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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

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