Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
03 08 2020
03 08 2020
Historique:
received:
23
07
2019
accepted:
25
06
2020
entrez:
5
8
2020
pubmed:
5
8
2020
medline:
7
5
2021
Statut:
epublish
Résumé
Atrazine is an herbicide and a pollutant of great environmental concern that is naturally biodegraded by microbial communities. Paenarthrobacter aurescens TC1 is one of the most studied degraders of this herbicide. Here, we developed a genome scale metabolic model for P. aurescens TC1, iRZ1179, to study the atrazine degradation process at organism level. Constraint based flux balance analysis and time dependent simulations were used to explore the organism's phenotypic landscape. Simulations aimed at designing media optimized for supporting growth and enhancing degradation, by passing the need in strain design via genetic modifications. Growth and degradation simulations were carried with more than 100 compounds consumed by P. aurescens TC1. In vitro validation confirmed the predicted classification of different compounds as efficient, moderate or poor stimulators of growth. Simulations successfully captured previous reports on the use of glucose and phosphate as bio-stimulators of atrazine degradation, supported by in vitro validation. Model predictions can go beyond supplementing the medium with a single compound and can predict the growth outcomes for higher complexity combinations. Hence, the analysis demonstrates that the exhaustive power of the genome scale metabolic reconstruction allows capturing complexities that are beyond common biochemical expertise and knowledge and further support the importance of computational platforms for the educated design of complex media. The model presented here can potentially serve as a predictive tool towards achieving optimal biodegradation efficiencies and for the development of ecologically friendly solutions for pollutant degradation.
Identifiants
pubmed: 32747737
doi: 10.1038/s41598-020-69509-7
pii: 10.1038/s41598-020-69509-7
pmc: PMC7398907
doi:
Substances chimiques
Herbicides
0
Soil Pollutants
0
Atrazine
QJA9M5H4IM
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
13019Références
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