Elemental formula annotation of polar and lipophilic metabolites using 13C, 15N and 34S isotope labelling, in combination with high-resolution mass spectrometry
Patrick Giavalisco,Yan Li,Annemarie Matthes,Aenne Eckhardt,Hans-Michael Hubberten,Holger Hesse,Shruthi Segu,Jan Hummel,Karin Köhl,Lothar Willmitzer +9 more
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TLDR
A comprehensive multi-isotope labelling-based strategy using fully labelled plant tissues, in combination with a fractionated metabolite extraction protocol, which can be applied in either an automated database-dependent or a database-independent analysis of the plant polar metabolome and lipidome.Abstract:
The unbiased and comprehensive analysis of metabolites in any organism presents a major challenge if proper peak annotation and unambiguous assignment of the biological origin of the peaks are required. Here we provide a comprehensive multi-isotope labelling-based strategy using fully labelled (13) C, (15) N and (34) S plant tissues, in combination with a fractionated metabolite extraction protocol. The extraction procedure allows for the simultaneous extraction of polar, semi-polar and hydrophobic metabolites, as well as for the extraction of proteins and starch. After labelling and extraction, the metabolites and lipids were analysed using a high-resolution mass spectrometer providing accurate MS and all-ion fragmentation data, providing an unambiguous readout for every detectable isotope-labelled peak. The isotope labelling assisted peak annotation process employed can be applied in either an automated database-dependent or a database-independent analysis of the plant polar metabolome and lipidome. As a proof of concept, the developed methods and technologies were applied and validated using Arabidopsis thaliana leaf and root extracts. Along with a large repository of assigned elemental compositions, which is provided, we show, using selected examples, the accuracy and reliability of the developed workflow.read more
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Medicinal Bioprospecting of the Amazon Rainforest: A Modern Eldorado?
Aleksandra Skirycz,Aleksandra Skirycz,Sylwia Kierszniowska,Michaël Méret,Lothar Willmitzer,George Tzotzos +5 more
TL;DR: The potential of new technologies to tap into the metabolic diversity of tropical plants is assessed and how regulations affect access to plant resources is considered.
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Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress
Noemi Ruiz-Lopez,Jessica Pérez-Sancho,Jessica Pérez-Sancho,Alicia Esteban del Valle,Richard P. Haslam,Steffen Vanneste,Rafael Catalá,Carlos Perea-Resa,Daniël Van Damme,Selene García-Hernández,Armando Albert,José G. Vallarino,Jinxing Lin,Jiří Friml,Alberto P. Macho,Julio Salinas,Abel Rosado,Johnathan A. Napier,Vitor Amorim-Silva,Miguel A. Botella +19 more
TL;DR: In this paper, the authors showed that the SYT-induced SYT3 is an ER-PM tether that also functions in maintaining PM integrity under multiple abiotic stresses, such as freezing, high salt, osmotic stress, and mechanical damage.
Journal ArticleDOI
Identification of a Solanum pennellii Chromosome 4 Fruit Flavor and Nutritional Quality-Associated Metabolite QTL
Zhongyuan Liu,Saleh Alseekh,Yariv Brotman,Yi Zheng,Zhangjun Fei,Zhangjun Fei,Denise M. Tieman,James J. Giovannoni,James J. Giovannoni,Alisdair R. Fernie,Harry J. Klee +10 more
TL;DR: This work provides comprehensive insights into IL4-4 fruit biochemistry, identifying a small region of the genome that has major effects on a large and diverse set of metabolites.
Journal ArticleDOI
Metabolomics should be deployed in the identification and characterization of gene-edited crops
Paul D. Fraser,Asaph Aharoni,Robert Hall,Sanwen Huang,James J. Giovannoni,Uwe Sonnewald,Alisdair R. Fernie +6 more
TL;DR: With the emergence of new edited crop varieties, concerted efforts in the advancement of 'omics' technologies such as metabolomics are advocated to redress the use of the technology in the regulatory assessment for metabolically-engineered biotech crops.
Journal ArticleDOI
Global mapping of protein–metabolite interactions in Saccharomyces cerevisiae reveals that Ser-Leu dipeptide regulates phosphoglycerate kinase activity
Marcin Luzarowski,Rubén Vicente,Andrei Kiselev,Andrei Kiselev,Mateusz Wagner,Mateusz Wagner,Dennis Schlossarek,Alexander Erban,Leonardo Perez de Souza,Dorothee Childs,Izabela Wojciechowska,Urszula Luzarowska,Urszula Luzarowska,Michal Gorka,Ewelina M. Sokolowska,Monika Kosmacz,Monika Kosmacz,Juan Moreno,Juan Moreno,Aleksandra Brzezińska,Bhavana Vegesna,Joachim Kopka,Alisdair R. Fernie,Lothar Willmitzer,Jennifer C. Ewald,Aleksandra Skirycz,Aleksandra Skirycz +26 more
TL;DR: In this paper, a biochemical approach named PROMIS was applied to address the complexity of the protein-small molecule interactome in the model yeast Saccharomyces cerevisiae.
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