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Towards a genome-scale metabolic model for the Kluyveromyces lactis yeast

The interest in Kluyveromyces lactis (K. lactis) has begun in academia due to its ability to metabolize the betaglycoside (1). Since then, this yeast has been considered a model organism for studies in genetics and physiology (2). This yeast had its genome sequenced back in 2004 (3) and recently we have published a full metabolic re-annotation of its genome (4). This re-annotation can be used, among other appli...

iOD962 - the first genome-scale metabolic model of Kluyveromyces lactis

The genome-scale metabolic model of Kluyveromyces lactis was reconstructed from its genome annotation. The result was the partially compartmentalized (5 compartments) iOD962 metabolic model composed of 2038 reactions and 1561 metabolites. Previous chemostate experiments were used to adjust the maintenance ATP parameter, and the model proved valuable when predicting the biomass, oxygen and carbon dioxide yields....

Reconstruction of the genome-scale metabolic network of Kluyveromyces lactis

System Biology proposes to study biological components, as well as the interactions between them, to understand and predict systems’ behaviour through the use of mathematical models. Under this scope, Genome-Scale Metabolic Models (GSMMs) can be regarded as mathematical representations of the intrinsic metabolic capabilities of a given organism, encoded in its genome, and can be used in a variety of application...

Reconstruction of a genome-scale metabolic model for the filamentous fungus Ash...

Metabolic models are an important tool for in silico simulation of cells’ behavior. Until now, a considerable number of metabolic models were released for several microorganisms. Ashbya gossypii is an industrially relevant fungus intensively used for riboflavin production with no model reported until now. Despite the high similarity with the Saccharomyces cerevisiae genome, A. gossypii contains only 4726 protei...

Assembling genome-wide transporter system annotations

Over the years, several genome-scale metabolic models have been released with compartmentation information. Models such as iMH805/775 [1] (15 compartments) and iMM904 [2] (8 compartments) for Saccharomyces cerevisiae or iRS1563 [3] for Zea mays (6 compartments) include reactions performed in specific cellular organelles, such as mitochondria, chloroplasts (in photosynthetic organisms), lysosomes, cell nucleus o...

Genome-wide metabolic (re-) annotation of Kluyveromyces lactis

Even before having its genome sequence published in 2004, Kluyveromyces lactis had long been considered a model organism for studies in genetics and physiology. Research on Kluyveromyces lactis is quite advanced and this yeast species is one of the few with which it is possible to perform formal genetic analysis. Nevertheless, until now, no complete metabolic functional annotation has been performed to the prot...

Reconstruction of a genome-scale metabolic model for the filamentous fungus Ash...

Systems biology has recently arisen as a promising and powerful tool for process development and optimization. Metabolic models are one of its different methodologies with high interest and applicability since it allows the simulation of cells behavior under different environments and/or specific genetic variations. The fast-growing number of sequenced genomes may have contributed to this phenomenon, as the seq...

Reconstructing genome-scale metabolic models with merlin : the Ashbya gossypii ...

Reconstruction of a genome-scale metabolic model for the riboflavin producer fu...

Metabolic models are an important tool for in silico simulation of cells’ behavior. Until now, a considerable number of metabolic models have been released for a wide range of microorganisms. Ashbya gossypii is an industrial-relevant fungus intensively used for riboflavin production with no model reported until now. Despite its high similarity with Saccharomyces cerevisiae genome, A. gossypii contains only 472...

Revealing new biotechnological potentialities of the riboflavin producer fungus...