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Open AccessArticle

Exploring Plant Sesquiterpene Diversity by Generating Chemical Networks

1
Federal Institute of Goiás, Rua 64, esq. c/ Rua 11, s/n, Expansão Parque Lago, Formosa, GO 73813-816, Brazil
2
Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF 70910-900, Brazil
3
Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany
4
Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
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Departamento de Ciência da Computação, Instituto de Ciências Exatas, Universidade de Brasília, Brasília, DF 70910-900, Brazil
6
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions Dresden-Leipzig, and Leipzig Research Center for Civilization Diseases, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany
7
Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria
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Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany
9
Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
*
Author to whom correspondence should be addressed.
Processes 2019, 7(4), 240; https://doi.org/10.3390/pr7040240
Received: 28 February 2019 / Revised: 6 April 2019 / Accepted: 11 April 2019 / Published: 25 April 2019
(This article belongs to the Special Issue In silico metabolic modeling and engineering)
Plants produce a diverse portfolio of sesquiterpenes that are important in their response to herbivores and the interaction with other plants. Their biosynthesis from farnesyl diphosphate depends on the sesquiterpene synthases that admit different cyclizations and rearrangements to yield a blend of sesquiterpenes. Here, we investigate to what extent sesquiterpene biosynthesis metabolic pathways can be reconstructed just from the knowledge of the final product and the reaction mechanisms catalyzed by sesquiterpene synthases. We use the software package MedØlDatschgerl (MØD) to generate chemical networks and to elucidate pathways contained in them. As examples, we successfully consider the reachability of the important plant sesquiterpenes β -caryophyllene, α -humulene, and β -farnesene. We also introduce a graph database to integrate the simulation results with experimental biological evidence for the selected predicted sesquiterpenes biosynthesis. View Full-Text
Keywords: plant; sesquiterpenes; biosynthesis; graph grammars; graph database plant; sesquiterpenes; biosynthesis; graph grammars; graph database
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Silva, W.M.C.; Andersen, J.L.; Holanda, M.T.; Walter, M.E.M.T.; Brigido, M.M.; Stadler, P.F.; Flamm, C. Exploring Plant Sesquiterpene Diversity by Generating Chemical Networks. Processes 2019, 7, 240.

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