Genome-scale model of Rhodotorula toruloides metabolism.

Modelo a escala genómica del metabolismo de Rhodotorula toruloides.

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ID: 44277
2019
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Abstract
The basidiomycete red yeast Rhodotorula toruloides is a promising platform organism for production of biooils. We present rhto-GEM, the first genome-scale model (GEM) of R. toruloides metabolism, that was largely reconstructed using RAVEN toolbox. The model includes 852 genes, 2731 reactions, and 2277 metabolites, while lipid metabolism is described using the SLIMEr formalism allowing direct integration of lipid class and acyl chain experimental distribution data. The simulation results confirmed that the R. toruloides model provides valid growth predictions on glucose, xylose and glycerol, while prediction of genetic engineering targets to increase production of linolenic acid, triacylglycerols and carotenoids identified genes - some of which have previously been engineered to successfully increase production. This renders rtho-GEM valuable for future studies to improve the production of other oleochemicals of industrial relevance including value-added fatty acids and carotenoids, in addition to facilitate system-wide omics-data analysis in R. toruloides. Expanding the portfolio of GEMs for lipid accumulating fungi contributes to both understanding of metabolic mechanisms of the oleaginous phenotype but also uncover particularities of the lipid production machinery in R. toruloides. This article is protected by copyright. All rights reserved.
La levadura roja basidiomiceta *Rhodotorula toruloides* es un organismo plataforma prometedor para la producción de bioaceites. Presentamos rhto-GEM, el primer modelo a escala genómica (GEM) del metabolismo de *R. toruloides*, reconstruido en gran parte mediante el conjunto de herramientas RAVEN toolbox. El modelo incluye 852 genes, 2731 reacciones y 2277 metabolitos, mientras que el metabolismo lipídico se describe mediante el formalismo SLIMEr, lo que permite la integración directa de datos experimentales de distribución de clases de lípidos y cadenas de acilo. Los resultados de las simulaciones confirmaron que el modelo de *R. toruloides* proporciona predicciones de crecimiento válidas en glucosa, xilosa y glicerol; asimismo, la predicción de dianas de ingeniería genética para aumentar la producción de ácido linolénico, triacilgliceroles y carotenoides identificó genes, algunos de los cuales ya se han modificado previamente con éxito para incrementar la producción. Esto hace que rtho-GEM sea valioso para futuros estudios dirigidos a mejorar la producción de otros compuestos oleoquímicos de relevancia industrial, incluidos ácidos grasos de alto valor añadido y carotenoides, además de facilitar el análisis integral de datos ómicos en *R. toruloides*. La ampliación del repertorio de GEM para hongos acumuladores de lípidos no solo contribuye a la comprensión de los mecanismos metabólicos del fenotipo oleaginoso, sino que también permite esclarecer particularidades de la maquinaria de producción de lípidos en *R. toruloides*. Este artículo está protegido por derechos de autor. Todos los derechos reservados.
Reference Key
tiukova2019genomescalebiotechnology Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Tiukova, Ievgeniia A;Prigent, Sylvain;Nielsen, Jens;Sandgren, Mats;Kerkhoven, Eduard J;
Journal Biotechnology and bioengineering
Year 2019
DOI
10.1002/bit.27162
URL
Keywords
metabolism yeast rhodotorula toruloides genome-scale model

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