics in Plant Research)
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22 pages, 10186 KiB  
Article
Long-Term Cd Exposure Alters the Metabolite Profile in Stem Tissue of Medicago sativa
by Annelie Gutsch, Sophie Hendrix, Gea Guerriero, Jenny Renaut, Stanley Lutts, Saleh Alseekh, Alisdair R. Fernie, Jean-Francois Hausman, Jaco Vangronsveld, Ann Cuypers and Kjell Sergeant
Cells 2020, 9(12), 2707; https://doi.org/10.3390/cells9122707 - 17 Dec 2020
Cited by 17 | Viewed by 3526
Abstract
As a common pollutant, cadmium (Cd) is one of the most toxic heavy metals accumulating in agricultural soils through anthropogenic activities. The uptake of Cd by plants is the main entry route into the human food chain, whilst in plants it elicits oxidative [...] Read more.
As a common pollutant, cadmium (Cd) is one of the most toxic heavy metals accumulating in agricultural soils through anthropogenic activities. The uptake of Cd by plants is the main entry route into the human food chain, whilst in plants it elicits oxidative stress by unbalancing the cellular redox status. Medicago sativa was subjected to chronic Cd stress for five months. Targeted and untargeted metabolic analyses were performed. Long-term Cd exposure altered the amino acid composition with levels of asparagine, histidine and proline decreasing in stems but increasing in leaves. This suggests tissue-specific metabolic stress responses, which are often not considered in environmental studies focused on leaves. In stem tissue, profiles of secondary metabolites were clearly separated between control and Cd-exposed plants. Fifty-one secondary metabolites were identified that changed significantly upon Cd exposure, of which the majority are (iso)flavonoid conjugates. Cadmium exposure stimulated the phenylpropanoid pathway that led to the accumulation of secondary metabolites in stems rather than cell wall lignification. Those metabolites are antioxidants mitigating oxidative stress and preventing cellular damage. By an adequate adjustment of its metabolic composition, M. sativa reaches a new steady state, which enables the plant to acclimate under chronic Cd stress. Full article
(This article belongs to the Special Issue Metabolomics in Plant Research)
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19 pages, 1983 KiB  
Article
Fructans Are Differentially Distributed in Root Tissues of Asparagus
by Katja Witzel and Andrea Matros
Cells 2020, 9(9), 1943; https://doi.org/10.3390/cells9091943 - 22 Aug 2020
Cited by 28 | Viewed by 3630
Abstract
Inulin- and neoseries-type fructans [fructooligosaccharides (FOS) and fructopolysaccharides] accumulate in storage roots of asparagus (Asparagus officinalis L.), which continue to grow throughout the lifespan of this perennial plant. However, little is known about the storage of fructans at the spatial level in [...] Read more.
Inulin- and neoseries-type fructans [fructooligosaccharides (FOS) and fructopolysaccharides] accumulate in storage roots of asparagus (Asparagus officinalis L.), which continue to grow throughout the lifespan of this perennial plant. However, little is known about the storage of fructans at the spatial level in planta, and the degree of control by the plant is largely uncertain. We have utilized mass spectrometry imaging (MSI) to resolve FOS distribution patterns in asparagus roots (inner, middle, and outer tissues). Fructan and proteome profiling were further applied to validate the differential abundance of various fructan structures and to correlate observed tissue-specific metabolite patterns with the abundance of related fructan biosynthesis enzymes. Our data revealed an increased abundance of FOS with higher degree of polymerization (DP > 5) and of fructopolysaccharides (DP11 to DP17) towards the inner root tissues. Three isoforms of fructan:fructan 6G-fructosyltransferase (6G-FFT), forming 6G-kestose with a β (2–6) linkage using sucrose as receptor and 1-kestose as donor, were similarly detected in all three root tissues. In contrast, one ß-fructofuranosidase, which likely exhibits fructan:fructan 1-fructosyltransferase (1-FFT) activity, showed very high abundance in the inner tissues and lower levels in the outer tissues. We concluded a tight induction of the biosynthesis of fructans with DP > 5, following a gradient from the outer root cortex to the inner vascular tissues, which also correlates with high levels of sucrose metabolism in inner tissues, observed in our study. Full article
(This article belongs to the Special Issue Metabolomics in Plant Research)
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25 pages, 4358 KiB  
Article
Metabolome Profiling Supports the Key Role of the Spike in Wheat Yield Performance
by Omar Vergara-Diaz, Thomas Vatter, Rubén Vicente, Toshihiro Obata, Maria Teresa Nieto-Taladriz, Nieves Aparicio, Shawn Carlisle Kefauver, Alisdair Fernie and José Luis Araus
Cells 2020, 9(4), 1025; https://doi.org/10.3390/cells9041025 - 21 Apr 2020
Cited by 26 | Viewed by 3778
Abstract
Although the relevance of spike bracts in stress acclimation and contribution to wheat yield was recently revealed, the metabolome of this organ and its response to water stress is still unknown. The metabolite profiles of flag leaves, glumes and lemmas were characterized under [...] Read more.
Although the relevance of spike bracts in stress acclimation and contribution to wheat yield was recently revealed, the metabolome of this organ and its response to water stress is still unknown. The metabolite profiles of flag leaves, glumes and lemmas were characterized under contrasting field water regimes in five durum wheat cultivars. Water conditions during growth were characterized through spectral vegetation indices, canopy temperature and isotope composition. Spike bracts exhibited better coordination of carbon and nitrogen metabolisms than the flag leaves in terms of photorespiration, nitrogen assimilation and respiration paths. This coordination facilitated an accumulation of organic and amino acids in spike bracts, especially under water stress. The metabolomic response to water stress also involved an accumulation of antioxidant and drought tolerance related sugars, particularly in the spikes. Furthermore, certain cell wall, respiratory and protective metabolites were associated with genotypic outperformance and yield stability. In addition, grain yield was strongly predicted by leaf and spike bracts metabolomes independently. This study supports the role of the spike as a key organ during wheat grain filling, particularly under stress conditions and provides relevant information to explore new ways to improve wheat productivity including potential biomarkers for yield prediction. Full article
(This article belongs to the Special Issue Metabolomics in Plant Research)
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Review

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19 pages, 1660 KiB  
Review
Analysis of Nucleosides and Nucleotides in Plants: An Update on Sample Preparation and LC–MS Techniques
by Henryk Straube, Claus-Peter Witte and Marco Herde
Cells 2021, 10(3), 689; https://doi.org/10.3390/cells10030689 - 20 Mar 2021
Cited by 16 | Viewed by 6244
Abstract
Nucleotides fulfill many essential functions in plants. Compared to non-plant systems, these hydrophilic metabolites have not been adequately investigated in plants, especially the less abundant nucleotide species such as deoxyribonucleotides and modified or damaged nucleotides. Until recently, this was mainly due to a [...] Read more.
Nucleotides fulfill many essential functions in plants. Compared to non-plant systems, these hydrophilic metabolites have not been adequately investigated in plants, especially the less abundant nucleotide species such as deoxyribonucleotides and modified or damaged nucleotides. Until recently, this was mainly due to a lack of adequate methods for in-depth analysis of nucleotides and nucleosides in plants. In this review, we focus on the current state-of-the-art of nucleotide analysis in plants with liquid chromatography coupled to mass spectrometry and describe recent major advances. Tissue disruption, quenching, liquid–liquid and solid-phase extraction, chromatographic strategies, and peculiarities of nucleotides and nucleosides in mass spectrometry are covered. We describe how the different steps of the analytical workflow influence each other, highlight the specific challenges of nucleotide analysis, and outline promising future developments. The metabolite matrix of plants is particularly complex. Therefore, it is likely that nucleotide analysis methods that work for plants can be applied to other organisms as well. Although this review focuses on plants, we also discuss advances in nucleotide analysis from non-plant systems to provide an overview of the analytical techniques available for this challenging class of metabolites. Full article
(This article belongs to the Special Issue Metabolomics in Plant Research)
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32 pages, 1051 KiB  
Review
Metabolomics Intervention Towards Better Understanding of Plant Traits
by Vinay Sharma, Prateek Gupta, Kagolla Priscilla, SharanKumar, Bhagyashree Hangargi, Akash Veershetty, Devade Pandurang Ramrao, Srinivas Suresh, Rahul Narasanna, Gajanana R. Naik, Anirudh Kumar, Baozhu Guo, Weijian Zhuang, Rajeev K. Varshney, Manish K. Pandey and Rakesh Kumar
Cells 2021, 10(2), 346; https://doi.org/10.3390/cells10020346 - 7 Feb 2021
Cited by 42 | Viewed by 6290
Abstract
The majority of the most economically important plant and crop species are enriched with the availability of high-quality reference genome sequences forming the basis of gene discovery which control the important biochemical pathways. The transcriptomics and proteomics resources have also been made available [...] Read more.
The majority of the most economically important plant and crop species are enriched with the availability of high-quality reference genome sequences forming the basis of gene discovery which control the important biochemical pathways. The transcriptomics and proteomics resources have also been made available for many of these plant species that intensify the understanding at expression levels. However, still we lack integrated studies spanning genomics–transcriptomics–proteomics, connected to metabolomics, the most complicated phase in phenotype expression. Nevertheless, for the past few decades, emphasis has been more on metabolome which plays a crucial role in defining the phenotype (trait) during crop improvement. The emergence of modern high throughput metabolome analyzing platforms have accelerated the discovery of a wide variety of biochemical types of metabolites and new pathways, also helped in improving the understanding of known existing pathways. Pinpointing the causal gene(s) and elucidation of metabolic pathways are very important for development of improved lines with high precision in crop breeding. Along with other -omics sciences, metabolomics studies have helped in characterization and annotation of a new gene(s) function. Hereby, we summarize several areas in the field of crop development where metabolomics studies have made its remarkable impact. We also assess the recent research on metabolomics, together with other omics, contributing toward genetic engineering to target traits and key pathway(s). Full article
(This article belongs to the Special Issue Metabolomics in Plant Research)
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26 pages, 2304 KiB  
Review
Enhancing Salt Tolerance of Plants: From Metabolic Reprogramming to Exogenous Chemical Treatments and Molecular Approaches
by Manish Kumar Patel, Manoj Kumar, Weiqiang Li, Yin Luo, David J. Burritt, Noam Alkan and Lam-Son Phan Tran
Cells 2020, 9(11), 2492; https://doi.org/10.3390/cells9112492 - 17 Nov 2020
Cited by 85 | Viewed by 9391
Abstract
Plants grow on soils that not only provide support for root anchorage but also act as a reservoir of water and nutrients important for plant growth and development. However, environmental factors, such as high salinity, hinder the uptake of nutrients and water from [...] Read more.
Plants grow on soils that not only provide support for root anchorage but also act as a reservoir of water and nutrients important for plant growth and development. However, environmental factors, such as high salinity, hinder the uptake of nutrients and water from the soil and reduce the quality and productivity of plants. Under high salinity, plants attempt to maintain cellular homeostasis through the production of numerous stress-associated endogenous metabolites that can help mitigate the stress. Both primary and secondary metabolites can significantly contribute to survival and the maintenance of growth and development of plants on saline soils. Existing studies have suggested that seed/plant-priming with exogenous metabolites is a promising approach to increase crop tolerance to salt stress without manipulation of the genome. Recent advancements have also been made in genetic engineering of various metabolic genes involved in regulation of plant responses and protection of the cells during salinity, which have therefore resulted in many more basic and applied studies in both model and crop plants. In this review, we discuss the recent findings of metabolic reprogramming, exogenous treatments with metabolites and genetic engineering of metabolic genes for the improvement of plant salt tolerance. Full article
(This article belongs to the Special Issue Metabolomics in Plant Research)
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