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doi:10.22028/D291-33429
Titel: | In-depth characterization of genome-scale network reconstructions for the in vitro synthesis in cell-free systems |
VerfasserIn: | Schuh, Lisa Katharina Weyler, Christian Heinzle, Elmar |
Sprache: | Englisch |
Titel: | Biotechnology and Bioengineering |
Bandnummer: | 117 |
Heft: | 4 |
Seiten: | 1137–1147 |
Verlag/Plattform: | Wiley |
Erscheinungsjahr: | 2019 |
Freie Schlagwörter: | biocatalysis genome‐scale network metabolic pathway search multienzyme systems network curation pan‐organism network |
DDC-Sachgruppe: | 540 Chemie |
Dokumenttyp: | Journalartikel / Zeitschriftenartikel |
Abstract: | Cell‐free systems containing multiple enzymes are becoming an increasingly interesting tool for one‐pot syntheses of biochemical compounds. To extensively explore the enormous wealth of enzymes in the biological space, we present methods for assembling and curing data from databases to apply them for the prediction of pathway candidates for directed enzymatic synthesis. We use Kyoto Encyclopedia of Genes and Genomes to establish single organism models and a pan‐organism model that is combining the available data from all organisms listed there. We introduce a filtering scheme to remove data that are not suitable, for example, generic metabolites and general reactions. In addition, a valid stoichiometry of reactions is required for acceptance. The networks created are analyzed by graph theoretical methods to identify a set of metabolites that are potentially reachable from a defined set of starting metabolites. Thus, metabolites not connected to such starting metabolites cannot be produced unless new starting metabolites or reactions are introduced. The network models also comprise stoichiometric and thermodynamic data that allow the definition of constraints to identify potential pathways. The resulting data can be directly applied using existing or future pathway finding tools. |
DOI der Erstveröffentlichung: | 10.1002/bit.27249 |
Link zu diesem Datensatz: | urn:nbn:de:bsz:291--ds-334295 hdl:20.500.11880/30740 http://dx.doi.org/10.22028/D291-33429 |
ISSN: | 1097-0290 0006-3592 |
Datum des Eintrags: | 26-Feb-2021 |
Bezeichnung des in Beziehung stehenden Objekts: | Supporting Information |
In Beziehung stehendes Objekt: | https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fbit.27249&file=bit27249-sup-0001-Supplementary1.pdf https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fbit.27249&file=bit27249-sup-0002-Supplementary2.pdf https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fbit.27249&file=bit27249-sup-0003-Supplementary3.txt https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fbit.27249&file=bit27249-sup-0004-Supplementary4.pdf https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fbit.27249&file=bit27249-sup-0005-Supplementary5.pdf https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fbit.27249&file=bit27249-sup-0006-Supplementary6.pdf |
Fakultät: | NT - Naturwissenschaftlich- Technische Fakultät |
Fachrichtung: | NT - Chemie |
Professur: | NT - Keiner Professur zugeordnet |
Sammlung: | SciDok - Der Wissenschaftsserver der Universität des Saarlandes |
Dateien zu diesem Datensatz:
Datei | Beschreibung | Größe | Format | |
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bit.27249.pdf | 1,89 MB | Adobe PDF | Öffnen/Anzeigen |
Diese Ressource wurde unter folgender Copyright-Bestimmung veröffentlicht: Lizenz von Creative Commons