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Peters K, Blatt-Janmaat KL, Tkach N, van Dam NM, Neumann S. Untargeted Metabolomics for Integrative Taxonomy: Metabolomics, DNA Marker-Based Sequencing, and Phenotype Bioimaging. PLANTS (BASEL, SWITZERLAND) 2023; 12:881. [PMID: 36840229 PMCID: PMC9965764 DOI: 10.3390/plants12040881] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Integrative taxonomy is a fundamental part of biodiversity and combines traditional morphology with additional methods such as DNA sequencing or biochemistry. Here, we aim to establish untargeted metabolomics for use in chemotaxonomy. We used three thallose liverwort species Riccia glauca, R. sorocarpa, and R. warnstorfii (order Marchantiales, Ricciaceae) with Lunularia cruciata (order Marchantiales, Lunulariacea) as an outgroup. Liquid chromatography high-resolution mass-spectrometry (UPLC/ESI-QTOF-MS) with data-dependent acquisition (DDA-MS) were integrated with DNA marker-based sequencing of the trnL-trnF region and high-resolution bioimaging. Our untargeted chemotaxonomy methodology enables us to distinguish taxa based on chemophenetic markers at different levels of complexity: (1) molecules, (2) compound classes, (3) compound superclasses, and (4) molecular descriptors. For the investigated Riccia species, we identified 71 chemophenetic markers at the molecular level, a characteristic composition in 21 compound classes, and 21 molecular descriptors largely indicating electron state, presence of chemical motifs, and hydrogen bonds. Our untargeted approach revealed many chemophenetic markers at different complexity levels that can provide more mechanistic insight into phylogenetic delimitation of species within a clade than genetic-based methods coupled with traditional morphology-based information. However, analytical and bioinformatics analysis methods still need to be better integrated to link the chemophenetic information at multiple scales.
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Affiliation(s)
- Kristian Peters
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany
- Bioinformatics and Scientific Data, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Kaitlyn L. Blatt-Janmaat
- Bioinformatics and Scientific Data, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
- Department of Chemistry, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Natalia Tkach
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany
| | - Nicole M. van Dam
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburgerstraße 159, 07743 Jena, Germany
- Plants Biotic Interactions, Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Steffen Neumann
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany
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Martínez-Abaigar J, Núñez-Olivera E. Bryophyte ultraviolet-omics: from genes to the environment. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4412-4426. [PMID: 35274697 DOI: 10.1093/jxb/erac090] [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: 01/02/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Ultraviolet (UV) radiation has contributed to the evolution of organisms since the origins of life. Bryophytes also have evolutionary importance as the first clearly identified lineage of land plants (embryophytes) colonizing the terrestrial environment, thus facing high UV and water scarcity, among other new challenges. Here we review bryophyte UV-omics, the discipline relating bryophytes and UV, with an integrative perspective from genes to the environment. We consider species and habitats investigated, methodology, response variables, protection mechanisms, environmental interactions, UV biomonitoring, molecular and evolutionary aspects, and applications. Bryophyte UV-omics shows convergences and divergences with the UV-omics of other photosynthetic organisms, from algae to tracheophytes. All these organisms converge in that UV damage may be limited under realistic UV levels, due to structural protection and/or physiological acclimation capacity. Nevertheless, bryophytes diverge because they have a unique combination of vegetative and reproductive characteristics to cope with high UV and other concomitant adverse processes, such as desiccation. This interaction has both evolutionary and ecological implications. In addition, UV effects on bryophytes depend on the species and the evolutionary lineage considered, with mosses more UV-tolerant than liverworts. Thus, bryophytes do not constitute a homogeneous functional type with respect to their UV tolerance.
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Affiliation(s)
- Javier Martínez-Abaigar
- Faculty of Science and Technology, University of La Rioja, Madre de Dios 53, 26006 Logroño, Spain
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Beyond Photoprotection: The Multifarious Roles of Flavonoids in Plant Terrestrialization. Int J Mol Sci 2022; 23:ijms23095284. [PMID: 35563675 PMCID: PMC9101737 DOI: 10.3390/ijms23095284] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/29/2022] [Accepted: 05/06/2022] [Indexed: 02/01/2023] Open
Abstract
Plants evolved an impressive arsenal of multifunctional specialized metabolites to cope with the novel environmental pressures imposed by the terrestrial habitat when moving from water. Here we examine the multifarious roles of flavonoids in plant terrestrialization. We reason on the environmental drivers, other than the increase in UV-B radiation, that were mostly responsible for the rise of flavonoid metabolism and how flavonoids helped plants in land conquest. We are reasonably based on a nutrient-deficiency hypothesis for the replacement of mycosporine-like amino acids, typical of streptophytic algae, with the flavonoid metabolism during the water-to-land transition. We suggest that flavonoids modulated auxin transport and signaling and promoted the symbiosis between plants and fungi (e.g., arbuscular mycorrhizal, AM), a central event for the conquest of land by plants. AM improved the ability of early plants to take up nutrients and water from highly impoverished soils. We offer evidence that flavonoids equipped early land plants with highly versatile “defense compounds”, essential for the new set of abiotic and biotic stressors imposed by the terrestrial environment. We conclude that flavonoids have been multifunctional since the appearance of plants on land, not only acting as UV filters but especially improving both nutrient acquisition and biotic stress defense.
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Soriano G, Kneeshaw S, Jimenez-Aleman G, Zamarreño ÁM, Franco-Zorrilla JM, Rey-Stolle MF, Barbas C, García-Mina JM, Solano R. An evolutionarily ancient fatty acid desaturase is required for the synthesis of hexadecatrienoic acid, which is the main source of the bioactive jasmonate in Marchantia polymorpha. THE NEW PHYTOLOGIST 2022; 233:1401-1413. [PMID: 34846752 DOI: 10.1111/nph.17850] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/02/2021] [Indexed: 06/13/2023]
Abstract
Jasmonates are fatty acid-derived hormones that regulate multiple aspects of plant development, growth and stress responses. Bioactive jasmonates, defined as the ligands of the conserved COI1 receptor, differ between vascular plants and bryophytes (jasmonoyl-l-isoleucine (JA-Ile) and dinor-12-oxo-10,15(Z)-phytodienoic acid (dn-OPDA), respectively). The biosynthetic pathways of JA-Ile in the model vascular plant Arabidopsis thaliana have been elucidated. However, the details of dn-OPDA biosynthesis in bryophytes are still unclear. Here, we identify an orthologue of Arabidopsis fatty-acid-desaturase 5 (AtFAD5) in the model liverwort Marchantia polymorpha and show that FAD5 function is ancient and conserved between species separated by more than 450 million years (Myr) of independent evolution. Similar to AtFAD5, MpFAD5 is required for the synthesis of 7Z-hexadecenoic acid. Consequently, in Mpfad5 mutants, the hexadecanoid pathway is blocked, dn-OPDA concentrations are almost completely depleted and normal chloroplast development is impaired. Our results demonstrate that the main source of wounding-induced dn-OPDA in Marchantia is the hexadecanoid pathway and the contribution of the octadecanoid pathway (i.e. from OPDA) is minimal. Remarkably, despite extremely low concentrations of dn-OPDA, MpCOI1-mediated responses to wounding and insect feeding can still be activated in Mpfad5, suggesting that dn-OPDA may not be the only bioactive jasmonate and COI1 ligand in Marchantia.
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Affiliation(s)
- Gonzalo Soriano
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, 28049, Spain
- Facultad de Ciencia y Tecnología, Universidad de La Rioja, Madre de Dios 53, Logroño (La Rioja), 26006, Spain
| | - Sophie Kneeshaw
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, 28049, Spain
| | - Guillermo Jimenez-Aleman
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, 28049, Spain
| | - Ángel M Zamarreño
- Department of Environmental Biology, University of Navarra, Navarra, 31008, Spain
| | - José Manuel Franco-Zorrilla
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, 28049, Spain
| | - Mª Fernanda Rey-Stolle
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty, Universidad San Pablo-CEU, Boadilla del Monte, Madrid, 28668, Spain
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty, Universidad San Pablo-CEU, Boadilla del Monte, Madrid, 28668, Spain
| | - Jose M García-Mina
- Department of Environmental Biology, University of Navarra, Navarra, 31008, Spain
| | - Roberto Solano
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, 28049, Spain
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