Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation

Abstract 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, iRZ1...

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Autores principales:	Shany Ofaim, Raphy Zarecki, Seema Porob, Daniella Gat, Tamar Lahav, Yechezkel Kashi, Radi Aly, Hanan Eizenberg, Zeev Ronen, Shiri Freilich
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2020
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/f75aee03dcd141b4ba4b4e5abf9cf208
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spelling	oai:doaj.org-article:f75aee03dcd141b4ba4b4e5abf9cf2082021-12-02T16:35:41ZGenome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation10.1038/s41598-020-69509-72045-2322https://doaj.org/article/f75aee03dcd141b4ba4b4e5abf9cf2082020-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-69509-7https://doaj.org/toc/2045-2322Abstract 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.Shany OfaimRaphy ZareckiSeema PorobDaniella GatTamar LahavYechezkel KashiRadi AlyHanan EizenbergZeev RonenShiri FreilichNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 10, Iss 1, Pp 1-11 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Shany Ofaim Raphy Zarecki Seema Porob Daniella Gat Tamar Lahav Yechezkel Kashi Radi Aly Hanan Eizenberg Zeev Ronen Shiri Freilich Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation
description	Abstract 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.
format	article
author	Shany Ofaim Raphy Zarecki Seema Porob Daniella Gat Tamar Lahav Yechezkel Kashi Radi Aly Hanan Eizenberg Zeev Ronen Shiri Freilich
author_facet	Shany Ofaim Raphy Zarecki Seema Porob Daniella Gat Tamar Lahav Yechezkel Kashi Radi Aly Hanan Eizenberg Zeev Ronen Shiri Freilich
author_sort	Shany Ofaim
title	Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation
title_short	Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation
title_full	Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation
title_fullStr	Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation
title_full_unstemmed	Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation
title_sort	genome-scale reconstruction of paenarthrobacter aurescens tc1 metabolic model towards the study of atrazine bioremediation
publisher	Nature Portfolio
publishDate	2020
url	https://doaj.org/article/f75aee03dcd141b4ba4b4e5abf9cf208
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Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation

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