Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
Jan Schellenberger,Richard Que,Ronan M. T. Fleming,Ines Thiele,Jeffrey D. Orth,Adam M. Feist,Daniel C. Zielinski,Aarash Bordbar,Nathan E. Lewis,Sorena Rahmanian,Joseph Kang,Daniel R. Hyduke,Bernhard O. Palsson +12 more
TLDR
The constraint-based reconstruction and analysis toolbox as discussed by the authors is a software package running in the Matlab environment, which allows for quantitative prediction of cellular behavior using a constraintbased approach and allows predictive computations of both steady-state and dynamic optimal growth behavior, the effects of gene deletions, comprehensive robustness analyses, sampling the range of possible cellular metabolic states and the determination of network modules.Abstract:
The manner in which microorganisms utilize their metabolic processes can be predicted using constraint-based analysis of genome-scale metabolic networks. Herein, we present the constraint-based reconstruction and analysis toolbox, a software package running in the Matlab environment, which allows for quantitative prediction of cellular behavior using a constraint-based approach. Specifically, this software allows predictive computations of both steady-state and dynamic optimal growth behavior, the effects of gene deletions, comprehensive robustness analyses, sampling the range of possible cellular metabolic states and the determination of network modules. Functions enabling these calculations are included in the toolbox, allowing a user to input a genome-scale metabolic model distributed in Systems Biology Markup Language format and perform these calculations with just a few lines of code. The results are predictions of cellular behavior that have been verified as accurate in a growing body of research. After software installation, calculation time is minimal, allowing the user to focus on the interpretation of the computational results.read more
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The metabolic network of Synechocystis sp. PCC 6803: systemic properties of autotrophic growth.
TL;DR: A detailed reconstruction of the primary metabolic network of the autotrophic prokaryote Synechocystis sp.
Journal ArticleDOI
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism
Hongzhong Lu,Feiran Li,Benjamin Sanchez,Zhengming Zhu,Zhengming Zhu,Gang Li,Iván Domenzain,Simonas Marcišauskas,Petre Mihail Anton,Dimitra Lappa,Christian Lieven,Moritz Emanuel Beber,Nikolaus Sonnenschein,Eduard J. Kerkhoven,Jens Nielsen,Jens Nielsen +15 more
TL;DR: Yast8 is introduced with its model ecosystem, a comprehensive computational resource for simulating the metabolism of Saccharomyces cerevisiae, and further facilitates the exploration of yeast metabolism at a multi-scale level.
Journal ArticleDOI
The sequence of a 1.8-Mb bacterial linear plasmid reveals a rich evolutionary reservoir of secondary metabolic pathways
Marnix H. Medema,Axel Christoph Trefzer,Andriy Kovalchuk,Marco A. van den Berg,Ulrike Müller,Wilbert H. M. Heijne,Liang Wu,Mohammad Tauqeer Alam,Catherine M. Ronning,William C. Nierman,Roel A. L. Bovenberg,Rainer Breitling,Rainer Breitling,Eriko Takano +13 more
TL;DR: Phylogenetic analysis indicates that heavy traffic of genetic information between Streptomyces plasmids and chromosomes may facilitate the rapid evolution of secondary metabolite repertoires in these bacteria.
Journal ArticleDOI
Metabolic Adaptation Establishes Disease Tolerance to Sepsis
Sebastian Weis,Ana Rita Carlos,Maria Raquel Moita,Sumnima Singh,Birte Blankenhaus,Silvia Cardoso,Rasmus Larsen,Sofia Rebelo,Sascha Schäuble,Laura del Barrio,Gilles Mithieux,Fabienne Rajas,Sandro Lindig,Michael Bauer,Miguel P. Soares +14 more
TL;DR: It is demonstrated that induction of the iron-sequestering ferritin H chain in response to polymicrobial infections is critical to establish disease tolerance to sepsis and a crosstalk between adaptive responses controlling iron and glucose metabolism is required to maintain blood glucose within a physiologic range compatible with host survival.
Journal ArticleDOI
Establishing a synthetic pathway for high-level production of 3-hydroxypropionic acid in Saccharomyces cerevisiae via β-alanine.
Irina Borodina,Kanchana Rueksomtawin Kildegaard,Niels Bjerg Jensen,Thomas Blicher,Jerome Maury,Svetlana Sherstyk,Konstantin Schneider,Pedro Lamosa,Markus J. Herrgård,Inger Rosenstand,Fredrik Öberg,Jochen Förster,Jens Nielsen +12 more
TL;DR: This work engineered and optimized a synthetic pathway for de novo biosynthesis of β-alanine and its subsequent conversion into 3HP using a novel β-Alanine-pyruvate aminotransferase discovered in Bacillus cereus.
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