Untargeted Metabolomics Sheds Light on the Diversity of Major Classes of Secondary Metabolites in the Malpighiaceae Botanical Family
Natural products produced by plants are one of the most investigated natural sources, which substantially contributed to the development of the natural products field. Even though these compounds are widely explored, the literature still lacks comprehensive investigations aiming to explore the evolu...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2022-04-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.854842/full |
| _version_ | 1818479733999927296 |
|---|---|
| author | Helena Mannochio-Russo Helena Mannochio-Russo Rafael F. de Almeida Rafael F. de Almeida Wilhan D. G. Nunes Paula C. P. Bueno Paula C. P. Bueno Andrés M. Caraballo-Rodríguez Anelize Bauermeister Pieter C. Dorrestein Vanderlan S. Bolzani |
| author_facet | Helena Mannochio-Russo Helena Mannochio-Russo Rafael F. de Almeida Rafael F. de Almeida Wilhan D. G. Nunes Paula C. P. Bueno Paula C. P. Bueno Andrés M. Caraballo-Rodríguez Anelize Bauermeister Pieter C. Dorrestein Vanderlan S. Bolzani |
| author_sort | Helena Mannochio-Russo |
| collection | DOAJ |
| description | Natural products produced by plants are one of the most investigated natural sources, which substantially contributed to the development of the natural products field. Even though these compounds are widely explored, the literature still lacks comprehensive investigations aiming to explore the evolution of secondary metabolites produced by plants, especially if classical methodologies are employed. The development of sensitive hyphenated techniques and computational tools for data processing has enabled the study of large datasets, being valuable assets for chemosystematic studies. Here, we describe a strategy for chemotaxonomic investigations using the Malpighiaceae botanical family as a model. Our workflow was based on MS/MS untargeted metabolomics, spectral searches, and recently described in silico classification tools, which were mapped into the latest molecular phylogeny accepted for this family. The metabolomic analysis revealed that different ionization modes and extraction protocols significantly impacted the chemical profiles, influencing the chemotaxonomic results. Spectral searches within public databases revealed several clades or genera-specific molecular families, being potential chemical markers for these taxa, while the in silico classification tools were able to expand the Malpighiaceae chemical space. The classes putatively annotated were used for ancestral character reconstructions, which recovered several classes of metabolites as homoplasies (i.e., non-exclusive) or synapomorphies (i.e., exclusive) for all sampled clades and genera. Our workflow combines several approaches to perform a comprehensive evolutionary chemical study. We expect it to be used on further chemotaxonomic investigations to expand chemical knowledge and reveal biological insights for compounds classes in different biological groups. |
| first_indexed | 2024-12-10T11:14:40Z |
| format | Article |
| id | doaj.art-dad464d51b0f4d43886e25caaf2ca2f4 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-10T11:14:40Z |
| publishDate | 2022-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-dad464d51b0f4d43886e25caaf2ca2f42022-12-22T01:51:15ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-04-011310.3389/fpls.2022.854842854842Untargeted Metabolomics Sheds Light on the Diversity of Major Classes of Secondary Metabolites in the Malpighiaceae Botanical FamilyHelena Mannochio-Russo0Helena Mannochio-Russo1Rafael F. de Almeida2Rafael F. de Almeida3Wilhan D. G. Nunes4Paula C. P. Bueno5Paula C. P. Bueno6Andrés M. Caraballo-Rodríguez7Anelize Bauermeister8Pieter C. Dorrestein9Vanderlan S. Bolzani10NuBBE, Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Araraquara, BrazilCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, United StatesRoyal Botanical Gardens Kew, Science, Ecosystem Stewardship, Diversity and Livelihoods, Richmond, United KingdomDepartment of Biological Sciences, Lamol Lab, Feira de Santana State University (UEFS), Feira de Santana, BrazilFederal Institute of Education, Science and Technology of Rondônia (IFRO), Ji-Paraná, BrazilMax Planck Institute of Molecular Plant Physiology, Potsdam, GermanyInstitute of Chemistry, Federal University of Alfenas (UNIFAL), Alfenas, BrazilCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, United StatesCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, United StatesCollaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, United StatesNuBBE, Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Araraquara, BrazilNatural products produced by plants are one of the most investigated natural sources, which substantially contributed to the development of the natural products field. Even though these compounds are widely explored, the literature still lacks comprehensive investigations aiming to explore the evolution of secondary metabolites produced by plants, especially if classical methodologies are employed. The development of sensitive hyphenated techniques and computational tools for data processing has enabled the study of large datasets, being valuable assets for chemosystematic studies. Here, we describe a strategy for chemotaxonomic investigations using the Malpighiaceae botanical family as a model. Our workflow was based on MS/MS untargeted metabolomics, spectral searches, and recently described in silico classification tools, which were mapped into the latest molecular phylogeny accepted for this family. The metabolomic analysis revealed that different ionization modes and extraction protocols significantly impacted the chemical profiles, influencing the chemotaxonomic results. Spectral searches within public databases revealed several clades or genera-specific molecular families, being potential chemical markers for these taxa, while the in silico classification tools were able to expand the Malpighiaceae chemical space. The classes putatively annotated were used for ancestral character reconstructions, which recovered several classes of metabolites as homoplasies (i.e., non-exclusive) or synapomorphies (i.e., exclusive) for all sampled clades and genera. Our workflow combines several approaches to perform a comprehensive evolutionary chemical study. We expect it to be used on further chemotaxonomic investigations to expand chemical knowledge and reveal biological insights for compounds classes in different biological groups.https://www.frontiersin.org/articles/10.3389/fpls.2022.854842/fullchemotaxonomymass spectrometrymetabolite annotationmetabolomicsevolutionancestral character reconstruction |
| spellingShingle | Helena Mannochio-Russo Helena Mannochio-Russo Rafael F. de Almeida Rafael F. de Almeida Wilhan D. G. Nunes Paula C. P. Bueno Paula C. P. Bueno Andrés M. Caraballo-Rodríguez Anelize Bauermeister Pieter C. Dorrestein Vanderlan S. Bolzani Untargeted Metabolomics Sheds Light on the Diversity of Major Classes of Secondary Metabolites in the Malpighiaceae Botanical Family Frontiers in Plant Science chemotaxonomy mass spectrometry metabolite annotation metabolomics evolution ancestral character reconstruction |
| title | Untargeted Metabolomics Sheds Light on the Diversity of Major Classes of Secondary Metabolites in the Malpighiaceae Botanical Family |
| title_full | Untargeted Metabolomics Sheds Light on the Diversity of Major Classes of Secondary Metabolites in the Malpighiaceae Botanical Family |
| title_fullStr | Untargeted Metabolomics Sheds Light on the Diversity of Major Classes of Secondary Metabolites in the Malpighiaceae Botanical Family |
| title_full_unstemmed | Untargeted Metabolomics Sheds Light on the Diversity of Major Classes of Secondary Metabolites in the Malpighiaceae Botanical Family |
| title_short | Untargeted Metabolomics Sheds Light on the Diversity of Major Classes of Secondary Metabolites in the Malpighiaceae Botanical Family |
| title_sort | untargeted metabolomics sheds light on the diversity of major classes of secondary metabolites in the malpighiaceae botanical family |
| topic | chemotaxonomy mass spectrometry metabolite annotation metabolomics evolution ancestral character reconstruction |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.854842/full |
| work_keys_str_mv | AT helenamannochiorusso untargetedmetabolomicsshedslightonthediversityofmajorclassesofsecondarymetabolitesinthemalpighiaceaebotanicalfamily AT helenamannochiorusso untargetedmetabolomicsshedslightonthediversityofmajorclassesofsecondarymetabolitesinthemalpighiaceaebotanicalfamily AT rafaelfdealmeida untargetedmetabolomicsshedslightonthediversityofmajorclassesofsecondarymetabolitesinthemalpighiaceaebotanicalfamily AT rafaelfdealmeida untargetedmetabolomicsshedslightonthediversityofmajorclassesofsecondarymetabolitesinthemalpighiaceaebotanicalfamily AT wilhandgnunes untargetedmetabolomicsshedslightonthediversityofmajorclassesofsecondarymetabolitesinthemalpighiaceaebotanicalfamily AT paulacpbueno untargetedmetabolomicsshedslightonthediversityofmajorclassesofsecondarymetabolitesinthemalpighiaceaebotanicalfamily AT paulacpbueno untargetedmetabolomicsshedslightonthediversityofmajorclassesofsecondarymetabolitesinthemalpighiaceaebotanicalfamily AT andresmcaraballorodriguez untargetedmetabolomicsshedslightonthediversityofmajorclassesofsecondarymetabolitesinthemalpighiaceaebotanicalfamily AT anelizebauermeister untargetedmetabolomicsshedslightonthediversityofmajorclassesofsecondarymetabolitesinthemalpighiaceaebotanicalfamily AT pietercdorrestein untargetedmetabolomicsshedslightonthediversityofmajorclassesofsecondarymetabolitesinthemalpighiaceaebotanicalfamily AT vanderlansbolzani untargetedmetabolomicsshedslightonthediversityofmajorclassesofsecondarymetabolitesinthemalpighiaceaebotanicalfamily |